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    PDB 1afv-3qjk
      1afv
      1b6g
      1e9n
      1efn
      1fjr
      1hd7
      1hqj
      1iw7
      1ka4
      1n0y
      1na0
      1nbs
      1ocx
      1ps1
      1qnv
      1qr7
      1sn8
      1syy
      1tif
      1tn1
      1tn2
      1v0d
      1xxa
      1y95
      1zhw
      1zhy
      1zhz
      2ani
      2ch7
      2ex3
      2fj9
      2fp1
      2g0a
      2o3c
      2oq1
      2qd5
      2qkl
      2v01
      2xal
      3ec8
      3fhh
      3qjk

Lead in the structure of Crystal Structure Of the Specificity Domain of Ribonuclease P Rna (pdb 1nbs)






The binding sites of Lead atom in the structure of Crystal Structure Of the Specificity Domain of Ribonuclease P Rna (pdb code 1nbs). This binding sites where shown with 5.0 Angstroms radius around Lead atom.
The 1nbs structure was solved by A.S.KRASILNIKOV, X.YANG, T.PAN, A.MONDRAGON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)33.0-3.1
Space groupC2221
a (A)126.500
b (A)145.300
c (A)144.600
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)28
Rfree (%)30.7


Lead Binding Sites:

Lead binding site 1 out of 23 in 1nbs


Lead binding site 1 out of 23 in 1nbs
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stereopicture of Lead binding site 1 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: A185, A: C186, A: G219, A: G220,

conact list:


AtomAtomDistance (A)
PbC6 A:A1854.99
PbN6 A:A1854.26
PbN3 A:C1863.28
PbC2 A:C1864.56
PbC5 A:C1864.77
PbC4 A:C1863.38
PbN4 A:C1862.58
PbC3' A:G2193.56
PbO3' A:G2192.42
PbC5' A:G2193.95
PbC2' A:G2194.63
PbC4' A:G2193.75
PbO5' A:G2194.88
PbO2' A:G2194.47
PbOP1 A:G2203.04
PbP A:G2203.17
PbOP2 A:G2203.77
PbO5' A:G2204.55

interactive model:


Lead binding site 2 out of 23 in 1nbs


Lead binding site 2 out of 23 in 1nbs
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stereopicture of Lead binding site 2 out of 23 in 1nbs
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: G90, A: G132, A: G133, A: Mg7,

conact list:


AtomAtomDistance (A)
PbC6 A:G904.12
PbN1 A:G904.94
PbC5 A:G904.31
PbN7 A:G904.31
PbO6 A:G903.83
PbC8 A:G1323.96
PbC6 A:G1323.49
PbN1 A:G1324.86
PbC5 A:G1323.45
PbN7 A:G1322.79
PbC4 A:G1324.77
PbO6 A:G1322.90
PbC6 A:G1334.61
PbC5 A:G1334.75
PbN7 A:G1334.21
PbO6 A:G1333.88
PbMG A:Mg72.72

interactive model:


Lead binding site 3 out of 23 in 1nbs


Lead binding site 3 out of 23 in 1nbs
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stereopicture of Lead binding site 3 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: G86, A: C87, A: A240,

conact list:


AtomAtomDistance (A)
PbN9 A:G864.62
PbC8 A:G863.52
PbC6 A:G863.37
PbN1 A:G864.76
PbC5 A:G863.17
PbP A:G864.97
PbN7 A:G862.38
PbC4 A:G864.46
PbOP2 A:G863.79
PbO6 A:G862.92
PbN4 A:C874.43
PbC6 A:A2404.97
PbN1 A:A2404.54
PbN6 A:A2404.66

interactive model:


Lead binding site 4 out of 23 in 1nbs


Lead binding site 4 out of 23 in 1nbs
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stereopicture of Lead binding site 4 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: C134, A: U181, A: G182, A: A231,

conact list:


AtomAtomDistance (A)
PbN3 A:C1344.46
PbC2 A:C1343.48
PbN1 A:C1344.19
PbC1' A:C1343.87
PbO2 A:C1342.27
PbC2' A:C1343.80
PbO2' A:C1343.13
PbN3 A:U1814.65
PbC5 A:U1814.03
PbC4 A:U1813.48
PbO4 A:U1812.41
PbC8 A:G1824.85
PbC6 A:G1824.22
PbC5 A:G1824.30
PbN7 A:G1823.81
PbO6 A:G1823.62
PbN6 A:A2314.31

interactive model:


Lead binding site 5 out of 23 in 1nbs


Lead binding site 5 out of 23 in 1nbs
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stereopicture of Lead binding site 5 out of 23 in 1nbs
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: G97, A: A98, A: U101, A: C102, A: A103, A: U104,

conact list:


AtomAtomDistance (A)
PbC8 A:G974.86
PbN7 A:G974.69
PbOP2 A:G974.49
PbOP2 A:A984.17
PbO3' A:U1014.97
PbC5' A:U1014.91
PbOP1 A:C1024.65
PbP A:C1024.10
PbOP2 A:C1022.70
PbOP2 A:A1034.68
PbO4 A:U1044.75

interactive model:


Lead binding site 6 out of 23 in 1nbs


Lead binding site 6 out of 23 in 1nbs
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stereopicture of Lead binding site 6 out of 23 in 1nbs
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: G219, A: A222,

conact list:


AtomAtomDistance (A)
PbC6 A:G2194.38
PbN1 A:G2194.47
PbO6 A:G2193.43
PbOP2 A:A2224.91

interactive model:


Lead binding site 7 out of 23 in 1nbs


Lead binding site 7 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 7 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: A187, A: G188,

conact list:


AtomAtomDistance (A)
PbOP1 A:A1874.41
PbP A:A1874.82
PbOP2 A:A1874.33
PbOP2 A:G1884.34

interactive model:


Lead binding site 8 out of 23 in 1nbs


Lead binding site 8 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 8 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: A135, A: G136, A: G137, A: C173, A: G180,

conact list:


AtomAtomDistance (A)
PbC6 A:A1354.52
PbC5 A:A1354.89
PbN6 A:A1353.89
PbN7 A:A1354.86
PbC8 A:G1364.99
PbC6 A:G1363.27
PbN1 A:G1364.50
PbC5 A:G1363.82
PbN7 A:G1363.69
PbO6 A:G1362.23
PbC6 A:G1374.76
PbC5 A:G1374.90
PbN7 A:G1374.38
PbO6 A:G1374.03
PbN4 A:C1734.18
PbOP2 A:G1804.77

interactive model:


Lead binding site 9 out of 23 in 1nbs


Lead binding site 9 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 9 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: U228, A: A229, A: A231,

conact list:


AtomAtomDistance (A)
PbC3' A:U2284.12
PbO3' A:U2283.20
PbO4' A:U2284.95
PbC5' A:U2284.69
PbC2' A:U2284.56
PbC4' A:U2283.94
PbO2' A:U2283.82
PbOP1 A:A2293.93
PbP A:A2294.23
PbO5' A:A2294.92
PbOP1 A:A2313.17
PbP A:A2314.54

interactive model:


Lead binding site 10 out of 23 in 1nbs


Lead binding site 10 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 10 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: A139, A: A140, A: G168,

conact list:


AtomAtomDistance (A)
PbOP2 A:A1394.94
PbOP2 A:A1404.94
PbN3 A:G1684.95
PbN2 A:G1683.73
PbC2 A:G1683.72
PbC6 A:G1683.50
PbN1 A:G1682.81
PbC5 A:G1684.79
PbO6 A:G1683.38

interactive model:


Lead binding site 11 out of 23 in 1nbs


Lead binding site 11 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 11 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: C96, A: G97, A: U104,

conact list:


AtomAtomDistance (A)
PbC5 A:C964.42
PbC4 A:C964.84
PbOP2 A:C964.64
PbN4 A:C964.53
PbC8 A:G974.84
PbC2 A:G974.94
PbC6 A:G972.56
PbN1 A:G973.67
PbC5 A:G973.36
PbN7 A:G973.55
PbC4 A:G974.69
PbO6 A:G971.45
PbOP2 A:U1044.39

interactive model:


Lead binding site 12 out of 23 in 1nbs


Lead binding site 12 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 12 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: G86,

conact list:


AtomAtomDistance (A)
PbOP1 A:G863.61
PbP A:G864.22
PbOP2 A:G864.56
PbC5' A:G864.08
PbO5' A:G863.75

interactive model:


Lead binding site 13 out of 23 in 1nbs


Lead binding site 13 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 13 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: A185, B: C186, B: G219, B: G220,

conact list:


AtomAtomDistance (A)
PbC6 B:A1854.73
PbN1 B:A1854.43
PbN6 B:A1854.37
PbN3 B:C1863.04
PbC2 B:C1863.05
PbN1 B:C1864.36
PbO2 B:C1862.42
PbC4 B:C1864.27
PbN4 B:C1864.81
PbO3' B:G2194.57
PbOP1 B:G2204.93
PbN7 B:G2204.60

interactive model:


Lead binding site 14 out of 23 in 1nbs


Lead binding site 14 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 14 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: G90, B: G132, B: G133, B: A230,

conact list:


AtomAtomDistance (A)
PbC8 B:G904.94
PbC6 B:G903.92
PbN1 B:G904.75
PbC5 B:G904.09
PbN7 B:G904.08
PbC4 B:G904.99
PbO6 B:G903.66
PbOP1 B:G1324.82
PbC8 B:G1324.35
PbC6 B:G1323.51
PbN1 B:G1324.84
PbC5 B:G1323.66
PbN7 B:G1323.15
PbO6 B:G1322.76
PbN7 B:G1334.57
PbO6 B:G1334.58
PbOP1 B:A2304.48

interactive model:


Lead binding site 15 out of 23 in 1nbs


Lead binding site 15 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 15 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: G86, B: C87,

conact list:


AtomAtomDistance (A)
PbN9 B:G864.40
PbC8 B:G863.19
PbC6 B:G863.96
PbC5 B:G863.42
PbP B:G864.82
PbN7 B:G862.36
PbC4 B:G864.52
PbOP2 B:G863.84
PbO5' B:G864.91
PbO6 B:G863.78
PbN4 B:C874.83

interactive model:


Lead binding site 16 out of 23 in 1nbs


Lead binding site 16 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 16 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: A160, B: G162, B: G163,

conact list:


AtomAtomDistance (A)
PbO2' B:A1603.66
PbC8 B:G1624.81
PbC5 B:G1624.81
PbN7 B:G1624.28
PbOP2 B:G1624.05
PbC8 B:G1634.07
PbC5 B:G1634.54
PbN7 B:G1633.40
PbO6 B:G1634.73

interactive model:


Lead binding site 17 out of 23 in 1nbs


Lead binding site 17 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 17 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: C134, B: U181, B: G182, B: U228, B: A231,

conact list:


AtomAtomDistance (A)
PbC3' B:C1344.70
PbC2 B:C1343.99
PbN1 B:C1344.39
PbC1' B:C1343.90
PbO2 B:C1343.00
PbO3' B:C1344.91
PbC2' B:C1343.29
PbO2' B:C1342.43
PbN3 B:U1814.91
PbC5 B:U1814.04
PbC4 B:U1813.69
PbO4 B:U1812.75
PbC6 B:G1824.31
PbC5 B:G1824.46
PbN7 B:G1823.95
PbO6 B:G1823.57
PbO4 B:U2284.82
PbN6 B:A2314.55

interactive model:


Lead binding site 18 out of 23 in 1nbs


Lead binding site 18 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 18 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: A98, B: U101, B: C102, B: U104,

conact list:


AtomAtomDistance (A)
PbOP2 B:A984.46
PbOP1 B:U1014.55
PbP B:U1014.23
PbOP2 B:U1013.23
PbC5' B:U1013.95
PbC4' B:U1014.92
PbO5' B:U1014.58
PbOP1 B:C1024.85
PbP B:C1024.10
PbOP2 B:C1022.66
PbO5' B:C1024.72
PbC5 B:U1044.57
PbC4 B:U1044.50
PbO4 B:U1043.69

interactive model:


Lead binding site 19 out of 23 in 1nbs


Lead binding site 19 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 19 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: U218, B: G219, B: A222,

conact list:


AtomAtomDistance (A)
PbO4 B:U2184.84
PbC6 B:G2194.34
PbC5 B:G2194.97
PbN7 B:G2194.87
PbO6 B:G2193.32
PbOP2 B:A2224.88

interactive model:


Lead binding site 20 out of 23 in 1nbs


Lead binding site 20 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 20 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 20 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: G188, B: G190,

conact list:


AtomAtomDistance (A)
PbN7 B:G1884.98
PbOP2 B:G1884.72
PbOP1 B:G1904.88
PbOP2 B:G1904.58

interactive model:


Lead binding site 21 out of 23 in 1nbs


Lead binding site 21 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 21 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 21 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: G137,

conact list:


AtomAtomDistance (A)
PbN7 B:G1374.65
PbO6 B:G1374.50

interactive model:


Lead binding site 22 out of 23 in 1nbs


Lead binding site 22 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 22 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 22 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: C96, A: C102, A: A103, B: U228, B: A229, B: A230, B: A231,

conact list:


AtomAtomDistance (A)
PbOP1 A:C964.82
PbOP1 A:C1024.13
PbP A:C1024.57
PbOP2 A:C1024.60
PbO5' A:C1024.48
PbOP2 A:A1034.51
PbC3' B:U2284.92
PbO3' B:U2283.86
PbC4' B:U2284.99
PbO2' B:U2284.26
PbOP1 B:A2294.31
PbP B:A2294.64
PbO5' B:A2294.91
PbC2' B:A2304.77
PbO2' B:A2304.97
PbOP1 B:A2312.56
PbP B:A2313.93
PbOP2 B:A2314.56
PbO5' B:A2314.53

interactive model:


Lead binding site 23 out of 23 in 1nbs


Lead binding site 23 out of 23 in 1nbs
Click to enlarge
stereopicture of Lead binding site 23 out of 23 in 1nbs
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 23 of Lead in the PDB 1nbs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Lead atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: C96, B: G97, B: U104,

conact list:


AtomAtomDistance (A)
PbC5 B:C964.29
PbC4 B:C964.74
PbOP2 B:C964.98
PbN4 B:C964.38
PbC2 B:G974.97
PbC6 B:G972.68
PbN1 B:G973.63
PbC5 B:G973.69
PbN7 B:G974.04
PbC4 B:G974.98
PbO6 B:G971.45
PbOP2 B:U1044.51

interactive model:




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