Lead in PDB 1nbs: Crystal Structure of the Specificity Domain of Ribonuclease P Rna

The structure of Crystal Structure of the Specificity Domain of Ribonuclease P Rna, PDB code: 1nbs was solved by A.S.Krasilnikov, X.Yang, T.Pan, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 3.15
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	126.500, 145.300, 144.600, 90.00, 90.00, 90.00
R / Rfree (%)	28 / 30.7

The structure of Crystal Structure of the Specificity Domain of Ribonuclease P Rna also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Lead atom in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna (pdb code 1nbs). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 23 binding sites of Lead where determined in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna, PDB code: 1nbs:
Jump to Lead binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Lead binding site 1 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb241 b:0.8 occ:0.23 O3' A:G219 2.4 0.7 1.0 N4 A:C186 2.6 0.1 1.0 OP1 A:G220 3.0 0.8 1.0 P A:G220 3.2 0.9 1.0 N3 A:C186 3.3 0.7 1.0 C4 A:C186 3.4 0.8 1.0 C3' A:G219 3.6 1.0 1.0 C4' A:G219 3.7 0.4 1.0 OP2 A:G220 3.8 0.2 1.0 C5' A:G219 4.0 0.3 1.0 N6 A:A185 4.3 0.6 1.0 O2' A:G219 4.5 0.6 1.0 O5' A:G220 4.6 0.7 1.0 C2 A:C186 4.6 0.4 1.0 C2' A:G219 4.6 0.4 1.0 C5 A:C186 4.8 0.5 1.0 O5' A:G219 4.9 0.7 1.0 C6 A:A185 5.0 0.4 1.0

Lead binding site 2 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb242 b:0.1 occ:0.23 MG A:MG7 2.7 57.2 1.0 N7 A:G132 2.8 53.1 1.0 O6 A:G132 2.9 59.0 1.0 C5 A:G132 3.5 54.4 1.0 C6 A:G132 3.5 55.6 1.0 O6 A:G90 3.8 52.8 1.0 O6 A:G133 3.9 53.3 1.0 C8 A:G132 4.0 53.2 1.0 C6 A:G90 4.1 52.1 1.0 N7 A:G133 4.2 55.8 1.0 N7 A:G90 4.3 53.4 1.0 C5 A:G90 4.3 52.1 1.0 C6 A:G133 4.6 55.6 1.0 C5 A:G133 4.8 54.2 1.0 C4 A:G132 4.8 53.7 1.0 N1 A:G132 4.9 56.2 1.0 N1 A:G90 4.9 51.1 1.0

Lead binding site 3 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb243 b:57.3 occ:0.19 N7 A:G86 2.4 82.4 1.0 O6 A:G86 2.9 85.4 1.0 C5 A:G86 3.2 82.1 1.0 C6 A:G86 3.4 82.6 1.0 C8 A:G86 3.5 81.6 1.0 OP2 A:G86 3.8 87.2 1.0 N4 A:C87 4.4 64.1 1.0 C4 A:G86 4.5 80.7 1.0 N1 A:A240 4.5 60.5 1.0 N9 A:G86 4.6 80.3 1.0 N6 A:A240 4.7 59.4 1.0 N1 A:G86 4.8 81.2 1.0 C6 A:A240 5.0 60.4 1.0 P A:G86 5.0 88.2 1.0

Lead binding site 4 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 4 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb244 b:63.8 occ:0.23 O2 A:C134 2.3 76.2 1.0 O4 A:U181 2.4 73.7 1.0 O2' A:C134 3.1 77.0 1.0 C4 A:U181 3.5 70.3 1.0 C2 A:C134 3.5 73.5 1.0 O6 A:G182 3.6 78.2 1.0 C2' A:C134 3.8 73.2 1.0 N7 A:G182 3.8 77.8 1.0 C1' A:C134 3.9 71.9 1.0 C5 A:U181 4.0 68.1 1.0 N1 A:C134 4.2 71.2 1.0 C6 A:G182 4.2 77.1 1.0 C5 A:G182 4.3 77.2 1.0 N6 A:A231 4.3 59.5 1.0 N3 A:C134 4.5 71.9 1.0 N3 A:U181 4.7 68.5 1.0 C8 A:G182 4.8 77.4 1.0

Lead binding site 5 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 5 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb245 b:62.0 occ:0.20 OP2 A:C102 2.7 50.9 1.0 P A:C102 4.1 46.9 1.0 OP2 A:A98 4.2 86.3 1.0 OP2 A:G97 4.5 84.8 1.0 OP1 A:C102 4.6 46.8 1.0 OP2 A:A103 4.7 37.7 1.0 N7 A:G97 4.7 89.6 1.0 O4 A:U104 4.8 71.1 1.0 C8 A:G97 4.9 88.9 1.0 C5' A:U101 4.9 53.5 0.0 O3' A:U101 5.0 51.6 1.0

Lead binding site 6 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 6 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb246 b:0.7 occ:0.04 O6 A:G219 3.4 0.9 1.0 C6 A:G219 4.4 0.8 1.0 N1 A:G219 4.5 0.2 1.0 OP2 A:A222 4.9 0.5 1.0

Lead binding site 7 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 7 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb247 b:0.4 occ:0.02 OP2 A:A187 4.3 0.2 1.0 OP2 A:G188 4.3 0.2 1.0 OP1 A:A187 4.4 0.7 1.0 P A:A187 4.8 0.5 1.0

Lead binding site 8 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 8 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb248 b:0.5 occ:0.03 O6 A:G136 2.2 80.7 1.0 C6 A:G136 3.3 79.9 1.0 N7 A:G136 3.7 80.0 1.0 C5 A:G136 3.8 80.0 1.0 N6 A:A135 3.9 71.3 1.0 O6 A:G137 4.0 86.8 1.0 N4 A:C173 4.2 72.3 1.0 N7 A:G137 4.4 87.2 1.0 N1 A:G136 4.5 79.0 1.0 C6 A:A135 4.5 72.7 1.0 C6 A:G137 4.8 87.2 1.0 OP2 A:G180 4.8 79.4 1.0 N7 A:A135 4.9 73.3 1.0 C5 A:A135 4.9 73.9 1.0 C5 A:G137 4.9 87.3 1.0 C8 A:G136 5.0 80.0 1.0

Lead binding site 9 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 9 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb249 b:0.8 occ:0.05 OP1 A:A231 3.2 96.6 1.0 O3' A:U228 3.2 64.6 1.0 O2' A:U228 3.8 62.8 1.0 OP1 A:A229 3.9 67.2 1.0 C4' A:U228 3.9 59.0 1.0 C3' A:U228 4.1 60.7 1.0 P A:A229 4.2 65.8 1.0 P A:A231 4.5 95.8 1.0 C2' A:U228 4.6 60.4 1.0 C5' A:U228 4.7 57.4 1.0 O5' A:A229 4.9 65.7 1.0 O4' A:U228 5.0 56.8 1.0

Lead binding site 10 out of 23 in the Crystal Structure of the Specificity Domain of Ribonuclease P Rna


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 10 of Crystal Structure of the Specificity Domain of Ribonuclease P Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb250 b:0.6 occ:0.08 N1 A:G168 2.8 0.3 1.0 O6 A:G168 3.4 0.6 1.0 C6 A:G168 3.5 0.7 1.0 C2 A:G168 3.7 0.9 1.0 N2 A:G168 3.7 0.1 1.0 C5 A:G168 4.8 0.0 1.0 OP2 A:A140 4.9 0.3 1.0 OP2 A:A139 4.9 97.7 1.0 N3 A:G168 5.0 1.0 1.0

A.S.Krasilnikov, X.Yang, T.Pan, A.Mondragon. Crystal Structure of the Specificity Domain of Ribonuclease P Nature V. 421 760 2003.
ISSN: ISSN 0028-0836
PubMed: 12610630
DOI: 10.1038/NATURE01386