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Lead in PDB 1iw7: Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution

Enzymatic activity of Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution

All present enzymatic activity of Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution, PDB code: 1iw7 was solved by Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.60
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 236.350, 236.350, 249.040, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 27.4

Other elements in 1iw7:

The structure of Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 485 atoms

Lead Binding Sites:

The binding sites of Lead atom in the Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution (pdb code 1iw7). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 4 binding sites of Lead where determined in the Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution, PDB code: 1iw7:
Jump to Lead binding site number: 1; 2; 3; 4;

Lead binding site 1 out of 4 in 1iw7

Go back to Lead Binding Sites List in 1iw7
Lead binding site 1 out of 4 in the Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution


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 Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pb6058

b:0.8
occ:1.00
 SG D:CYS58 3.0 66.0 1.0
CB D:CYS60 3.1 80.1 1.0
SG D:CYS60 3.3 84.2 1.0
N D:CYS60 3.5 79.1 1.0
SG D:CYS73 3.5 73.9 1.0
CA D:CYS60 3.8 80.0 1.0
N D:GLY61 3.8 80.5 1.0
CB D:CYS73 4.0 74.8 1.0
CB D:CYS76 4.1 76.6 1.0
CB D:CYS58 4.1 69.4 1.0
N D:LYS62 4.1 79.8 1.0
C D:CYS60 4.2 80.4 1.0
CB D:LYS62 4.3 78.0 1.0
O D:CYS76 4.3 76.2 1.0
N D:ALA59 4.6 74.3 1.0
C D:ALA59 4.7 78.1 1.0
CG D:LYS62 4.8 75.4 1.0
CA D:CYS76 4.9 76.1 1.0
CA D:LYS62 4.9 79.5 1.0
C D:CYS76 4.9 75.3 1.0
N D:CYS76 4.9 76.0 1.0
CA D:GLY61 4.9 80.1 1.0

Lead binding site 2 out of 4 in 1iw7

Go back to Lead Binding Sites List in 1iw7
Lead binding site 2 out of 4 in the Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution


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 Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pb6112

b:71.9
occ:1.00
 CB D:CYS1112 2.8 58.9 1.0
SG D:CYS1194 3.2 63.7 1.0
SG D:CYS1204 3.2 46.6 1.0
CB D:CYS1201 3.2 46.0 1.0
CB D:CYS1204 3.4 41.0 1.0
SG D:CYS1201 3.4 52.4 1.0
SG D:CYS1112 3.4 61.4 1.0
OG1 D:THR1196 3.6 54.8 1.0
N D:CYS1201 3.6 44.7 1.0
CA D:CYS1201 4.0 43.5 1.0
CA D:CYS1112 4.1 57.6 1.0
CB D:CYS1194 4.2 60.0 1.0
CA D:CYS1194 4.3 57.2 1.0
N D:CYS1112 4.4 57.2 1.0
N D:GLN1195 4.4 58.4 1.0
NH1 D:ARG1189 4.5 43.5 1.0
CA D:CYS1204 4.7 39.6 1.0
C D:VAL1200 4.7 45.7 1.0
N D:CYS1204 4.7 39.4 1.0
C D:CYS1201 4.9 41.8 1.0
N D:THR1196 4.9 58.8 1.0
C D:CYS1112 4.9 57.2 1.0
O D:CYS1112 4.9 57.2 1.0
CA D:VAL1200 5.0 46.6 1.0
C D:CYS1194 5.0 57.9 1.0
CB D:THR1196 5.0 57.0 1.0

Lead binding site 3 out of 4 in 1iw7

Go back to Lead Binding Sites List in 1iw7
Lead binding site 3 out of 4 in the Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution


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 Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Pb7058

b:91.4
occ:1.00
 CB N:CYS73 2.7 63.9 1.0
SG N:CYS73 2.8 61.6 1.0
SG N:CYS60 2.9 62.5 1.0
SG N:CYS58 3.0 67.6 1.0
O N:CYS76 3.2 68.6 1.0
O N:HOH2407 3.3 35.4 1.0
SG N:CYS76 3.5 73.0 1.0
CB N:CYS76 3.9 70.2 1.0
C N:CYS76 4.0 68.2 1.0
CB N:CYS58 4.1 63.3 1.0
CA N:CYS73 4.2 66.0 1.0
CA N:CYS76 4.3 69.8 1.0
N N:CYS76 4.3 70.8 1.0
CB N:LYS62 4.3 60.1 1.0
CB N:CYS60 4.6 61.4 1.0
O N:HOH2038 4.7 60.7 1.0
N N:LYS62 4.7 60.8 1.0
N N:CYS60 4.8 62.6 1.0
C N:CYS73 4.8 66.8 1.0
N N:CYS73 4.9 67.0 1.0
N N:GLY61 4.9 61.9 1.0

Lead binding site 4 out of 4 in 1iw7

Go back to Lead Binding Sites List in 1iw7
Lead binding site 4 out of 4 in the Crystal Structure of the Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution


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 Rna Polymerase Holoenzyme From Thermus Thermophilus at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Pb7112

b:93.0
occ:1.00
 SG N:CYS1112 2.8 62.2 1.0
CA N:CYS1194 3.1 52.8 1.0
MG N:MG9257 3.1 91.4 1.0
CB N:CYS1194 3.2 52.9 1.0
SG N:CYS1204 3.3 45.2 1.0
MG N:MG9396 3.4 95.9 1.0
CB N:CYS1204 3.5 40.8 1.0
CB N:CYS1112 3.5 59.8 1.0
SG N:CYS1194 3.5 57.4 1.0
N N:GLN1195 3.6 57.8 1.0
C N:CYS1194 3.9 54.7 1.0
N N:CYS1194 4.2 48.8 1.0
NH1 N:ARG1189 4.3 28.9 1.0
CB N:CYS1201 4.4 40.0 1.0
N N:CYS1201 4.4 43.4 1.0
OG1 N:THR1196 4.5 63.8 1.0
N N:THR1196 4.7 63.5 1.0
O N:THR1193 4.9 45.7 1.0
C N:THR1193 4.9 45.3 1.0
CA N:GLN1195 4.9 60.7 1.0
CA N:CYS1204 4.9 40.6 1.0
CA N:CYS1112 5.0 59.4 1.0

Reference:

D.G.Vassylyev, S.Sekine, O.Laptenko, J.Lee, M.N.Vassylyeva, S.Borukhov, S.Yokoyama. Crystal Structure of A Bacterial Rna Polymerase Holoenzyme at 2.6 A Resolution Nature V. 417 712 2002.
ISSN: ISSN 0028-0836
PubMed: 12000971
DOI: 10.1038/NATURE752
Page generated: Thu Oct 10 09:59:45 2024

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