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Zinc in PDB 5tmc: Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure

Enzymatic activity of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure

All present enzymatic activity of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure:
2.7.7.6;

Protein crystallography data

The structure of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure, PDB code: 5tmc was solved by J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.51 / 2.71
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 236.350, 236.350, 249.040, 90.00, 90.00, 120.00
R / Rfree (%) 26.5 / 28.6

Other elements in 5tmc:

The structure of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure (pdb code 5tmc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure, PDB code: 5tmc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5tmc

Go back to Zinc Binding Sites List in 5tmc
Zinc binding site 1 out of 2 in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1602

b:0.6
occ:1.00
SG D:CYS73 2.4 0.8 1.0
SG D:CYS76 2.4 0.8 1.0
SG D:CYS58 2.4 0.0 1.0
SG D:CYS60 2.4 0.5 1.0
CB D:CYS73 2.9 0.1 1.0
CB D:CYS58 3.2 0.6 1.0
N D:GLY61 3.8 0.3 1.0
N D:LYS62 3.9 0.5 1.0
CB D:CYS76 3.9 0.7 1.0
N D:CYS60 4.0 0.2 1.0
CB D:CYS60 4.0 0.1 1.0
CB D:LYS62 4.2 0.7 1.0
N D:ALA59 4.3 0.3 1.0
N D:CYS76 4.3 0.6 1.0
CA D:CYS60 4.4 0.7 1.0
CA D:CYS73 4.4 0.6 1.0
CA D:CYS58 4.5 0.7 1.0
C D:CYS60 4.6 0.9 1.0
CA D:GLY61 4.6 0.8 1.0
CA D:LYS62 4.6 0.1 1.0
C D:GLY61 4.7 0.2 1.0
C D:CYS58 4.7 0.2 1.0
CA D:CYS76 4.7 0.4 1.0
N D:TYR63 4.9 0.6 1.0
C D:ALA59 4.9 0.8 1.0
N D:GLY77 4.9 0.3 1.0

Zinc binding site 2 out of 2 in 5tmc

Go back to Zinc Binding Sites List in 5tmc
Zinc binding site 2 out of 2 in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1603

b:0.6
occ:1.00
SG D:CYS1201 2.4 0.8 1.0
SG D:CYS1112 2.4 0.9 1.0
SG D:CYS1204 2.4 0.5 1.0
SG D:CYS1194 2.4 0.1 1.0
CA D:CYS1194 2.8 0.7 1.0
CB D:CYS1194 2.9 0.3 1.0
N D:GLN1195 3.0 0.5 1.0
CB D:CYS1204 3.0 87.5 1.0
C D:CYS1194 3.4 0.9 1.0
N D:CYS1194 4.0 0.6 1.0
CB D:CYS1112 4.2 0.7 1.0
CB D:CYS1201 4.2 79.4 1.0
CA D:GLN1195 4.2 0.6 1.0
O D:THR1193 4.3 84.6 1.0
CG2 D:THR1114 4.4 0.5 1.0
N D:CYS1201 4.5 64.8 1.0
CA D:CYS1204 4.5 85.7 1.0
N D:THR1196 4.5 0.6 1.0
OG1 D:THR1196 4.5 0.1 1.0
C D:GLN1195 4.5 0.9 1.0
C D:THR1193 4.6 89.7 1.0
O D:SER1190 4.6 72.3 1.0
O D:CYS1194 4.6 0.1 1.0
CB D:GLN1195 4.9 0.5 1.0
CA D:CYS1201 4.9 71.7 1.0
NH1 D:ARG1189 4.9 98.6 1.0
N D:CYS1204 5.0 82.6 1.0

Reference:

J.Wang, J.Wang. N/A N/A.
ISSN: ESSN 1469-896X
PubMed: 25352397
DOI: 10.1002/PRO.2595
Page generated: Wed Dec 16 10:56:10 2020

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