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Zinc in PDB 4wqs: Thermus Thermophilus Rna Polymerase Backtracked Complex

Enzymatic activity of Thermus Thermophilus Rna Polymerase Backtracked Complex

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Backtracked Complex:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Rna Polymerase Backtracked Complex, PDB code: 4wqs was solved by Y.Murayama, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.15 / 4.31
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 155.983, 155.983, 495.000, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 31.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Rna Polymerase Backtracked Complex (pdb code 4wqs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Thermus Thermophilus Rna Polymerase Backtracked Complex, PDB code: 4wqs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4wqs

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Zinc binding site 1 out of 4 in the Thermus Thermophilus Rna Polymerase Backtracked Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Rna Polymerase Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1601

b:72.1
occ:1.00
SG D:CYS73 2.5 0.9 1.0
CB D:LYS62 2.8 0.7 1.0
CG D:LYS62 2.8 0.2 1.0
N D:LYS62 3.0 0.2 1.0
CB D:CYS73 3.3 0.9 1.0
CA D:LYS62 3.4 0.2 1.0
SG D:CYS58 3.6 0.4 1.0
N D:GLY61 4.0 0.8 1.0
SG D:CYS76 4.1 0.5 1.0
C D:GLY61 4.1 0.8 1.0
N D:TYR63 4.3 0.4 1.0
CD D:LYS62 4.4 0.9 1.0
SG D:CYS60 4.4 0.4 1.0
C D:LYS62 4.4 0.2 1.0
CA D:GLY61 4.5 0.8 1.0
O D:CYS76 4.6 0.3 1.0
CD1 D:TYR63 4.6 0.7 1.0
CA D:CYS73 4.7 0.4 1.0
CG D:ARG75 4.7 0.9 1.0
CB D:ARG75 4.9 0.9 1.0
N D:CYS76 4.9 0.3 1.0
CB D:CYS60 4.9 0.9 1.0

Zinc binding site 2 out of 4 in 4wqs

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Zinc binding site 2 out of 4 in the Thermus Thermophilus Rna Polymerase Backtracked Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Rna Polymerase Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1602

b:72.1
occ:1.00
CB D:CYS1204 1.9 0.7 1.0
SG D:CYS1204 2.0 0.7 1.0
SG D:CYS1112 2.1 0.1 1.0
NH1 D:ARG1189 2.2 0.8 1.0
SG D:CYS1201 2.5 0.7 1.0
CB D:CYS1194 2.5 0.9 1.0
SG D:CYS1194 2.9 0.9 1.0
CZ D:ARG1189 3.0 0.5 1.0
CA D:CYS1194 3.0 0.5 1.0
CA D:CYS1204 3.1 0.2 1.0
CB D:CYS1112 3.2 0.1 1.0
N D:CYS1204 3.5 0.2 1.0
NH2 D:ARG1189 3.5 0.7 1.0
NE D:ARG1189 3.8 0.1 1.0
CG1 D:VAL1200 3.8 0.2 1.0
N D:CYS1201 3.9 0.3 1.0
N D:CYS1194 4.0 0.5 1.0
CB D:CYS1201 4.1 0.6 1.0
C D:CYS1194 4.1 0.5 1.0
CD D:ARG1189 4.2 0.0 1.0
N D:GLN1195 4.3 0.5 1.0
O D:SER1190 4.3 0.5 1.0
CA D:CYS1112 4.3 0.0 1.0
C D:CYS1204 4.3 0.2 1.0
O D:CYS1112 4.4 0.0 1.0
CA D:CYS1201 4.5 0.3 1.0
N D:CYS1112 4.5 0.0 1.0
O D:CYS1201 4.6 0.3 1.0
C D:LYS1203 4.7 0.9 1.0
CG D:ARG1189 4.7 0.3 1.0
C D:CYS1112 4.8 0.0 1.0
C D:SER1190 4.8 0.5 1.0
C D:THR1193 4.9 0.4 1.0
C D:CYS1201 4.9 0.3 1.0
CB D:VAL1200 4.9 0.2 1.0
CA D:PRO1191 4.9 0.3 1.0
O D:THR1193 5.0 0.4 1.0
C D:VAL1200 5.0 0.3 1.0
O D:CYS1204 5.0 0.2 1.0

Zinc binding site 3 out of 4 in 4wqs

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Zinc binding site 3 out of 4 in the Thermus Thermophilus Rna Polymerase Backtracked Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus Rna Polymerase Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1601

b:72.1
occ:1.00
SG N:CYS60 2.1 0.4 1.0
SG N:CYS76 2.4 0.8 1.0
CB N:CYS76 2.7 0.8 1.0
SG N:CYS73 2.9 0.9 1.0
N N:CYS60 3.5 0.9 1.0
SG N:CYS58 3.7 0.9 1.0
CB N:CYS60 3.7 0.8 1.0
CB N:CYS73 3.9 0.2 1.0
CA N:CYS76 4.0 0.1 1.0
N N:GLY61 4.0 0.9 1.0
CB N:ALA59 4.1 0.5 1.0
N N:CYS76 4.1 0.1 1.0
CA N:CYS60 4.1 0.9 1.0
N N:ALA59 4.3 0.8 1.0
N N:LYS62 4.3 0.6 1.0
CB N:LYS62 4.4 0.6 1.0
C N:ALA59 4.5 0.7 1.0
CB N:CYS58 4.5 0.9 1.0
O N:CYS76 4.5 0.1 1.0
CA N:ALA59 4.5 0.3 1.0
CG N:LYS62 4.5 0.6 1.0
C N:CYS60 4.6 0.9 1.0
C N:CYS76 4.7 0.1 1.0
C N:ARG75 4.9 0.8 1.0
CG N:ARG75 4.9 0.1 1.0
CA N:LYS62 5.0 0.6 1.0

Zinc binding site 4 out of 4 in 4wqs

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Zinc binding site 4 out of 4 in the Thermus Thermophilus Rna Polymerase Backtracked Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermus Thermophilus Rna Polymerase Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1602

b:72.1
occ:1.00
CB N:CYS1201 1.8 0.6 1.0
SG N:CYS1201 1.9 0.6 1.0
SG N:CYS1204 1.9 0.3 1.0
CB N:CYS1112 2.1 0.5 1.0
SG N:CYS1112 2.1 0.5 1.0
N N:CYS1112 2.3 0.7 1.0
SG N:CYS1194 2.3 0.5 1.0
CA N:CYS1112 2.6 0.7 1.0
CA N:CYS1201 2.8 0.3 1.0
N N:CYS1201 2.9 0.1 1.0
O N:CYS1112 3.4 0.7 1.0
CB N:CYS1204 3.4 0.3 1.0
C N:CYS1112 3.5 0.7 1.0
C N:ASP1111 3.5 0.7 1.0
C N:CYS1201 3.8 0.8 1.0
NH1 N:ARG1189 3.9 0.2 1.0
OD1 N:ASP1111 3.9 0.9 1.0
CB N:CYS1194 4.0 0.3 1.0
N N:CYS1204 4.1 0.0 1.0
CA N:ASP1111 4.1 0.7 1.0
OG1 N:THR1196 4.1 0.6 1.0
C N:VAL1200 4.2 0.8 1.0
O N:CYS1201 4.2 0.7 1.0
CA N:CYS1204 4.4 0.0 1.0
CZ N:ARG1189 4.4 0.2 1.0
O N:ASP1111 4.5 0.7 1.0
CG1 N:VAL1200 4.6 0.6 1.0
N N:GLN1202 4.6 0.9 1.0
CA N:CYS1194 4.6 0.1 1.0
O N:ALA1110 4.7 0.3 1.0
OE1 N:GLU1109 4.7 0.5 1.0
N N:GLY1113 4.7 0.5 1.0
N N:GLN1195 4.8 0.3 1.0
CG N:ASP1111 4.8 0.9 1.0
CA N:VAL1200 4.8 0.8 1.0
NH2 N:ARG1189 4.8 0.2 1.0
N N:LYS1203 4.8 0.2 1.0

Reference:

S.I.Sekine, Y.Murayama, V.Svetlov, E.Nudler, S.Yokoyama. The Ratcheted and Ratchetable Structural States of Rna Polymerase Underlie Multiple Transcriptional Functions. Mol.Cell V. 57 408 2015.
ISSN: ISSN 1097-2765
PubMed: 25601758
DOI: 10.1016/J.MOLCEL.2014.12.014
Page generated: Wed Dec 16 05:51:31 2020

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