Zinc in PDB 6h67: Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)

Enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd):
2.7.7.6;

Other elements in 6h67:

The structure of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) (pdb code 6h67). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd), PDB code: 6h67:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6h67

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Zinc binding site 1 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:49.8
occ:1.00
 NE2 A:HIS75 2.2 46.4 1.0
SG A:CYS65 2.5 57.2 1.0
CD2 A:HIS75 2.5 46.4 1.0
SG A:CYS62 2.5 57.3 1.0
SG A:CYS72 2.9 48.4 1.0
CB A:CYS65 3.1 57.2 1.0
CE1 A:HIS75 3.5 46.4 1.0
CB A:CYS62 3.5 57.3 1.0
N A:CYS65 3.6 57.2 1.0
CG A:HIS75 3.8 46.4 1.0
CA A:CYS65 3.9 57.2 1.0
CA A:GLY55 4.1 46.8 1.0
ND1 A:HIS75 4.2 46.4 1.0
CB A:THR64 4.3 53.9 1.0
CB A:CYS72 4.5 48.4 1.0
N A:GLY55 4.5 46.8 1.0
N A:GLY74 4.5 42.5 1.0
C A:THR64 4.6 53.9 1.0
CA A:GLY74 4.6 42.5 1.0
C A:GLY55 4.7 46.8 1.0
C A:GLY74 4.8 42.5 1.0
C A:CYS65 4.8 57.2 1.0
N A:GLY66 4.9 58.2 1.0
CA A:THR64 4.9 53.9 1.0
CG2 A:THR64 4.9 53.9 1.0
N A:HIS75 5.0 46.4 1.0
CA A:CYS62 5.0 57.3 1.0
N A:THR64 5.0 53.9 1.0
CB A:HIS75 5.0 46.4 1.0

Zinc binding site 2 out of 6 in 6h67

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Zinc binding site 2 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:0.7
occ:1.00
 SG A:CYS105 2.5 83.3 1.0
SG A:CYS102 2.5 81.3 1.0
SG A:CYS236 2.6 81.6 1.0
SG A:CYS233 2.8 78.2 1.0
CB A:CYS105 3.0 83.3 1.0
N A:CYS105 3.5 83.3 1.0
CB A:CYS102 3.7 81.3 1.0
CB A:CYS236 3.7 81.6 1.0
CA A:CYS105 3.8 83.3 1.0
CB A:CYS233 4.0 78.2 1.0
N A:CYS236 4.0 81.6 1.0
CB A:ASN235 4.2 75.3 1.0
CB A:PHE104 4.5 83.0 1.0
CA A:CYS236 4.5 81.6 1.0
C A:PHE104 4.6 83.0 1.0
C A:ASN235 4.6 75.3 1.0
CA A:ASN235 4.9 75.3 1.0
C A:CYS105 4.9 83.3 1.0
CA A:PHE104 4.9 83.0 1.0
N A:PHE104 4.9 83.0 1.0

Zinc binding site 3 out of 6 in 6h67

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Zinc binding site 3 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:87.3
occ:1.00
 SG B:CYS1104 2.5 53.7 1.0
SG B:CYS1107 2.5 57.0 1.0
SG B:CYS1131 2.5 63.7 1.0
SG B:CYS1128 2.5 62.5 1.0
CB B:CYS1131 3.0 63.7 1.0
CB B:CYS1107 3.2 57.0 1.0
CB B:CYS1104 3.4 53.7 1.0
CB B:CYS1128 3.6 62.5 1.0
N B:CYS1107 3.6 57.0 1.0
N B:CYS1131 3.6 63.7 1.0
CA B:CYS1131 3.9 63.7 1.0
CA B:CYS1107 4.0 57.0 1.0
CB B:GLU1106 4.3 59.2 1.0
C B:GLU1106 4.5 59.2 1.0
C B:ARG1130 4.7 55.3 1.0
CB B:ARG1130 4.7 55.3 1.0
CA B:GLU1106 4.8 59.2 1.0
N B:ARG1130 4.8 55.3 1.0
CA B:CYS1104 4.9 53.7 1.0
N B:GLU1106 4.9 59.2 1.0
OE1 B:GLU1106 4.9 59.2 1.0
C B:CYS1107 5.0 57.0 1.0
CG B:GLU1106 5.0 59.2 1.0
CA B:CYS1128 5.0 62.5 1.0
CA B:ARG1130 5.0 55.3 1.0

Zinc binding site 4 out of 6 in 6h67

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Zinc binding site 4 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:0.2
occ:1.00
 SG I:CYS13 2.2 0.0 1.0
SG I:CYS33 2.5 0.0 1.0
SG I:CYS30 2.9 0.5 1.0
SG I:CYS10 3.1 0.1 1.0
CB I:CYS10 3.3 0.1 1.0
CB I:CYS30 3.4 0.5 1.0
CB I:CYS13 3.9 0.0 1.0
OD2 I:ASP15 4.0 98.3 1.0
CB I:CYS33 4.1 0.0 1.0
CB I:ASP15 4.3 98.3 1.0
CD2 I:LEU17 4.5 0.5 1.0
N I:CYS13 4.5 0.0 1.0
CG I:ASP15 4.6 98.3 1.0
N I:CYS33 4.7 0.0 1.0
CA I:CYS13 4.7 0.0 1.0
OH I:TYR37 4.7 0.1 1.0
CA I:CYS10 4.8 0.1 1.0
CA I:CYS30 4.8 0.5 1.0
CB I:ALA35 4.8 0.6 1.0
CA I:CYS33 4.9 0.0 1.0
N I:LYS34 4.9 0.4 1.0

Zinc binding site 5 out of 6 in 6h67

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Zinc binding site 5 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:16.9
occ:1.00
 N J:CYS46 2.2 24.7 1.0
SG J:CYS45 2.4 23.9 1.0
SG J:CYS46 2.5 24.7 1.0
SG J:CYS7 2.5 21.0 1.0
CA J:CYS46 2.6 24.7 1.0
C J:CYS45 2.6 23.9 1.0
SG J:CYS10 2.9 19.7 1.0
O J:CYS45 3.0 23.9 1.0
CB J:CYS46 3.0 24.7 1.0
CB J:CYS45 3.3 23.9 1.0
CB J:CYS7 3.4 21.0 1.0
CA J:CYS45 3.5 23.9 1.0
C J:CYS46 4.0 24.7 1.0
CB J:CYS10 4.3 19.7 1.0
N J:CYS45 4.3 23.9 1.0
N J:CYS10 4.6 19.7 1.0
O J:CYS46 4.7 24.7 1.0
N J:ARG47 4.8 25.6 1.0
CA J:CYS7 4.8 21.0 1.0
CB J:SER9 4.9 18.0 1.0
CB J:ARG43 5.0 26.0 1.0
O J:ARG43 5.0 26.0 1.0

Zinc binding site 6 out of 6 in 6h67

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Zinc binding site 6 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:0.7
occ:1.00
 SG L:CYS51 2.5 71.0 1.0
SG L:CYS48 2.5 74.8 1.0
SG L:CYS31 2.5 50.3 1.0
SG L:CYS34 2.5 56.5 1.0
CB L:CYS48 3.1 74.8 1.0
CB L:CYS34 3.6 56.5 1.0
N L:CYS34 3.7 56.5 1.0
CB L:CYS31 3.8 50.3 1.0
CB L:HIS53 4.0 66.6 1.0
CB L:CYS51 4.1 71.0 1.0
CA L:CYS34 4.2 56.5 1.0
OG L:SER36 4.3 52.5 1.0
N L:CYS51 4.5 71.0 1.0
CB L:GLU33 4.5 56.3 1.0
O L:CYS51 4.5 71.0 1.0
N L:GLU33 4.6 56.3 1.0
C L:GLU33 4.6 56.3 1.0
CA L:CYS48 4.6 74.8 1.0
CG L:HIS53 4.7 66.6 1.0
CA L:CYS51 4.7 71.0 1.0
CD2 L:HIS53 4.7 66.6 1.0
C L:CYS51 4.8 71.0 1.0
CA L:GLU33 4.8 56.3 1.0
C L:CYS34 4.9 56.5 1.0
N L:SER35 5.0 50.1 1.0

Reference:

M.Sanz-Murillo, J.Xu, G.A.Belogurov, O.Calvo, D.Gil-Carton, M.Moreno-Morcillo, D.Wang, C.Fernandez-Tornero. Structural Basis of Rna Polymerase I Stalling at Uv Light-Induced Dna Damage. Proc. Natl. Acad. Sci. V. 115 8972 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30127008
DOI: 10.1073/PNAS.1802626115
Page generated: Wed Dec 16 11:55:51 2020

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