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Zinc in PDB 6h68: Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) with Fully-Ordered A49

Enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) with Fully-Ordered A49

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) with Fully-Ordered A49:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Rna Polymerase I Elongation Complex Stalled By Cyclobutane Pyrimidine Dimer (Cpd) with Fully-Ordered A49 (pdb code 6h68). 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) with Fully-Ordered A49, PDB code: 6h68:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6h68

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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) with Fully-Ordered A49


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) with Fully-Ordered A49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:0.7
occ:1.00
 NE2 A:HIS75 2.1 75.7 1.0
SG A:CYS65 2.4 95.8 1.0
SG A:CYS62 2.5 90.7 1.0
SG A:CYS72 2.5 79.0 1.0
CD2 A:HIS75 2.8 75.7 1.0
CB A:CYS65 2.9 95.8 1.0
N A:CYS65 3.1 95.8 1.0
CE1 A:HIS75 3.3 75.7 1.0
CA A:CYS65 3.6 95.8 1.0
CB A:CYS62 3.6 90.7 1.0
CB A:CYS72 3.6 79.0 1.0
CB A:THR64 4.0 87.1 1.0
CG A:HIS75 4.1 75.7 1.0
C A:THR64 4.1 87.1 1.0
ND1 A:HIS75 4.3 75.7 1.0
C A:CYS65 4.5 95.8 1.0
CA A:THR64 4.5 87.1 1.0
N A:GLY66 4.5 92.7 1.0
CA A:GLY55 4.6 81.6 1.0
CG2 A:THR64 4.6 87.1 1.0
N A:THR64 4.7 87.1 1.0
CA A:CYS72 4.7 79.0 1.0
N A:GLY55 5.0 81.6 1.0

Zinc binding site 2 out of 6 in 6h68

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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) with Fully-Ordered A49


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) with Fully-Ordered A49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:0.3
occ:1.00
 SG A:CYS105 2.5 62.2 1.0
SG A:CYS102 2.5 57.6 1.0
SG A:CYS236 2.6 70.9 1.0
SG A:CYS233 2.6 67.2 1.0
CB A:CYS105 3.2 62.2 1.0
CB A:CYS102 3.5 57.6 1.0
CB A:CYS233 3.7 67.2 1.0
N A:CYS105 3.8 62.2 1.0
CA A:CYS105 4.1 62.2 1.0
CB A:CYS236 4.2 70.9 1.0
CB A:ASN235 4.3 65.8 1.0
N A:CYS236 4.3 70.9 1.0
CG A:MET238 4.6 74.7 1.0
ND2 A:ASN235 4.7 65.8 1.0
CB A:MET238 4.7 74.7 1.0
CA A:CYS236 4.8 70.9 1.0
CB A:PHE104 4.8 63.8 1.0
C A:PHE104 4.9 63.8 1.0
CA A:CYS102 5.0 57.6 1.0

Zinc binding site 3 out of 6 in 6h68

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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) with Fully-Ordered A49


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) with Fully-Ordered A49 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:0.4
occ:1.00
 SG B:CYS1128 2.6 84.2 1.0
SG B:CYS1131 2.6 80.7 1.0
SG B:CYS1104 2.6 81.6 1.0
CB B:CYS1107 2.7 78.9 1.0
SG B:CYS1107 2.9 78.9 1.0
CB B:CYS1131 3.2 80.7 1.0
N B:CYS1107 3.3 78.9 1.0
CB B:CYS1104 3.3 81.6 1.0
CB B:CYS1128 3.4 84.2 1.0
CA B:CYS1107 3.6 78.9 1.0
N B:CYS1131 3.8 80.7 1.0
C B:GLU1106 4.1 83.2 1.0
CA B:CYS1131 4.1 80.7 1.0
O B:CYS1104 4.5 81.6 1.0
CB B:GLU1106 4.6 83.2 1.0
CA B:CYS1104 4.6 81.6 1.0
C B:CYS1104 4.7 81.6 1.0
C B:ARG1130 4.7 77.5 1.0
CA B:GLU1106 4.7 83.2 1.0
C B:CYS1107 4.7 78.9 1.0
CB B:ARG1130 4.8 77.5 1.0
N B:GLU1106 4.8 83.2 1.0
O B:GLU1106 4.8 83.2 1.0
CA B:CYS1128 4.9 84.2 1.0

Zinc binding site 4 out of 6 in 6h68

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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) with Fully-Ordered A49


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) with Fully-Ordered A49 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:0.7
occ:1.00
 SG I:CYS13 2.4 0.1 1.0
SG I:CYS33 2.4 0.3 1.0
SG I:CYS10 3.1 0.2 1.0
SG I:CYS30 3.1 0.1 1.0
CB I:CYS10 3.1 0.2 1.0
CB I:CYS30 3.4 0.1 1.0
CB I:CYS13 4.0 0.1 1.0
CB I:CYS33 4.0 0.3 1.0
CA I:CYS10 4.6 0.2 1.0
OD2 I:ASP15 4.6 0.2 1.0
N I:CYS13 4.7 0.1 1.0
CB I:ALA35 4.7 0.0 1.0
CB I:ASP15 4.7 0.2 1.0
N I:CYS33 4.8 0.3 1.0
CA I:CYS13 4.8 0.1 1.0
N I:ASP15 4.9 0.2 1.0
CA I:CYS30 4.9 0.1 1.0
CA I:CYS33 4.9 0.3 1.0

Zinc binding site 5 out of 6 in 6h68

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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) with Fully-Ordered A49


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) with Fully-Ordered A49 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:51.7
occ:1.00
 C J:CYS45 2.4 51.2 1.0
SG J:CYS7 2.5 45.2 1.0
CB J:CYS45 2.6 51.2 1.0
SG J:CYS10 2.6 59.7 1.0
N J:CYS46 2.6 51.6 1.0
O J:CYS45 2.8 51.2 1.0
SG J:CYS46 2.9 51.6 1.0
CA J:CYS45 3.0 51.2 1.0
SG J:CYS45 3.0 51.2 1.0
CA J:CYS46 3.4 51.6 1.0
CB J:CYS7 3.6 45.2 1.0
CB J:CYS10 3.6 59.7 1.0
CB J:CYS46 3.7 51.6 1.0
N J:CYS45 3.8 51.2 1.0
N J:CYS10 4.4 59.7 1.0
CA J:CYS10 4.6 59.7 1.0
NE J:ARG43 4.8 49.4 1.0
C J:CYS46 4.8 51.6 1.0
CG J:MET49 4.9 45.4 1.0
C J:TYR44 4.9 45.0 1.0
CA J:CYS7 4.9 45.2 1.0

Zinc binding site 6 out of 6 in 6h68

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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) with Fully-Ordered A49


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) with Fully-Ordered A49 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:0.6
occ:1.00
 SG L:CYS34 2.5 74.2 1.0
SG L:CYS51 2.5 0.8 1.0
CB L:CYS51 2.5 0.8 1.0
SG L:CYS48 2.6 0.5 1.0
SG L:CYS31 3.0 72.8 1.0
N L:CYS51 3.2 0.8 1.0
CB L:CYS34 3.2 74.2 1.0
CB L:CYS48 3.4 0.5 1.0
CA L:CYS51 3.5 0.8 1.0
C L:ASP50 3.9 0.0 1.0
CB L:CYS31 3.9 72.8 1.0
CB L:ASP50 4.1 0.0 1.0
N L:CYS34 4.2 74.2 1.0
C L:CYS51 4.4 0.8 1.0
CA L:CYS34 4.4 74.2 1.0
O L:CYS51 4.4 0.8 1.0
CA L:ASP50 4.4 0.0 1.0
N L:ASP50 4.5 0.0 1.0
O L:ASP50 4.6 0.0 1.0
OG L:SER36 4.7 62.4 1.0
CA L:CYS48 4.8 0.5 1.0
CB L:HIS53 4.8 97.2 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: Mon Oct 28 22:38:32 2024

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