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Zinc in PDB 5vvr: Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26

Enzymatic activity of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26

All present enzymatic activity of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26:
2.7.7.6; 3.6.4.12;

Other elements in 5vvr:

The structure of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 (pdb code 5vvr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26, PDB code: 5vvr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vvr

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Zinc binding site 1 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.5
occ:1.00
 O A:MET108 2.1 0.8 1.0
SG A:CYS107 2.6 0.7 1.0
N A:CYS167 2.6 0.3 1.0
N A:GLY166 3.0 0.5 1.0
CB A:CYS110 3.1 0.1 1.0
C A:GLY166 3.2 0.3 1.0
CB A:CYS167 3.3 0.9 1.0
C A:MET108 3.3 0.8 1.0
CA A:GLY166 3.4 0.8 1.0
CA A:CYS167 3.4 0.1 1.0
C A:GLY165 3.6 0.5 1.0
CB A:CYS148 3.8 0.6 1.0
N A:MET108 3.9 0.8 1.0
N A:CYS110 3.9 0.5 1.0
C A:CYS107 4.0 0.4 1.0
C A:HIS109 4.0 0.1 1.0
CA A:GLY165 4.0 0.4 1.0
CB A:CYS107 4.0 0.6 1.0
SG A:CYS148 4.0 0.2 1.0
O A:GLY166 4.1 0.1 1.0
C A:CYS167 4.1 0.3 1.0
CA A:CYS110 4.1 0.8 1.0
O A:CYS167 4.1 0.1 1.0
O A:CYS107 4.2 0.9 1.0
CA A:MET108 4.2 0.1 1.0
O A:HIS109 4.2 0.6 1.0
O A:GLY165 4.3 0.5 1.0
N A:HIS109 4.3 0.7 1.0
SG A:CYS110 4.3 0.5 1.0
CA A:CYS107 4.5 0.9 1.0
CA A:HIS109 4.5 0.7 1.0
O A:CYS148 4.6 0.4 1.0
CB A:HIS109 4.7 0.8 1.0
CA A:CYS148 4.9 0.3 1.0
CB A:MET108 4.9 0.2 1.0
O A:ARG164 5.0 0.8 1.0

Zinc binding site 2 out of 8 in 5vvr

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Zinc binding site 2 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.7
occ:1.00
 O A:CYS67 2.5 0.3 1.0
O A:PRO78 2.6 0.9 1.0
CB A:CYS67 2.9 0.6 1.0
SG A:CYS77 3.0 0.4 1.0
C A:CYS67 3.2 0.8 1.0
CE1 A:HIS80 3.3 0.6 1.0
CA A:CYS67 3.6 0.1 1.0
ND1 A:HIS80 3.6 0.7 1.0
CB A:CYS70 3.7 0.2 1.0
SG A:CYS70 3.7 0.4 1.0
C A:PRO78 3.9 0.8 1.0
N A:GLN68 4.1 0.0 1.0
CB A:GLN68 4.2 0.1 1.0
SG A:CYS67 4.4 0.9 1.0
C A:CYS77 4.4 0.2 1.0
N A:PRO78 4.4 0.3 1.0
O A:CYS77 4.5 0.8 1.0
CB A:CYS77 4.5 0.1 1.0
CD A:PRO78 4.6 0.8 1.0
NE2 A:HIS80 4.6 0.1 1.0
OE1 A:GLN68 4.7 0.6 1.0
CA A:GLN68 4.7 0.4 1.0
N A:GLY79 4.7 0.1 1.0
CA A:GLY79 4.7 0.7 1.0
CA A:PRO78 4.8 0.7 1.0
CA A:CYS77 4.8 0.4 1.0
CA A:CYS70 4.9 1.0 1.0
N A:CYS67 4.9 1.0 1.0
O A:LYS66 4.9 0.3 1.0
N A:CYS70 5.0 0.7 1.0
CG A:PRO78 5.0 0.7 1.0

Zinc binding site 3 out of 8 in 5vvr

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Zinc binding site 3 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.8
occ:1.00
 SG B:CYS1163 2.5 1.0 1.0
SG B:CYS1166 2.5 0.2 1.0
SG B:CYS1185 2.6 0.4 1.0
CB B:CYS1185 2.9 1.0 1.0
CB B:CYS1166 3.2 0.8 1.0
CB B:CYS1163 3.4 0.5 1.0
N B:CYS1166 3.4 0.2 1.0
O B:CYS1163 3.8 0.5 1.0
CB B:ILE1165 3.9 1.0 1.0
OG1 B:THR1170 3.9 0.8 1.0
CA B:CYS1166 4.0 0.8 1.0
CB B:CYS1182 4.0 0.7 1.0
SG B:CYS1182 4.1 0.7 1.0
C B:ILE1165 4.2 0.4 1.0
C B:CYS1163 4.3 0.9 1.0
CG2 B:ILE1165 4.3 0.6 1.0
CA B:ILE1165 4.4 0.5 1.0
CA B:CYS1185 4.4 0.3 1.0
N B:ILE1165 4.4 0.6 1.0
CA B:CYS1163 4.5 0.7 1.0
OD2 B:ASP1190 4.6 0.9 1.0
N B:CYS1185 4.9 0.6 1.0
CG1 B:ILE1165 4.9 0.8 1.0
C B:CYS1166 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 5vvr

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Zinc binding site 4 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.1
occ:1.00
 OE1 C:GLU81 2.1 0.5 1.0
OE2 C:GLU81 2.5 0.2 1.0
CD C:GLU81 2.6 0.6 1.0
SG C:CYS92 2.6 0.8 1.0
SG C:CYS88 2.7 0.5 1.0
SG C:CYS86 2.7 0.3 1.0
CB C:CYS88 2.8 0.2 1.0
N C:CYS88 3.1 0.4 1.0
SG C:CYS95 3.2 0.1 1.0
CA C:CYS88 3.5 0.6 1.0
CB C:CYS86 3.7 0.1 1.0
CA C:CYS86 3.7 1.0 1.0
CB C:CYS92 3.7 0.8 1.0
N C:PHE87 3.7 0.1 1.0
CG C:GLU81 4.0 0.9 1.0
C C:CYS86 4.0 0.3 1.0
CB C:CYS95 4.3 0.9 1.0
O C:CYS88 4.3 0.5 1.0
C C:PHE87 4.3 0.0 1.0
N C:CYS95 4.4 0.7 1.0
C C:CYS88 4.4 0.3 1.0
CB C:LYS94 4.6 0.9 1.0
CA C:CYS92 4.6 0.9 1.0
CA C:PHE87 4.7 0.1 1.0
CB C:GLU81 4.7 0.6 1.0
N C:LYS94 4.8 0.6 1.0
C C:LYS94 4.9 0.4 1.0
CA C:CYS95 4.9 0.1 1.0
O C:CYS86 5.0 0.2 1.0
N C:CYS86 5.0 0.0 1.0
CA C:LYS94 5.0 0.5 1.0

Zinc binding site 5 out of 8 in 5vvr

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Zinc binding site 5 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.7
occ:1.00
 SG I:CYS7 2.9 0.1 1.0
SG I:CYS29 2.9 0.9 1.0
SG I:CYS10 3.0 0.3 1.0
CB I:CYS32 3.0 0.7 1.0
CB I:ASN12 3.2 0.4 1.0
SG I:CYS32 3.6 0.2 1.0
O I:ASN12 3.9 0.9 1.0
CB I:CYS29 3.9 0.7 1.0
CB I:CYS7 3.9 0.0 1.0
ND2 I:ASN12 4.0 0.6 1.0
CA I:ASN12 4.0 0.2 1.0
CG I:ASN12 4.1 0.1 1.0
C I:ASN12 4.2 1.0 1.0
N I:ASN12 4.3 0.9 1.0
CA I:CYS32 4.4 0.8 1.0
CB I:CYS10 4.7 0.4 1.0
N I:CYS32 4.7 0.8 1.0
OG1 I:THR31 4.8 0.8 1.0
O I:THR31 4.8 0.5 1.0
C I:THR31 4.9 0.2 1.0

Zinc binding site 6 out of 8 in 5vvr

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Zinc binding site 6 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.3
occ:1.00
 ND1 I:HIS108 2.3 0.7 1.0
SG I:CYS103 2.8 0.9 1.0
CB I:CYS78 2.9 0.8 1.0
CG I:HIS108 3.1 0.4 1.0
CB I:CYS106 3.2 0.4 1.0
CE1 I:HIS108 3.3 0.0 1.0
CB I:HIS108 3.4 0.2 1.0
CB I:CYS103 3.5 0.8 1.0
SG I:CYS106 3.6 0.2 1.0
N I:CYS78 3.6 0.1 1.0
C I:LYS77 3.7 0.4 1.0
CA I:CYS78 3.8 0.1 1.0
O I:LYS77 3.9 0.5 1.0
O I:CYS103 4.1 0.6 1.0
SG I:CYS78 4.1 0.6 1.0
N I:CYS106 4.1 0.5 1.0
CA I:CYS106 4.2 0.5 1.0
CD2 I:HIS108 4.2 0.5 1.0
O I:CYS75 4.2 0.0 1.0
NE2 I:HIS108 4.3 0.6 1.0
CB I:LYS77 4.3 0.9 1.0
CE1 I:PHE110 4.4 0.3 1.0
CZ I:PHE110 4.5 0.9 1.0
CA I:LYS77 4.5 0.0 1.0
C I:CYS106 4.6 0.8 1.0
N I:HIS108 4.6 0.7 1.0
CB I:CYS75 4.6 0.5 1.0
CA I:HIS108 4.6 0.8 1.0
O I:CYS106 4.7 0.0 1.0
N I:LYS77 4.8 0.5 1.0
CA I:CYS103 4.8 0.4 1.0
C I:CYS103 4.9 0.4 1.0

Zinc binding site 7 out of 8 in 5vvr

Go back to Zinc Binding Sites List in 5vvr
Zinc binding site 7 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.5
occ:1.00
 N J:CYS46 2.4 0.2 1.0
SG J:CYS46 2.5 0.6 1.0
SG J:CYS10 2.5 0.2 1.0
C J:CYS45 2.6 0.9 1.0
O J:ARG43 3.0 0.5 1.0
CB J:CYS45 3.0 0.4 1.0
CA J:CYS45 3.0 0.8 1.0
N J:CYS45 3.1 0.5 1.0
CA J:CYS46 3.1 0.9 1.0
CB J:CYS46 3.2 0.4 1.0
O J:CYS45 3.3 0.4 1.0
CG J:ARG43 3.4 0.5 1.0
SG J:CYS7 3.5 0.9 1.0
CB J:CYS10 3.7 0.7 1.0
C J:ARG43 3.8 0.5 1.0
CD J:ARG43 3.9 0.5 1.0
CB J:ARG43 4.0 0.4 1.0
C J:TYR44 4.1 0.1 1.0
OG J:SER9 4.5 0.9 1.0
CA J:ARG43 4.5 1.0 1.0
N J:TYR44 4.5 0.2 1.0
SG J:CYS45 4.5 0.0 1.0
C J:CYS46 4.6 0.7 1.0
CB J:CYS7 4.6 0.6 1.0
O J:TYR44 4.7 0.1 1.0
CA J:TYR44 4.9 0.3 1.0
N J:ARG47 4.9 0.7 1.0
CA J:CYS10 5.0 0.0 1.0

Zinc binding site 8 out of 8 in 5vvr

Go back to Zinc Binding Sites List in 5vvr
Zinc binding site 8 out of 8 in the Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ternary Complex of Rna Pol II, Transcription Scaffold and RAD26 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.1
occ:1.00
 OD2 L:ASP50 2.2 0.1 1.0
SG L:CYS31 2.5 0.6 1.0
N L:CYS51 2.9 0.6 1.0
CG L:ASP50 3.0 0.1 1.0
CB L:CYS31 3.1 0.9 1.0
CB L:ASP50 3.1 0.5 1.0
CB L:CYS51 3.4 0.2 1.0
SG L:CYS34 3.6 0.1 1.0
CA L:CYS51 3.6 0.6 1.0
O L:CYS51 3.8 0.7 1.0
C L:ASP50 3.9 0.2 1.0
SG L:CYS48 4.0 1.0 1.0
CA L:ASP50 4.0 0.5 1.0
CB L:CYS48 4.0 0.8 1.0
C L:CYS51 4.1 0.7 1.0
CB L:SER36 4.1 0.9 1.0
OG L:SER36 4.1 0.4 1.0
OD1 L:ASP50 4.2 0.1 1.0
CA L:CYS31 4.5 0.1 1.0
O L:ALA32 4.6 0.6 1.0
N L:ASP50 4.6 0.1 1.0
O L:CYS31 4.6 0.2 1.0
C L:CYS31 4.7 0.1 1.0
CD1 L:LEU38 4.8 0.2 1.0

Reference:

J.Xu, I.Lahiri, W.Wang, A.Wier, M.A.Cianfrocco, J.Chong, A.A.Hare, P.B.Dervan, F.Dimaio, A.E.Leschziner, D.Wang. Structural Basis For the Initiation of Eukaryotic Transcription-Coupled Dna Repair. Nature V. 551 653 2017.
ISSN: ESSN 1476-4687
PubMed: 29168508
DOI: 10.1038/NATURE24658
Page generated: Mon Oct 28 13:31:55 2024

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