Zinc in PDB 5vvs: Rna Pol II Elongation Complex

Enzymatic activity of Rna Pol II Elongation Complex

All present enzymatic activity of Rna Pol II Elongation Complex:
2.7.7.6;

Other elements in 5vvs:

The structure of Rna Pol II Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 5vvs

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Zinc binding site 1 out of 8 in the Rna Pol II Elongation Complex


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Stereo pair view

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

b:0.1
occ:1.00
 O A:CYS107 2.2 0.3 1.0
O A:MET108 2.2 0.7 1.0
SG A:CYS110 2.5 0.3 1.0
C A:CYS107 2.5 0.0 1.0
SG A:CYS107 2.6 0.7 1.0
C A:MET108 2.7 0.0 1.0
CB A:CYS110 2.8 0.3 1.0
N A:CYS110 2.8 0.7 1.0
N A:MET108 3.0 0.3 1.0
CB A:CYS107 3.1 0.1 1.0
CA A:CYS110 3.3 0.2 1.0
CA A:MET108 3.4 0.5 1.0
CA A:CYS107 3.4 0.7 1.0
N A:HIS109 3.5 0.9 1.0
C A:HIS109 3.6 0.3 1.0
SG A:CYS148 3.9 0.2 1.0
CA A:HIS109 4.0 0.3 1.0
N A:GLY166 4.3 0.0 1.0
C A:CYS110 4.4 0.6 1.0
N A:CYS107 4.5 0.9 1.0
O A:HIS109 4.5 1.0 1.0
N A:GLY111 4.6 0.5 1.0
SG A:CYS167 4.6 0.5 1.0
O A:LYS112 4.7 0.9 1.0
CB A:MET108 4.7 0.1 1.0
N A:CYS167 4.7 0.0 1.0
CB A:HIS109 4.8 0.1 1.0
O A:ARG164 4.8 0.7 1.0
CA A:GLY166 4.8 0.0 1.0
CB A:CYS148 4.9 0.3 1.0
C A:GLY165 5.0 0.7 1.0
CA A:GLY165 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 5vvs

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Zinc binding site 2 out of 8 in the Rna Pol II Elongation Complex


Mono view


Stereo pair view

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

b:0.1
occ:1.00
 OE1 A:GLU72 2.1 0.6 1.0
O A:PRO78 2.4 0.1 1.0
SG A:CYS67 2.6 0.2 1.0
SG A:CYS77 2.6 0.5 1.0
N A:PRO78 2.9 0.4 1.0
CA A:CYS77 3.0 0.9 1.0
C A:CYS77 3.1 0.3 1.0
CD A:PRO78 3.1 0.0 1.0
CD A:GLU72 3.2 0.2 1.0
CB A:CYS77 3.3 0.8 1.0
C A:PRO78 3.4 0.4 1.0
CG A:PRO78 3.7 0.5 1.0
CA A:PRO78 3.8 0.6 1.0
OE2 A:GLU72 3.8 0.9 1.0
O A:CYS77 3.9 0.6 1.0
CB A:CYS67 4.1 0.0 1.0
CB A:GLU72 4.2 0.4 1.0
CG A:GLU72 4.2 0.6 1.0
N A:CYS77 4.3 0.2 1.0
CB A:PRO78 4.4 0.8 1.0
O A:GLU76 4.5 1.0 1.0
N A:GLY79 4.6 0.3 1.0
O A:GLN71 4.6 0.1 1.0
CE1 A:HIS80 4.7 0.3 1.0
C A:GLU76 4.9 0.8 1.0

Zinc binding site 3 out of 8 in 5vvs

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Zinc binding site 3 out of 8 in the Rna Pol II Elongation Complex


Mono view


Stereo pair view

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

b:1.0
occ:1.00
 O B:CYS1163 2.2 0.0 1.0
SG B:CYS1166 2.4 0.6 1.0
CB B:CYS1163 2.5 1.0 1.0
SG B:CYS1163 2.6 0.6 1.0
C B:CYS1163 2.9 0.8 1.0
O B:LEU1168 3.2 0.8 1.0
CA B:CYS1163 3.2 1.0 1.0
SG B:CYS1182 3.3 0.9 1.0
N B:CYS1166 3.4 0.6 1.0
CB B:CYS1166 3.5 1.0 1.0
CG2 B:ILE1165 3.5 0.3 1.0
CB B:THR1170 3.8 0.6 1.0
CA B:CYS1166 3.9 0.2 1.0
N B:CYS1163 4.0 0.8 1.0
N B:LEU1168 4.1 0.7 1.0
N B:GLY1164 4.1 0.2 1.0
N B:GLY1167 4.2 0.5 1.0
OG1 B:THR1170 4.2 0.1 1.0
N B:THR1170 4.2 0.6 1.0
C B:LEU1168 4.2 0.8 1.0
O B:THR1170 4.3 0.7 1.0
N B:ILE1165 4.3 0.1 1.0
C B:CYS1166 4.4 0.1 1.0
C B:ILE1165 4.4 1.0 1.0
CA B:THR1170 4.5 0.7 1.0
C B:GLY1164 4.5 0.5 1.0
CB B:CYS1182 4.5 0.6 1.0
CA B:LEU1168 4.6 0.3 1.0
CB B:ILE1165 4.7 0.6 1.0
CA B:ILE1165 4.7 0.4 1.0
C B:THR1170 4.8 0.9 1.0
SG B:CYS1185 4.8 0.3 1.0
CB B:LEU1168 4.8 0.1 1.0
CA B:GLY1164 4.9 0.1 1.0
O B:GLY1164 4.9 0.4 1.0
CG2 B:THR1170 4.9 0.4 1.0

Zinc binding site 4 out of 8 in 5vvs

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Zinc binding site 4 out of 8 in the Rna Pol II Elongation Complex


Mono view


Stereo pair view

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

b:0.5
occ:1.00
 OD1 C:ASP93 2.1 0.2 1.0
SG C:CYS86 2.8 0.1 1.0
CA C:CYS88 3.1 0.7 1.0
CB C:CYS88 3.1 0.9 1.0
N C:LYS94 3.1 0.8 1.0
CG C:LYS94 3.2 0.8 1.0
CB C:LYS94 3.2 0.7 1.0
N C:ASP93 3.3 0.7 1.0
CD C:LYS94 3.3 0.1 1.0
CG C:ASP93 3.3 0.2 1.0
C C:CYS92 3.5 0.5 1.0
N C:CYS88 3.5 0.2 1.0
CA C:CYS92 3.6 0.6 1.0
CA C:LYS94 3.8 0.5 1.0
C C:ASP93 3.8 0.0 1.0
CA C:ASP93 3.9 0.5 1.0
O C:CYS92 4.1 0.4 1.0
OD2 C:ASP93 4.1 0.6 1.0
CE C:LYS94 4.1 0.5 1.0
C C:PHE87 4.1 0.2 1.0
CB C:CYS92 4.2 0.2 1.0
CB C:ASP93 4.3 0.8 1.0
O C:PHE87 4.3 0.1 1.0
N C:CYS95 4.4 0.9 1.0
C C:CYS88 4.4 0.3 1.0
O C:HIS91 4.4 0.1 1.0
CB C:CYS86 4.5 0.6 1.0
C C:LYS94 4.6 0.3 1.0
N C:PHE87 4.7 0.9 1.0
N C:GLU89 4.7 0.1 1.0
O C:ASP93 4.7 0.9 1.0
N C:CYS92 4.8 0.0 1.0
SG C:CYS88 4.8 0.4 1.0
NZ C:LYS94 4.9 0.1 1.0
SG C:CYS92 4.9 0.8 1.0
SG C:CYS95 4.9 0.0 1.0
C C:CYS86 5.0 0.7 1.0

Zinc binding site 5 out of 8 in 5vvs

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Zinc binding site 5 out of 8 in the Rna Pol II Elongation Complex


Mono view


Stereo pair view

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

b:0.4
occ:1.01
 OD1 I:ASN12 2.2 0.9 1.0
SG I:CYS29 2.6 0.7 1.0
SG I:CYS32 2.8 0.4 1.0
CB I:CYS29 2.9 0.8 1.0
CG I:ASN12 3.3 0.8 1.0
O I:MET13 3.4 0.8 1.0
CB I:CYS32 4.0 0.5 1.0
ND2 I:ASN12 4.0 0.0 1.0
C I:MET13 4.2 0.6 1.0
OG1 I:THR31 4.3 0.8 1.0
O I:ASN12 4.3 0.8 1.0
CB I:ASN12 4.3 0.1 1.0
CA I:CYS29 4.4 0.6 1.0
CB I:CYS7 4.4 0.3 1.0
C I:ASN12 4.4 0.4 1.0
N I:MET13 4.6 0.1 1.0
CD2 I:LEU14 4.8 0.6 1.0
N I:CYS32 4.8 0.3 1.0
N I:LEU14 4.9 0.7 1.0
CA I:MET13 4.9 0.2 1.0
CA I:ASN12 4.9 0.3 1.0
CE2 B:PHE322 5.0 0.8 1.0

Zinc binding site 6 out of 8 in 5vvs

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Zinc binding site 6 out of 8 in the Rna Pol II Elongation Complex


Mono view


Stereo pair view

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

b:0.3
occ:1.00
 CB I:CYS103 2.5 0.9 1.0
SG I:CYS106 2.5 0.6 1.0
OG I:SER105 3.1 0.5 1.0
O I:CYS103 3.2 0.3 1.0
SG I:CYS103 3.6 0.6 1.0
CA I:CYS103 3.7 0.5 1.0
C I:CYS103 3.7 0.0 1.0
N I:CYS106 3.8 0.4 1.0
CB I:CYS106 3.9 0.4 1.0
CE1 I:PHE110 4.0 0.1 1.0
O I:GLU82 4.1 0.7 1.0
CB I:CYS75 4.2 0.7 1.0
CB I:HIS108 4.3 0.8 1.0
CA I:CYS106 4.3 0.1 1.0
OE1 I:GLU82 4.4 0.7 1.0
CB I:SER105 4.4 0.3 1.0
CZ I:PHE110 4.4 0.2 1.0
N I:HIS108 4.5 0.3 1.0
CB I:SER80 4.5 0.7 1.0
OG I:SER80 4.6 1.0 1.0
C I:SER105 4.6 0.3 1.0
N I:SER105 4.6 0.7 1.0
N I:CYS103 4.6 0.7 1.0
O I:HIS108 4.6 0.5 1.0
O I:SER80 4.7 0.0 1.0
N I:SER107 4.7 0.1 1.0
C I:CYS106 4.8 0.0 1.0
CA I:SER105 4.8 0.1 1.0
CG I:HIS108 4.8 0.1 1.0
CA I:HIS108 4.9 0.6 1.0
N I:LEU104 4.9 0.6 1.0
ND1 I:HIS108 4.9 0.5 1.0
SG I:CYS75 4.9 1.0 1.0

Zinc binding site 7 out of 8 in 5vvs

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Zinc binding site 7 out of 8 in the Rna Pol II Elongation Complex


Mono view


Stereo pair view

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

b:0.3
occ:1.00
 OG J:SER9 2.1 0.2 1.0
SG J:CYS10 2.4 0.7 1.0
C J:SER9 2.6 0.6 1.0
SG J:CYS7 2.6 0.3 1.0
O J:SER9 2.7 0.7 1.0
N J:CYS10 2.9 0.9 1.0
SG J:CYS45 2.9 0.1 1.0
CB J:SER9 2.9 0.9 1.0
CA J:SER9 3.1 0.5 1.0
CB J:CYS10 3.2 0.2 1.0
SG J:CYS46 3.3 0.3 1.0
CA J:CYS10 3.5 0.5 1.0
N J:SER9 3.6 0.9 1.0
O J:CYS45 4.0 0.2 1.0
CB J:CYS45 4.1 0.9 1.0
CB J:CYS7 4.1 0.3 1.0
C J:CYS45 4.1 1.0 1.0
N J:CYS46 4.3 0.8 1.0
CA J:CYS46 4.4 0.7 1.0
CB J:CYS46 4.5 0.0 1.0
CA J:CYS45 4.8 0.2 1.0
O J:CYS7 4.8 0.5 1.0
C J:CYS10 4.9 0.0 1.0
C J:CYS7 4.9 0.4 1.0
C J:PHE8 4.9 0.7 1.0
NE J:ARG43 5.0 1.0 1.0

Zinc binding site 8 out of 8 in 5vvs

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Zinc binding site 8 out of 8 in the Rna Pol II Elongation Complex


Mono view


Stereo pair view

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

b:0.1
occ:1.00
 O L:ALA32 2.1 0.7 1.0
O L:CYS31 2.2 1.0 1.0
SG L:CYS34 2.6 0.2 1.0
C L:ALA32 2.7 0.3 1.0
C L:CYS31 2.7 0.3 1.0
O L:CYS34 2.9 0.2 1.0
SG L:CYS51 2.9 0.5 1.0
N L:CYS34 3.0 0.3 1.0
N L:ALA32 3.3 0.1 1.0
CA L:ALA32 3.4 0.1 1.0
CB L:CYS31 3.5 1.0 1.0
N L:GLU33 3.5 0.9 1.0
SG L:CYS31 3.5 0.6 1.0
C L:CYS34 3.5 0.3 1.0
OG L:SER36 3.6 0.6 1.0
CA L:CYS34 3.6 0.4 1.0
C L:GLU33 3.6 0.5 1.0
CB L:CYS34 3.7 0.1 1.0
CA L:CYS31 3.7 0.4 1.0
CB L:SER36 3.8 0.8 1.0
CA L:GLU33 3.9 0.7 1.0
N L:SER36 4.0 0.9 1.0
CB L:GLU33 4.3 0.5 1.0
O L:GLU33 4.4 0.7 1.0
CB L:CYS51 4.4 0.3 1.0
N L:CYS31 4.5 0.1 1.0
CA L:SER36 4.5 0.8 1.0
SG L:CYS48 4.6 0.4 1.0
N L:SER35 4.6 0.8 1.0
CB L:ALA32 4.8 0.0 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: Wed Dec 16 11:13:28 2020

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