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Zinc in PDB 3i4n: 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E

Enzymatic activity of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E

All present enzymatic activity of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E:
2.7.7.6;

Protein crystallography data

The structure of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E, PDB code: 3i4n was solved by G.E.Damsma, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.173, 394.148, 282.339, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.6

Other elements in 3i4n:

The structure of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E (pdb code 3i4n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E, PDB code: 3i4n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3i4n

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Zinc binding site 1 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.1
occ:1.00
 SG A:CYS110 2.4 1.0 1.0
SG A:CYS167 2.6 0.6 1.0
SG A:CYS148 2.7 0.3 1.0
SG A:CYS107 2.8 0.8 1.0
O A:CYS167 3.3 0.2 1.0
O A:MET108 3.3 1.0 1.0
CB A:CYS148 3.3 1.0 1.0
CB A:CYS110 3.5 0.3 1.0
CB A:CYS107 3.6 0.3 1.0
CB A:CYS167 3.9 0.9 1.0
N A:CYS110 4.0 0.8 1.0
O A:GLY166 4.1 0.5 1.0
C A:CYS167 4.2 0.9 1.0
CA A:CYS110 4.4 0.3 1.0
CB A:HIS109 4.4 0.3 1.0
C A:MET108 4.5 0.7 1.0
C A:CYS107 4.5 0.5 1.0
O A:CYS107 4.6 0.2 1.0
CA A:CYS167 4.6 1.0 1.0
CA A:CYS107 4.7 0.6 1.0
CA A:CYS148 4.8 0.7 1.0
N A:GLY111 4.8 0.3 1.0
C A:GLY166 4.9 0.5 1.0
O A:CYS148 4.9 0.2 1.0
C A:HIS109 4.9 0.1 1.0
N A:MET108 5.0 0.7 1.0
ND2 A:ASN169 5.0 0.8 1.0

Zinc binding site 2 out of 8 in 3i4n

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Zinc binding site 2 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:0.6
occ:1.00
 NE2 A:HIS80 2.2 0.5 1.0
SG A:CYS70 2.3 0.8 1.0
SG A:CYS77 2.3 0.8 1.0
SG A:CYS67 2.5 0.9 1.0
CD2 A:HIS80 2.8 0.1 1.0
O A:CYS67 2.8 0.8 1.0
CB A:CYS70 3.0 0.2 1.0
CE1 A:HIS80 3.4 0.8 1.0
CB A:CYS77 3.5 0.7 1.0
CB A:CYS67 3.7 0.1 1.0
C A:CYS67 3.9 0.8 1.0
CG A:HIS80 4.0 0.1 1.0
CA A:CYS70 4.2 1.0 1.0
ND1 A:HIS80 4.3 0.9 1.0
C A:CYS70 4.4 0.6 1.0
CA A:CYS67 4.4 0.5 1.0
O A:GLN71 4.5 0.5 1.0
N A:GLN71 4.5 0.6 1.0
CA A:CYS77 4.6 0.4 1.0
OE1 A:GLN68 4.7 1.0 1.0
CB A:GLN68 4.7 0.7 1.0
N A:CYS70 4.7 0.8 1.0
O A:CYS70 4.9 0.9 1.0

Zinc binding site 3 out of 8 in 3i4n

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Zinc binding site 3 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:0.1
occ:1.00
 SG B:CYS1166 2.4 98.0 1.0
SG B:CYS1163 2.5 0.6 1.0
CB B:CYS1185 2.5 0.9 1.0
SG B:CYS1182 2.5 0.2 1.0
CB B:CYS1163 2.8 0.1 1.0
SG B:CYS1185 2.9 0.7 1.0
CA B:CYS1185 3.9 0.7 1.0
CB B:CYS1166 4.1 0.1 1.0
OG1 B:THR1170 4.1 0.5 1.0
CA B:CYS1163 4.2 0.4 1.0
O B:LYS1183 4.3 0.0 1.0
CB B:CYS1182 4.3 0.3 1.0
O B:CYS1166 4.4 0.8 1.0
N B:CYS1185 4.4 0.4 1.0
N B:CYS1166 4.4 0.6 1.0
C B:CYS1185 4.6 0.6 1.0
O B:CYS1182 4.6 0.4 1.0
CB B:THR1170 4.7 0.1 1.0
CA B:CYS1166 4.8 0.9 1.0
N B:ASP1186 5.0 0.6 1.0

Zinc binding site 4 out of 8 in 3i4n

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Zinc binding site 4 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:0.4
occ:1.00
 SG C:CYS88 2.3 0.2 1.0
SG C:CYS86 2.5 0.7 1.0
SG C:CYS92 2.5 0.5 1.0
SG C:CYS95 2.6 0.2 1.0
CB C:CYS86 2.9 1.0 1.0
CB C:CYS95 3.0 0.6 1.0
N C:CYS92 3.4 0.0 1.0
CB C:CYS88 3.4 0.5 1.0
CB C:CYS92 3.6 0.9 1.0
CA C:CYS92 4.0 0.2 1.0
C C:HIS91 4.0 0.5 1.0
N C:CYS95 4.1 0.9 1.0
O C:CYS92 4.1 0.1 1.0
N C:CYS88 4.1 0.8 1.0
CA C:HIS91 4.2 0.3 1.0
CA C:CYS95 4.2 0.3 1.0
CA C:CYS86 4.3 0.1 1.0
CA C:CYS88 4.3 0.6 1.0
C C:CYS92 4.3 0.5 1.0
C C:LYS94 4.4 0.2 1.0
O C:CYS88 4.6 0.5 1.0
C C:CYS86 4.6 0.8 1.0
O C:HIS91 4.8 0.3 1.0
O C:LYS94 4.8 0.2 1.0
O C:SER83 4.9 0.5 1.0
N C:LYS94 4.9 0.2 1.0
N C:PHE87 4.9 0.8 1.0
CB C:LYS94 4.9 0.9 1.0
C C:CYS88 4.9 0.9 1.0
CA C:SER83 5.0 0.3 1.0
O C:CYS86 5.0 0.9 1.0

Zinc binding site 5 out of 8 in 3i4n

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Zinc binding site 5 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.2
occ:1.00
 SG I:CYS10 2.2 0.4 1.0
SG I:CYS32 2.3 1.0 1.0
SG I:CYS29 2.4 0.5 1.0
SG I:CYS7 2.5 0.6 1.0
CB I:CYS29 3.0 0.9 1.0
O I:CYS10 3.5 0.4 1.0
CB I:CYS32 3.6 0.3 1.0
CB I:CYS10 3.7 0.5 1.0
N I:CYS10 3.8 0.1 1.0
O I:ARG8 4.0 0.7 1.0
CB I:TYR34 4.0 0.8 1.0
CB I:CYS7 4.0 0.2 1.0
CA I:CYS10 4.1 0.9 1.0
C I:CYS10 4.1 0.8 1.0
CB I:ASP9 4.5 0.9 1.0
CA I:CYS29 4.6 0.6 1.0
N I:CYS32 4.6 0.0 1.0
C I:THR31 4.6 0.4 1.0
O I:THR31 4.6 0.2 1.0
CA I:CYS32 4.7 0.1 1.0
CG I:TYR34 4.9 0.6 1.0
CB I:THR31 4.9 0.9 1.0
O I:CYS7 4.9 0.1 1.0

Zinc binding site 6 out of 8 in 3i4n

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Zinc binding site 6 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.6
occ:1.00
 SG I:CYS75 2.4 0.8 1.0
SG I:CYS106 2.5 0.5 1.0
SG I:CYS78 2.9 0.2 1.0
SG I:CYS103 3.0 0.7 1.0
CB I:CYS75 3.1 0.8 1.0
CB I:CYS103 3.2 0.8 1.0
CB I:HIS108 3.4 0.2 1.0
N I:CYS78 3.7 0.5 1.0
CB I:CYS78 3.9 0.0 1.0
CB I:CYS106 4.0 0.1 1.0
CG I:HIS108 4.0 0.0 1.0
CA I:CYS78 4.3 0.5 1.0
CD2 I:HIS108 4.4 0.3 1.0
CA I:CYS75 4.5 0.7 1.0
N I:LYS77 4.6 0.6 1.0
CB I:LYS77 4.6 0.8 1.0
N I:HIS108 4.7 0.5 1.0
CA I:HIS108 4.7 0.9 1.0
C I:LYS77 4.7 0.1 1.0
CA I:CYS103 4.7 0.1 1.0
O I:SER105 4.8 0.1 1.0
C I:CYS78 4.8 0.8 1.0
CA I:LYS77 4.8 0.2 1.0
ND1 I:HIS108 4.9 0.6 1.0
C I:CYS75 5.0 0.9 1.0

Zinc binding site 7 out of 8 in 3i4n

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Zinc binding site 7 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:0.4
occ:1.00
 SG J:CYS10 2.3 0.1 1.0
SG J:CYS45 2.4 0.2 1.0
SG J:CYS7 2.4 0.0 1.0
SG J:CYS46 2.5 0.3 1.0
N J:CYS46 2.7 0.6 1.0
CB J:CYS46 2.9 0.3 1.0
CA J:CYS46 3.0 0.5 1.0
CB J:CYS7 3.2 0.4 1.0
CB J:CYS45 3.3 0.6 1.0
C J:CYS45 3.3 0.8 1.0
N J:CYS10 3.7 0.8 1.0
CB J:CYS10 3.8 0.3 1.0
CA J:CYS45 3.9 0.1 1.0
O J:CYS45 4.0 0.5 1.0
CA J:CYS10 4.2 0.3 1.0
CB J:SER9 4.2 0.7 1.0
C J:CYS46 4.5 0.7 1.0
N J:GLY11 4.6 0.3 1.0
N J:CYS45 4.7 0.1 1.0
OG J:SER9 4.7 0.3 1.0
CA J:CYS7 4.7 0.8 1.0
C J:CYS10 4.8 0.7 1.0
C J:SER9 4.8 0.9 1.0
NE J:ARG43 4.9 0.6 1.0
N J:SER9 4.9 0.9 1.0
CA J:SER9 4.9 0.8 1.0
CE J:MET49 5.0 0.7 1.0

Zinc binding site 8 out of 8 in 3i4n

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Zinc binding site 8 out of 8 in the 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex E within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.5
occ:1.00
 SG L:CYS34 2.3 0.9 1.0
SG L:CYS48 2.4 0.5 1.0
SG L:CYS31 2.5 0.2 1.0
CB L:CYS48 2.6 0.3 1.0
CB L:CYS51 2.7 0.2 1.0
N L:CYS51 3.1 0.4 1.0
CB L:CYS31 3.3 0.5 1.0
SG L:CYS51 3.4 1.0 1.0
CA L:CYS51 3.4 0.7 1.0
CB L:CYS34 3.4 0.8 1.0
O L:CYS51 3.5 0.1 1.0
C L:CYS51 3.9 0.5 1.0
CA L:CYS48 4.1 0.1 1.0
C L:ASP50 4.2 0.7 1.0
CB L:ASP50 4.3 0.4 1.0
CA L:CYS34 4.4 0.4 1.0
C L:CYS48 4.4 0.2 1.0
N L:CYS34 4.6 0.8 1.0
CA L:CYS31 4.6 0.1 1.0
C L:CYS34 4.6 0.9 1.0
O L:CYS34 4.6 0.5 1.0
CA L:ASP50 4.6 0.3 1.0
N L:ASP50 4.7 0.1 1.0
OD2 L:ASP50 4.7 1.0 1.0
N L:CYS48 4.8 0.2 1.0
N L:LYS49 4.8 0.1 1.0
O L:HIS53 4.8 0.8 1.0
O L:CYS48 4.9 0.0 1.0

Reference:

G.E.Damsma, P.Cramer. Molecular Basis of Transcriptional Mutagenesis at 8-Oxoguanine J.Biol.Chem. V. 284 31658 2009.
ISSN: ISSN 0021-9258
PubMed: 19758983
DOI: 10.1074/JBC.M109.022764
Page generated: Sat Oct 26 06:50:53 2024

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