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Zinc in PDB 3i4m: 8-Oxoguanine Containing Rna Polymerase II Elongation Complex D

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

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

Protein crystallography data

The structure of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex D, PDB code: 3i4m 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 / 3.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.646, 392.003, 281.455, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 25.8

Other elements in 3i4m:

The structure of 8-Oxoguanine Containing Rna Polymerase II Elongation Complex D 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 D (pdb code 3i4m). 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 D, PDB code: 3i4m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3i4m

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:96.4
occ:1.00
 SG A:CYS110 2.4 0.8 1.0
SG A:CYS167 2.5 0.2 1.0
SG A:CYS148 2.6 0.1 1.0
SG A:CYS107 2.7 0.7 1.0
CB A:CYS148 3.0 0.7 1.0
O A:CYS167 3.1 0.1 1.0
CB A:CYS107 3.3 1.0 1.0
O A:MET108 3.3 0.2 1.0
CB A:CYS110 3.4 0.8 1.0
CB A:CYS167 3.8 0.6 1.0
N A:CYS110 4.0 0.9 1.0
C A:CYS167 4.1 1.0 1.0
CA A:CYS110 4.3 0.1 1.0
CA A:CYS167 4.5 0.1 1.0
C A:CYS107 4.5 0.1 1.0
C A:MET108 4.5 0.5 1.0
CA A:CYS148 4.5 0.0 1.0
O A:GLY166 4.5 0.4 1.0
CA A:CYS107 4.5 0.4 1.0
CB A:HIS109 4.6 0.8 1.0
O A:CYS107 4.7 0.9 1.0
O A:CYS148 4.7 1.0 1.0
N A:GLY111 4.8 1.0 1.0
N A:MET108 4.8 0.7 1.0
ND2 A:ASN169 4.9 0.2 1.0

Zinc binding site 2 out of 8 in 3i4m

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


Mono view


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:38.4
occ:1.00
 NE2 A:HIS80 2.2 47.5 1.0
SG A:CYS77 2.3 40.8 1.0
SG A:CYS70 2.3 93.9 1.0
SG A:CYS67 2.4 93.2 1.0
CD2 A:HIS80 2.6 46.7 1.0
CB A:CYS70 2.7 99.2 1.0
CB A:CYS77 3.4 41.3 1.0
CE1 A:HIS80 3.4 47.9 1.0
O A:CYS67 3.5 97.5 1.0
CB A:CYS67 3.7 94.1 1.0
OE1 A:GLN68 3.8 94.2 1.0
CG A:HIS80 3.9 48.0 1.0
CD A:GLN68 4.1 95.5 1.0
CA A:CYS70 4.1 0.2 1.0
ND1 A:HIS80 4.2 47.9 1.0
NE2 A:GLN68 4.3 94.0 1.0
O A:GLN71 4.4 99.7 1.0
C A:CYS67 4.4 98.0 1.0
C A:CYS70 4.4 0.1 1.0
CA A:CYS77 4.4 41.8 1.0
O A:PRO78 4.7 40.4 1.0
CA A:CYS67 4.7 96.8 1.0
O A:CYS70 4.8 0.1 1.0
N A:CYS70 4.8 1.0 1.0
N A:GLN71 4.8 0.1 1.0
CG A:GLN68 4.8 98.0 1.0
C A:CYS77 4.9 39.5 1.0

Zinc binding site 3 out of 8 in 3i4m

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:43.3
occ:1.00
 SG B:CYS1166 2.3 40.1 1.0
CB B:CYS1185 2.3 69.7 1.0
SG B:CYS1182 2.5 70.8 1.0
SG B:CYS1185 2.5 66.1 1.0
SG B:CYS1163 2.7 50.5 1.0
CB B:CYS1163 2.8 49.1 1.0
O B:CYS1182 3.7 70.5 1.0
CA B:CYS1185 3.9 70.2 1.0
CB B:CYS1166 4.0 46.8 1.0
OG1 B:THR1170 4.2 41.0 1.0
CB B:CYS1182 4.3 71.7 1.0
O B:CYS1166 4.3 48.6 1.0
CA B:CYS1163 4.3 47.7 1.0
N B:CYS1166 4.4 48.2 1.0
N B:CYS1185 4.4 72.3 1.0
CB B:THR1170 4.5 38.3 1.0
C B:CYS1185 4.6 70.0 1.0
CA B:CYS1166 4.7 47.8 1.0
C B:CYS1182 4.7 71.8 1.0
CG2 B:THR1170 4.9 41.4 1.0

Zinc binding site 4 out of 8 in 3i4m

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:39.9
occ:1.00
 SG C:CYS88 2.2 46.2 1.0
SG C:CYS86 2.4 48.9 1.0
SG C:CYS92 2.5 58.3 1.0
SG C:CYS95 2.5 57.8 1.0
CB C:CYS95 2.9 58.1 1.0
CB C:CYS86 2.9 50.3 1.0
CB C:CYS88 3.5 50.8 1.0
N C:CYS92 3.5 60.1 1.0
N C:CYS95 3.6 58.8 1.0
CB C:CYS92 3.8 60.4 1.0
CA C:CYS95 3.9 57.4 1.0
C C:HIS91 4.0 59.6 1.0
CA C:CYS92 4.1 61.4 1.0
CA C:HIS91 4.1 60.3 1.0
O C:CYS92 4.2 62.5 1.0
N C:CYS88 4.2 49.7 1.0
CB C:LYS94 4.2 61.1 1.0
C C:LYS94 4.2 60.1 1.0
CA C:CYS86 4.4 51.0 1.0
CA C:CYS88 4.4 51.3 1.0
C C:CYS92 4.4 62.6 1.0
CA C:LYS94 4.6 60.9 1.0
C C:CYS86 4.7 51.4 1.0
O C:CYS88 4.7 52.3 1.0
O C:HIS91 4.7 59.2 1.0
N C:LYS94 4.7 61.6 1.0
O C:SER83 4.7 56.0 1.0
N C:PHE87 4.8 50.1 1.0
CA C:SER83 4.9 60.0 1.0
N C:HIS91 5.0 61.1 1.0
C C:CYS95 5.0 56.4 1.0
O C:LYS94 5.0 60.7 1.0

Zinc binding site 5 out of 8 in 3i4m

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:70.8
occ:1.00
 SG I:CYS10 2.2 88.8 1.0
SG I:CYS32 2.3 82.9 1.0
SG I:CYS7 2.4 81.1 1.0
SG I:CYS29 2.5 88.9 1.0
O I:CYS10 3.4 93.2 1.0
CB I:CYS32 3.5 84.1 1.0
CB I:CYS29 3.5 87.1 1.0
O I:THR31 3.6 89.0 1.0
CB I:CYS7 3.8 90.7 1.0
C I:THR31 3.9 88.0 1.0
CB I:CYS10 3.9 93.0 1.0
O I:ARG8 4.2 97.1 1.0
CB I:TYR34 4.2 64.9 1.0
N I:CYS32 4.2 86.4 1.0
CB I:THR31 4.3 90.1 1.0
C I:CYS10 4.3 93.0 1.0
N I:CYS10 4.3 96.7 1.0
CA I:CYS32 4.4 84.3 1.0
CA I:CYS10 4.4 94.0 1.0
CA I:THR31 4.6 89.0 1.0
N I:THR31 4.7 88.5 1.0
C I:CYS32 4.9 83.5 1.0
O I:CYS7 4.9 94.4 1.0
CA I:CYS29 5.0 86.5 1.0
OG1 I:THR31 5.0 91.5 1.0

Zinc binding site 6 out of 8 in 3i4m

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:1.0
occ:1.00
 SG I:CYS75 2.4 0.3 1.0
SG I:CYS106 2.6 0.7 1.0
SG I:CYS78 2.9 0.8 1.0
SG I:CYS103 3.0 0.8 1.0
CB I:CYS75 3.0 0.3 1.0
CB I:CYS103 3.2 0.4 1.0
CB I:HIS108 3.4 1.0 1.0
N I:CYS78 3.6 1.0 1.0
CB I:CYS78 4.0 0.7 1.0
CG I:HIS108 4.1 0.8 1.0
CB I:CYS106 4.1 0.2 1.0
CD2 I:HIS108 4.1 0.9 1.0
CA I:CYS78 4.2 0.7 1.0
N I:LYS77 4.4 0.6 1.0
CA I:CYS75 4.5 0.5 1.0
CB I:LYS77 4.5 0.4 1.0
C I:LYS77 4.6 0.8 1.0
C I:CYS78 4.6 0.0 1.0
CA I:HIS108 4.7 0.7 1.0
N I:HIS108 4.7 0.4 1.0
CA I:CYS103 4.7 0.8 1.0
CA I:LYS77 4.7 0.5 1.0
C I:CYS75 4.8 0.8 1.0
OG I:SER80 4.9 0.5 1.0
N I:PRO76 5.0 0.4 1.0

Zinc binding site 7 out of 8 in 3i4m

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:47.4
occ:1.00
 SG J:CYS7 2.4 52.1 1.0
SG J:CYS10 2.4 58.2 1.0
SG J:CYS45 2.4 54.6 1.0
SG J:CYS46 2.5 73.2 1.0
N J:CYS46 2.7 63.9 1.0
CA J:CYS46 3.1 66.2 1.0
CB J:CYS7 3.2 50.0 1.0
C J:CYS45 3.2 61.7 1.0
CB J:CYS45 3.2 58.7 1.0
CB J:CYS46 3.2 67.8 1.0
CB J:CYS10 3.7 57.7 1.0
N J:CYS10 3.7 54.7 1.0
O J:CYS45 3.8 61.0 1.0
CA J:CYS45 3.8 59.9 1.0
CA J:CYS10 4.2 55.9 1.0
CB J:SER9 4.2 49.8 1.0
N J:GLY11 4.4 56.5 1.0
C J:CYS46 4.6 66.7 1.0
CA J:CYS7 4.6 49.3 1.0
N J:CYS45 4.6 60.3 1.0
C J:CYS10 4.8 55.2 1.0
C J:SER9 4.8 52.2 1.0
NE J:ARG43 4.8 63.0 1.0
OG J:SER9 4.9 50.9 1.0
CB J:LYS12 4.9 66.8 1.0
CA J:SER9 4.9 50.1 1.0
C J:CYS7 4.9 48.3 1.0
N J:LYS12 5.0 63.2 1.0
O J:CYS7 5.0 48.4 1.0

Zinc binding site 8 out of 8 in 3i4m

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.7
occ:1.00
 SG L:CYS34 2.3 0.2 1.0
SG L:CYS48 2.5 0.4 1.0
SG L:CYS31 2.6 0.2 1.0
CB L:CYS51 2.6 0.3 1.0
CB L:CYS48 2.6 0.8 1.0
N L:CYS51 3.1 0.0 1.0
CB L:CYS31 3.3 0.9 1.0
CA L:CYS51 3.3 0.3 1.0
O L:CYS51 3.4 0.8 1.0
SG L:CYS51 3.4 0.1 1.0
CB L:CYS34 3.4 0.4 1.0
C L:CYS51 3.8 0.9 1.0
CA L:CYS48 4.1 0.6 1.0
C L:ASP50 4.2 0.2 1.0
CA L:CYS34 4.5 0.9 1.0
C L:CYS48 4.5 0.3 1.0
CB L:ASP50 4.5 0.6 1.0
N L:CYS34 4.6 0.1 1.0
CA L:CYS31 4.7 0.3 1.0
OE1 L:GLU33 4.7 0.5 1.0
O L:CYS34 4.7 0.8 1.0
N L:CYS48 4.7 0.3 1.0
C L:CYS34 4.7 0.5 1.0
CA L:ASP50 4.8 0.7 1.0
N L:ASP50 4.8 0.4 1.0
O L:CYS48 4.9 0.1 1.0
OD2 L:ASP50 4.9 0.6 1.0
N L:LYS49 5.0 0.4 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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