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Zinc in PDB 9n5f: Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp

Enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp

All present enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp, PDB code: 9n5f was solved by J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.54, 223.101, 195.002, 90, 100.38, 90
R / Rfree (%) 24.8 / 28.1

Other elements in 9n5f:

The structure of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp (pdb code 9n5f). 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 Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp, PDB code: 9n5f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9n5f

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:321.9
occ:1.00
 SG A:CYS107 2.3 285.4 1.0
SG A:CYS167 2.3 264.5 1.0
CB A:CYS167 2.7 271.9 1.0
N A:CYS167 2.8 279.8 1.0
CB A:CYS110 2.9 260.1 1.0
SG A:CYS148 3.1 231.2 1.0
SG A:CYS110 3.2 265.9 1.0
CA A:CYS167 3.3 275.5 1.0
O A:MET108 3.5 237.2 1.0
CB A:CYS148 3.5 224.2 1.0
C A:GLY166 3.9 241.4 1.0
CB A:CYS107 4.0 261.5 1.0
N A:GLY168 4.2 223.9 1.0
CA A:GLY166 4.2 245.2 1.0
C A:CYS167 4.3 262.9 1.0
CA A:CYS110 4.3 251.6 1.0
N A:CYS110 4.6 248.7 1.0
C A:MET108 4.7 237.8 1.0
O A:CYS110 4.8 238.6 1.0
C A:CYS110 4.9 239.2 1.0

Zinc binding site 2 out of 8 in 9n5f

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:217.3
occ:1.00
 NE2 A:HIS80 2.1 231.2 1.0
CE1 A:HIS80 2.2 225.9 1.0
SG A:CYS77 2.3 197.9 1.0
SG A:CYS67 2.3 240.4 1.0
SG A:CYS70 2.4 192.8 1.0
CB A:CYS70 2.6 216.1 1.0
CB A:CYS77 3.4 169.3 1.0
NE2 A:GLN68 3.5 234.3 1.0
CD2 A:HIS80 3.5 215.5 1.0
ND1 A:HIS80 3.5 215.0 1.0
CB A:CYS67 3.9 213.0 1.0
CG A:HIS80 4.1 211.3 1.0
CA A:CYS70 4.2 237.8 1.0
CA A:CYS77 4.3 174.8 1.0
O A:CYS67 4.3 244.4 1.0
CD A:PRO78 4.4 205.3 1.0
CD A:GLN68 4.5 244.6 1.0
CG A:GLN68 4.5 243.4 1.0
N A:GLY79 4.7 176.0 1.0
N A:PRO78 4.8 197.4 1.0
N A:CYS70 4.9 253.2 1.0
C A:CYS70 4.9 236.9 1.0
C A:CYS77 4.9 170.9 1.0
C A:CYS67 4.9 226.3 1.0

Zinc binding site 3 out of 8 in 9n5f

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:245.8
occ:1.00
 SG B:CYS1166 2.3 198.0 1.0
SG B:CYS1182 2.3 236.5 1.0
SG B:CYS1185 2.4 198.6 1.0
SG B:CYS1163 2.4 225.2 1.0
CB B:CYS1185 2.6 199.8 1.0
CB B:CYS1166 2.7 171.6 1.0
N B:CYS1166 2.9 156.9 1.0
CA B:CYS1166 3.2 156.6 1.0
CB B:CYS1163 3.7 202.4 1.0
CB B:CYS1182 3.8 226.7 1.0
CA B:CYS1185 3.9 198.9 1.0
C B:ILE1165 3.9 166.0 1.0
N B:CYS1185 4.0 194.3 1.0
O B:LYS1183 4.1 209.3 1.0
ND2 B:ASN1187 4.1 208.7 1.0
CB B:ILE1165 4.3 193.6 1.0
CA B:ILE1165 4.5 181.5 1.0
C B:CYS1166 4.6 165.7 1.0
O B:ILE1165 4.7 177.4 1.0
C B:CYS1185 4.7 201.5 1.0
N B:ILE1165 4.8 184.5 1.0
N B:ASP1186 4.9 206.5 1.0
CA B:CYS1182 5.0 228.2 1.0
CA B:CYS1163 5.0 189.5 1.0
C B:LYS1183 5.0 212.2 1.0

Zinc binding site 4 out of 8 in 9n5f

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:117.3
occ:1.00
 SG C:CYS88 2.3 107.3 1.0
SG C:CYS95 2.3 148.3 1.0
SG C:CYS86 2.3 112.4 1.0
CB C:CYS92 2.4 110.4 1.0
CB C:CYS95 2.4 108.3 1.0
CB C:CYS86 2.9 116.6 1.0
N C:CYS92 3.0 105.2 1.0
CB C:CYS88 3.2 68.3 1.0
CA C:CYS92 3.2 121.0 1.0
CA C:CYS95 3.7 99.3 1.0
SG C:CYS92 3.9 192.3 1.0
N C:CYS95 3.9 115.6 1.0
N C:CYS88 4.1 95.3 1.0
C C:CYS92 4.1 119.1 1.0
C C:HIS91 4.1 123.6 1.0
CA C:CYS88 4.3 77.3 1.0
O C:CYS92 4.3 98.8 1.0
CA C:CYS86 4.4 123.8 1.0
C C:CYS95 4.5 92.3 1.0
CA C:HIS91 4.6 111.8 1.0
N C:PHE87 4.8 97.9 1.0
C C:CYS86 4.8 118.1 1.0
N C:SER96 4.9 104.0 1.0
O C:SER83 4.9 76.5 1.0
C C:LYS94 5.0 119.7 1.0

Zinc binding site 5 out of 8 in 9n5f

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:132.9
occ:1.00
 SG I:CYS32 2.3 153.9 1.0
SG I:CYS10 2.3 146.8 1.0
SG I:CYS7 2.3 130.1 1.0
SG I:CYS29 2.4 153.4 1.0
CB I:CYS7 2.5 136.2 1.0
CB I:CYS32 2.8 127.6 1.0
CB I:CYS29 3.1 121.3 1.0
O I:CYS10 3.2 159.9 1.0
N I:CYS32 3.5 107.3 1.0
CA I:CYS32 3.7 111.4 1.0
CB I:CYS10 3.8 163.2 1.0
N I:CYS10 4.0 182.7 1.0
CA I:CYS7 4.0 126.9 1.0
C I:CYS10 4.0 149.8 1.0
CA I:CYS10 4.2 167.9 1.0
CA I:CYS29 4.5 111.8 1.0
C I:CYS7 4.6 133.5 1.0
C I:THR31 4.6 132.8 1.0
C I:CYS32 4.7 128.2 1.0
N I:CYS7 4.7 125.5 1.0
C I:CYS29 4.8 116.0 1.0
CB I:THR31 4.8 139.2 1.0
O I:CYS7 4.8 147.3 1.0
CD2 I:TYR34 4.8 100.2 1.0
O I:CYS29 5.0 155.0 1.0

Zinc binding site 6 out of 8 in 9n5f

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:146.5
occ:1.00
 CB I:CYS106 2.0 118.3 1.0
CB I:CYS78 2.2 103.1 1.0
SG I:CYS106 2.3 127.6 1.0
SG I:CYS78 2.3 164.7 1.0
SG I:CYS75 2.3 212.8 1.0
N I:CYS78 2.4 168.8 1.0
CA I:CYS78 2.8 132.4 1.0
CA I:CYS106 3.3 150.2 1.0
N I:CYS106 3.5 177.0 1.0
C I:LYS77 3.6 152.2 1.0
SG I:CYS103 4.0 157.3 1.0
CB I:LYS77 4.0 124.3 1.0
C I:CYS78 4.0 130.9 1.0
CB I:CYS75 4.1 169.6 1.0
CA I:LYS77 4.2 120.7 1.0
N I:HIS79 4.2 168.3 1.0
N I:LYS77 4.3 123.2 1.0
CB I:CYS103 4.3 163.1 1.0
O I:CYS75 4.3 180.5 1.0
C I:CYS106 4.5 144.5 1.0
C I:SER105 4.5 255.8 1.0
CB I:HIS108 4.6 118.2 1.0
O I:LYS77 4.6 150.5 1.0
C I:CYS75 4.7 178.2 1.0
CG I:LYS77 4.8 124.6 1.0
CA I:CYS75 4.9 171.8 1.0
N I:SER107 5.0 109.1 1.0

Zinc binding site 7 out of 8 in 9n5f

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:365.3
occ:1.00
 N J:CYS46 2.2 163.1 1.0
SG J:CYS10 2.3 59.7 1.0
SG J:CYS7 2.3 98.3 1.0
CB J:CYS10 2.5 94.6 1.0
CA J:CYS46 2.5 165.8 1.0
C J:CYS45 2.6 151.0 1.0
CB J:CYS7 2.8 85.2 1.0
CB J:CYS46 2.8 157.4 1.0
O J:CYS45 2.9 147.2 1.0
N J:CYS10 3.3 77.7 1.0
CA J:CYS10 3.4 92.3 1.0
CB J:CYS45 3.5 132.4 1.0
CA J:CYS45 3.5 127.3 1.0
SG J:CYS45 3.7 189.4 1.0
OG J:SER9 3.8 90.5 1.0
SG J:CYS46 3.9 173.3 1.0
C J:CYS46 4.0 156.6 1.0
CA J:CYS7 4.3 103.7 1.0
N J:CYS45 4.3 123.7 1.0
C J:SER9 4.5 78.6 1.0
C J:CYS10 4.6 99.0 1.0
N J:ARG47 4.7 131.3 1.0
O J:CYS46 4.8 150.1 1.0
C J:CYS7 4.8 94.4 1.0
N J:GLY11 4.8 93.9 1.0
N J:SER9 4.9 81.0 1.0
CB J:SER9 5.0 98.1 1.0

Zinc binding site 8 out of 8 in 9n5f

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog in Syn-Conformation with Added Amp


Mono view


Stereo pair view

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

b:212.5
occ:1.00
 SG L:CYS51 2.3 267.3 1.0
SG L:CYS48 2.3 231.5 1.0
SG L:CYS34 2.3 263.6 1.0
CB L:CYS34 2.6 224.6 1.0
CB L:CYS48 2.6 181.1 1.0
CB L:CYS51 3.1 240.6 1.0
SG L:CYS31 3.2 290.0 1.0
CB L:CYS31 3.5 265.9 1.0
N L:CYS34 3.6 233.9 1.0
CA L:CYS34 3.7 221.3 1.0
N L:CYS51 3.7 259.9 1.0
CA L:CYS51 3.9 246.8 1.0
CA L:CYS48 4.1 186.2 1.0
N L:GLY52 4.2 203.0 1.0
C L:CYS51 4.4 245.1 1.0
C L:CYS48 4.6 214.3 1.0
N L:HIS53 4.6 213.9 1.0
OG L:SER36 4.6 252.8 1.0
C L:GLU33 4.7 229.2 1.0
O L:CYS48 4.7 224.8 1.0
C L:ASP50 4.8 230.2 1.0
C L:CYS34 4.8 237.3 1.0
O L:HIS53 4.8 205.6 1.0
CA L:CYS31 4.8 259.4 1.0
N L:CYS48 4.9 185.3 1.0
N L:ASP50 5.0 216.4 1.0
C L:CYS31 5.0 264.3 1.0
CB L:HIS53 5.0 193.2 1.0

Reference:

J.Oh, K.A.Konovalov, P.Hou, J.Chong, X.Huang, D.Wang. Transcription-Coupled Template Reconfiguration of 8-Oxoguanine For Error-Prone Transcription Revealed By Time-Resolved X-Ray Crystallography and Molecular Dynamics. J.Am.Chem.Soc. V. 147 16396 2025.
ISSN: ESSN 1520-5126
PubMed: 40305462
DOI: 10.1021/JACS.5C02687
Page generated: Fri Aug 22 18:47:26 2025

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