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Zinc in PDB 9n5c: Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound

Enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound

All present enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound, PDB code: 9n5c 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) 48.77 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.638, 222.985, 192.256, 90, 98.55, 90
R / Rfree (%) 25.2 / 29.7

Other elements in 9n5c:

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound 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 at +1 Site, Cmpcpp- Bound (pdb code 9n5c). 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 at +1 Site, Cmpcpp- Bound, PDB code: 9n5c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9n5c

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:240.7
occ:1.00
 NZ A:LYS112 2.2 188.3 1.0
SG A:CYS107 2.3 177.2 1.0
SG A:CYS110 2.5 216.3 1.0
CB A:CYS167 2.5 195.8 1.0
O A:CYS110 2.6 219.6 1.0
CB A:CYS107 3.1 182.0 1.0
N A:CYS167 3.2 201.2 1.0
CE A:LYS112 3.4 171.0 1.0
CA A:CYS167 3.4 202.8 1.0
C A:CYS110 3.4 215.3 1.0
CD A:LYS112 3.8 166.9 1.0
CB A:CYS110 3.9 206.5 1.0
SG A:CYS167 3.9 218.0 1.0
O A:MET108 4.0 210.8 1.0
CG A:LYS112 4.1 162.9 1.0
CA A:CYS110 4.1 217.6 1.0
SG A:CYS148 4.2 175.2 1.0
CB A:CYS148 4.3 177.6 1.0
N A:GLY111 4.3 195.8 1.0
CA A:CYS107 4.4 173.7 1.0
C A:GLY166 4.4 180.6 1.0
N A:CYS110 4.5 216.0 1.0
C A:CYS107 4.6 179.5 1.0
N A:LYS112 4.6 164.6 1.0
CA A:GLY111 4.7 177.4 1.0
C A:CYS167 4.7 192.0 1.0
O A:CYS107 4.8 185.6 1.0
C A:GLY111 4.9 170.8 1.0
CA A:GLY166 4.9 178.0 1.0

Zinc binding site 2 out of 8 in 9n5c

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:121.8
occ:1.00
 SG A:CYS70 2.3 202.7 1.0
SG A:CYS77 2.3 100.7 1.0
SG A:CYS67 2.4 201.6 1.0
CB A:CYS70 2.4 195.3 1.0
CB A:CYS67 2.5 178.6 1.0
O A:CYS67 3.0 188.0 1.0
NE2 A:HIS80 3.5 175.5 1.0
CA A:CYS67 3.5 173.0 1.0
C A:CYS67 3.6 191.1 1.0
CB A:CYS77 3.8 123.4 1.0
CA A:CYS70 3.8 203.4 1.0
NE2 A:GLN68 4.0 209.7 1.0
CD2 A:HIS80 4.1 171.4 1.0
N A:CYS70 4.1 214.0 1.0
N A:CYS67 4.2 156.4 1.0
CE1 A:HIS80 4.5 155.9 1.0
CA A:CYS77 4.6 131.0 1.0
C A:CYS70 4.8 192.4 1.0
CG A:GLN68 4.8 202.7 1.0
N A:GLN68 4.8 208.4 1.0
CD A:GLN68 5.0 205.8 1.0

Zinc binding site 3 out of 8 in 9n5c

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2102

b:163.3
occ:1.00
 N B:CYS1166 2.3 144.7 1.0
SG B:CYS1166 2.4 130.5 1.0
CB B:CYS1185 2.5 166.7 1.0
SG B:CYS1163 2.6 161.6 1.0
CB B:CYS1166 2.6 118.0 1.0
SG B:CYS1182 2.7 194.1 1.0
CA B:CYS1166 2.8 128.3 1.0
SG B:CYS1185 3.1 186.3 1.0
C B:ILE1165 3.2 139.2 1.0
CB B:CYS1163 3.5 133.8 1.0
CB B:ILE1165 3.7 133.5 1.0
CA B:ILE1165 3.8 124.7 1.0
CA B:CYS1185 3.8 161.4 1.0
N B:ILE1165 4.0 126.5 1.0
O B:ILE1165 4.1 143.1 1.0
CB B:CYS1182 4.2 174.1 1.0
N B:CYS1185 4.2 150.3 1.0
C B:CYS1166 4.2 132.2 1.0
CG2 B:ILE1165 4.5 137.3 1.0
C B:CYS1185 4.5 171.2 1.0
O B:LYS1183 4.5 182.8 1.0
N B:GLY1167 4.7 134.4 1.0
C B:CYS1163 4.8 138.8 1.0
CG1 B:ILE1165 4.8 119.2 1.0
CA B:CYS1163 4.8 131.3 1.0
O B:CYS1163 4.8 139.9 1.0
N B:ASP1186 4.9 174.2 1.0
CB B:ASN1187 5.0 163.6 1.0
C B:GLY1164 5.0 130.7 1.0

Zinc binding site 4 out of 8 in 9n5c

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:148.3
occ:1.00
 SG C:CYS88 2.3 102.6 1.0
CB C:CYS92 2.4 95.9 1.0
SG C:CYS95 2.4 169.5 1.0
CB C:CYS95 2.4 142.9 1.0
N C:CYS92 2.7 114.6 1.0
CB C:CYS86 3.0 104.6 1.0
CA C:CYS92 3.1 93.9 1.0
SG C:CYS86 3.2 121.0 1.0
CB C:CYS88 3.7 102.4 1.0
CA C:CYS95 3.8 127.5 1.0
C C:HIS91 3.9 118.8 1.0
SG C:CYS92 3.9 170.2 1.0
N C:CYS95 4.0 131.2 1.0
C C:CYS92 4.1 93.1 1.0
O C:CYS92 4.2 116.8 1.0
CA C:CYS86 4.3 107.2 1.0
O C:SER83 4.4 103.1 1.0
CA C:HIS91 4.4 98.6 1.0
N C:CYS88 4.5 102.7 1.0
CA C:SER83 4.6 103.2 1.0
C C:CYS95 4.7 119.2 1.0
CA C:CYS88 4.7 102.5 1.0
N C:CYS86 4.8 109.8 1.0
O C:TYR82 4.8 103.6 1.0
C C:CYS86 4.8 118.6 1.0
N C:PHE87 4.9 103.5 1.0
O C:HIS91 4.9 130.7 1.0
C C:SER83 5.0 103.3 1.0

Zinc binding site 5 out of 8 in 9n5c

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:110.1
occ:1.00
 CB I:CYS32 2.4 137.3 1.0
SG I:CYS32 2.7 179.9 1.0
SG I:CYS29 2.8 203.7 1.0
CB I:CYS7 2.9 115.3 1.0
O I:ASP9 3.0 134.0 1.0
N I:CYS32 3.0 117.7 1.0
SG I:CYS10 3.1 158.0 1.0
SG I:CYS7 3.1 140.1 1.0
OG1 I:THR31 3.2 148.3 1.0
CA I:CYS32 3.3 129.1 1.0
O I:CYS10 3.5 153.6 1.0
CB I:CYS29 3.5 118.5 1.0
C I:THR31 4.1 120.0 1.0
C I:ASP9 4.2 142.1 1.0
C I:CYS10 4.2 138.2 1.0
CA I:CYS7 4.3 115.2 1.0
CB I:THR31 4.4 124.7 1.0
C I:CYS32 4.4 131.6 1.0
CB I:CYS10 4.5 160.1 1.0
O I:CYS29 4.5 121.7 1.0
CA I:THR31 4.7 120.1 1.0
C I:CYS29 4.7 122.4 1.0
CA I:CYS29 4.7 121.5 1.0
N I:THR31 4.7 123.8 1.0
N I:ASN12 4.7 118.7 1.0
C I:CYS7 4.8 119.7 1.0
N I:CYS7 4.8 126.6 1.0
O I:CYS7 4.8 137.3 1.0
CA I:CYS10 4.8 142.7 1.0
CB I:ASN12 4.9 120.5 1.0
N I:CYS10 4.9 155.1 1.0
O I:CYS32 5.0 130.1 1.0

Zinc binding site 6 out of 8 in 9n5c

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:209.4
occ:1.00
 CB I:CYS78 2.3 109.0 1.0
CA I:CYS106 2.3 149.9 1.0
N I:CYS106 2.5 152.7 1.0
CB I:CYS106 2.6 147.1 1.0
CA I:CYS78 2.8 155.4 1.0
C I:SER105 2.8 172.2 1.0
O I:SER105 3.0 178.4 1.0
SG I:CYS106 3.1 206.3 1.0
N I:CYS78 3.5 180.2 1.0
CB I:SER105 3.8 176.6 1.0
C I:CYS106 3.8 148.4 1.0
SG I:CYS78 3.8 129.6 1.0
CA I:SER105 3.9 184.3 1.0
C I:CYS78 4.1 156.9 1.0
C I:LYS77 4.4 162.4 1.0
O I:CYS106 4.4 170.0 1.0
SG I:CYS103 4.4 182.7 1.0
O I:CYS78 4.5 153.0 1.0
O I:LYS77 4.6 157.4 1.0
OG I:SER80 4.7 180.0 1.0
N I:SER105 4.7 187.7 1.0
N I:SER107 4.7 167.7 1.0

Zinc binding site 7 out of 8 in 9n5c

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:145.7
occ:1.00
 C J:CYS45 2.1 148.9 1.0
CB J:CYS10 2.1 50.5 1.0
N J:CYS46 2.2 128.8 1.0
SG J:CYS7 2.3 125.8 1.0
O J:CYS45 2.3 138.1 1.0
CA J:CYS46 2.5 120.7 1.0
CB J:CYS7 2.5 86.7 1.0
CB J:CYS45 2.9 134.1 1.0
CA J:CYS45 3.0 131.5 1.0
N J:CYS10 3.2 78.2 1.0
CA J:CYS10 3.2 79.6 1.0
SG J:CYS10 3.3 127.7 1.0
CB J:CYS46 3.4 97.5 1.0
SG J:CYS46 3.6 67.1 1.0
SG J:CYS45 3.7 140.5 1.0
C J:CYS46 3.7 98.2 1.0
CA J:CYS7 4.0 101.3 1.0
N J:CYS45 4.2 125.7 1.0
O J:CYS46 4.3 91.0 1.0
C J:CYS10 4.4 104.8 1.0
C J:SER9 4.4 86.7 1.0
N J:ARG47 4.5 95.9 1.0
N J:GLY11 4.6 107.2 1.0
C J:CYS7 4.6 105.4 1.0
N J:SER9 4.8 69.6 1.0
CB J:SER9 4.8 76.2 1.0
NE J:ARG48 4.8 50.0 1.0
N J:CYS7 4.8 131.0 1.0
CG J:MET49 4.9 70.9 1.0
C J:TYR44 4.9 85.0 1.0
CA J:SER9 4.9 86.4 1.0
O J:TYR44 4.9 74.0 1.0
O J:ARG43 4.9 116.3 1.0
O J:CYS7 4.9 117.7 1.0

Zinc binding site 8 out of 8 in 9n5c

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmpcpp- Bound


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 at +1 Site, Cmpcpp- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:309.9
occ:1.00
 N L:CYS51 2.1 270.3 1.0
SG L:CYS48 2.2 305.5 1.0
CB L:CYS51 2.3 252.5 1.0
CB L:CYS34 2.3 273.6 1.0
CA L:CYS51 2.6 259.6 1.0
CB L:CYS48 2.6 244.9 1.0
SG L:CYS34 2.8 305.4 1.0
C L:ASP50 3.1 259.7 1.0
CA L:ASP50 3.6 246.6 1.0
N L:ASP50 3.6 246.7 1.0
CB L:ASP50 3.7 238.0 1.0
C L:CYS48 3.7 244.6 1.0
CA L:CYS48 3.7 227.8 1.0
CA L:CYS34 3.7 265.1 1.0
O L:CYS48 3.7 259.5 1.0
SG L:CYS51 3.8 280.5 1.0
C L:CYS51 3.9 256.7 1.0
OG L:SER36 4.0 244.0 1.0
O L:ASP50 4.1 257.0 1.0
N L:GLY52 4.2 257.3 1.0
N L:CYS34 4.2 262.4 1.0
N L:LYS49 4.4 231.5 1.0
CB L:CYS31 4.4 226.5 1.0
N L:CYS48 4.5 205.6 1.0
C L:LYS49 4.6 235.1 1.0
CG L:ASP50 4.7 220.6 1.0
OD2 L:ASP50 4.7 208.6 1.0
C L:CYS34 4.8 263.6 1.0
O L:CYS51 5.0 252.8 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 18:45:33 2025

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