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Zinc in PDB 9n5d: Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added, PDB code: 9n5d 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) 49.31 / 3.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 165.899, 222.27, 193.145, 90, 100.27, 90
R / Rfree (%) 26.5 / 30

Other elements in 9n5d:

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added 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, Cmp Added (pdb code 9n5d). 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, Cmp Added, PDB code: 9n5d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9n5d

Go back to Zinc Binding Sites List in 9n5d
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:233.4
occ:1.00
 O A:CYS110 2.0 194.6 1.0
CB A:CYS167 2.4 194.4 1.0
CB A:CYS110 2.6 201.7 1.0
SG A:CYS167 2.6 190.4 1.0
C A:CYS110 2.8 187.3 1.0
CA A:CYS110 3.0 198.7 1.0
SG A:CYS110 3.0 209.9 1.0
CB A:CYS107 3.1 195.7 1.0
N A:CYS110 3.4 199.7 1.0
SG A:CYS107 3.5 178.6 1.0
O A:MET108 3.5 197.1 1.0
CA A:CYS167 3.7 197.4 1.0
O A:CYS107 3.7 182.9 1.0
C A:CYS107 3.8 187.7 1.0
CA A:CYS107 4.1 189.3 1.0
N A:GLY111 4.1 166.8 1.0
C A:MET108 4.3 191.9 1.0
N A:CYS167 4.4 182.9 1.0
N A:MET108 4.4 187.1 1.0
C A:HIS109 4.5 193.2 1.0
N A:LYS112 4.7 162.2 1.0
CA A:GLY111 4.7 159.1 1.0
C A:CYS167 4.8 192.3 1.0
N A:CYS107 4.8 180.7 1.0
CB A:LYS112 4.9 163.3 1.0
C A:GLY111 4.9 160.6 1.0

Zinc binding site 2 out of 8 in 9n5d

Go back to Zinc Binding Sites List in 9n5d
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:161.9
occ:1.00
 SG A:CYS67 2.3 166.1 1.0
CB A:CYS70 2.4 152.0 1.0
SG A:CYS77 2.4 150.4 1.0
SG A:CYS70 2.4 145.2 1.0
CB A:CYS77 2.4 139.3 1.0
CB A:CYS67 3.1 168.0 1.0
O A:CYS67 3.6 175.6 1.0
NE2 A:HIS80 3.7 147.2 1.0
CA A:CYS77 3.9 140.4 1.0
CA A:CYS70 3.9 160.7 1.0
CA A:CYS67 4.3 163.6 1.0
C A:CYS67 4.3 171.2 1.0
CB A:GLU72 4.4 153.4 1.0
N A:CYS70 4.5 172.2 1.0
NE2 A:GLN68 4.5 160.7 1.0
CE1 A:HIS80 4.5 149.4 1.0
O A:GLU72 4.6 120.4 1.0
CD2 A:HIS80 4.6 146.9 1.0
C A:CYS70 4.6 160.8 1.0
N A:CYS77 4.7 144.5 1.0
C A:CYS77 4.7 145.1 1.0
CG A:GLN68 4.8 161.6 1.0

Zinc binding site 3 out of 8 in 9n5d

Go back to Zinc Binding Sites List in 9n5d
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:163.7
occ:1.00
 SG B:CYS1166 2.3 169.3 1.0
SG B:CYS1185 2.3 184.3 1.0
N B:CYS1166 2.3 169.8 1.0
CB B:CYS1166 2.5 148.7 1.0
SG B:CYS1182 2.5 169.6 1.0
CA B:CYS1166 2.7 159.1 1.0
CB B:CYS1185 3.1 168.2 1.0
C B:ILE1165 3.3 169.1 1.0
SG B:CYS1163 3.4 174.4 1.0
O B:LYS1183 3.8 155.0 1.0
O B:ILE1165 4.0 171.0 1.0
CB B:ILE1165 4.0 161.8 1.0
CB B:CYS1163 4.0 158.8 1.0
CA B:ILE1165 4.1 159.7 1.0
N B:CYS1185 4.1 155.9 1.0
C B:CYS1166 4.2 157.1 1.0
CB B:CYS1182 4.2 153.8 1.0
CA B:CYS1185 4.2 165.1 1.0
OD1 B:ASN1187 4.2 162.8 1.0
N B:ILE1165 4.5 157.0 1.0
CG2 B:ILE1165 4.7 171.0 1.0
N B:GLY1167 4.8 160.8 1.0
O B:CYS1163 4.8 160.8 1.0
C B:LYS1183 5.0 154.8 1.0

Zinc binding site 4 out of 8 in 9n5d

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


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:100.9
occ:1.00
 SG C:CYS92 2.3 93.2 1.0
SG C:CYS88 2.3 119.5 1.0
CB C:CYS88 2.6 48.2 1.0
SG C:CYS95 2.8 103.3 1.0
CB C:CYS95 2.9 71.1 1.0
SG C:CYS86 3.0 129.3 1.0
CB C:CYS86 3.2 92.2 1.0
CB C:CYS92 3.3 88.2 1.0
N C:CYS92 3.4 93.6 1.0
N C:CYS88 3.5 65.0 1.0
CA C:CYS88 3.6 48.7 1.0
CA C:CYS92 3.9 87.9 1.0
CA C:CYS95 4.1 70.5 1.0
N C:CYS95 4.2 84.7 1.0
C C:HIS91 4.2 93.1 1.0
C C:CYS92 4.4 72.7 1.0
C C:CYS86 4.4 94.0 1.0
CA C:CYS86 4.4 101.5 1.0
CA C:HIS91 4.5 84.6 1.0
N C:PHE87 4.5 85.1 1.0
O C:CYS92 4.6 70.1 1.0
C C:CYS88 4.8 79.3 1.0
C C:PHE87 4.8 77.4 1.0
O C:CYS86 4.9 102.5 1.0
CG C:LYS94 4.9 68.9 1.0
O C:HIS91 5.0 90.4 1.0

Zinc binding site 5 out of 8 in 9n5d

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


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:90.0
occ:1.00
 SG I:CYS32 2.3 109.2 1.0
SG I:CYS7 2.4 108.1 1.0
SG I:CYS29 2.6 122.5 1.0
SG I:CYS10 2.6 119.0 1.0
N I:CYS32 2.8 99.4 1.0
CB I:CYS32 3.0 105.3 1.0
O I:ASP9 3.1 120.8 1.0
CB I:CYS29 3.3 83.5 1.0
CA I:CYS32 3.4 94.9 1.0
O I:CYS10 3.5 109.4 1.0
O I:CYS32 3.7 125.2 1.0
C I:THR31 3.7 105.6 1.0
CB I:CYS7 3.8 98.8 1.0
CB I:THR31 3.9 104.0 1.0
C I:CYS32 4.0 107.5 1.0
CB I:CYS10 4.2 135.3 1.0
CA I:THR31 4.2 97.5 1.0
C I:ASP9 4.3 126.6 1.0
C I:CYS10 4.3 104.9 1.0
N I:THR31 4.4 82.6 1.0
O I:THR31 4.6 103.0 1.0
CA I:CYS10 4.7 122.7 1.0
CA I:CYS29 4.8 91.7 1.0
OG1 I:THR31 4.8 115.9 1.0
CG2 I:THR31 4.8 110.7 1.0
N I:CYS10 4.9 128.7 1.0
CB I:ASN12 5.0 70.9 1.0

Zinc binding site 6 out of 8 in 9n5d

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


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:157.7
occ:1.00
 SG I:CYS78 2.2 152.6 1.0
SG I:CYS106 2.2 117.4 1.0
CB I:CYS78 2.4 87.0 1.0
CB I:CYS106 2.6 95.3 1.0
CB I:CYS75 2.9 122.7 1.0
SG I:CYS75 2.9 149.3 1.0
CB I:CYS103 3.0 97.4 1.0
SG I:CYS103 3.1 143.8 1.0
N I:CYS78 3.4 126.5 1.0
CA I:CYS78 3.5 99.4 1.0
N I:CYS106 3.6 120.0 1.0
CA I:CYS106 3.7 106.8 1.0
CA I:CYS75 4.2 114.8 1.0
CA I:CYS103 4.2 96.8 1.0
OG I:SER80 4.3 129.6 1.0
OG I:SER105 4.4 133.1 1.0
C I:CYS78 4.5 111.5 1.0
C I:CYS75 4.5 127.5 1.0
O I:CYS75 4.5 115.2 1.0
C I:CYS103 4.5 107.7 1.0
N I:CYS75 4.6 107.8 1.0
N I:HIS79 4.6 120.3 1.0
O I:CYS103 4.7 112.6 1.0
O I:SER80 4.7 98.9 1.0
N I:CYS103 4.7 75.2 1.0
C I:CYS106 4.7 110.7 1.0
C I:LYS77 4.7 126.6 1.0
N I:SER107 4.8 97.5 1.0
CE1 I:PHE110 4.8 97.8 1.0
C I:SER105 4.9 122.4 1.0
CB I:HIS108 4.9 97.1 1.0
N I:SER80 5.0 125.2 1.0

Zinc binding site 7 out of 8 in 9n5d

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


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:88.5
occ:1.00
 SG J:CYS10 2.2 79.3 1.0
CB J:CYS46 2.4 92.9 1.0
SG J:CYS7 2.4 69.1 1.0
CA J:CYS46 2.6 86.6 1.0
N J:CYS46 2.6 82.4 1.0
CB J:CYS7 2.8 75.3 1.0
C J:CYS45 3.3 70.3 1.0
CB J:CYS10 3.4 54.5 1.0
SG J:CYS46 3.5 101.9 1.0
SG J:CYS45 3.6 74.6 1.0
O J:CYS45 3.7 69.0 1.0
N J:CYS10 3.8 65.8 1.0
CB J:CYS45 4.1 66.1 1.0
C J:CYS46 4.1 74.1 1.0
CA J:CYS10 4.2 66.6 1.0
NH2 J:ARG43 4.2 91.4 1.0
CA J:CYS45 4.3 63.1 1.0
CA J:CYS7 4.3 79.8 1.0
O J:CYS46 4.8 69.3 1.0
CB J:SER9 4.8 58.4 1.0
C J:CYS7 4.9 67.7 1.0
N J:ARG47 4.9 73.4 1.0
C J:SER9 4.9 67.3 1.0
CB J:LYS12 5.0 45.1 1.0
CZ J:ARG43 5.0 107.0 1.0
N J:GLY11 5.0 67.1 1.0

Zinc binding site 8 out of 8 in 9n5d

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


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, Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:174.8
occ:1.00
 SG L:CYS34 2.3 173.7 1.0
CB L:CYS51 2.3 133.7 1.0
SG L:CYS48 2.4 206.7 1.0
N L:CYS51 2.5 173.7 1.0
CA L:CYS51 2.8 156.3 1.0
CB L:CYS34 2.8 133.3 1.0
OG L:SER36 3.2 144.9 1.0
CB L:CYS48 3.3 155.3 1.0
C L:ASP50 3.4 165.5 1.0
SG L:CYS51 3.5 145.2 1.0
CB L:SER36 3.7 148.9 1.0
CB L:ASP50 3.9 128.1 1.0
CA L:ASP50 4.1 147.6 1.0
C L:CYS51 4.2 158.2 1.0
CA L:CYS34 4.3 134.3 1.0
O L:ASP50 4.3 156.2 1.0
N L:ASP50 4.3 151.8 1.0
CB L:CYS31 4.3 135.6 1.0
SG L:CYS31 4.6 177.7 1.0
O L:CYS48 4.6 161.5 1.0
CA L:CYS48 4.6 157.4 1.0
N L:SER36 4.6 141.4 1.0
C L:CYS48 4.6 167.2 1.0
CA L:SER36 4.7 139.6 1.0
N L:GLY52 4.7 154.3 1.0
N L:CYS34 4.8 148.7 1.0
C L:CYS34 5.0 146.4 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 18:45:56 2025

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