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Zinc in PDB 9n5e: Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Ampcpp in E-Site

Enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Ampcpp in E-Site

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Ampcpp in E-Site, PDB code: 9n5e 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) 48.96 / 3.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.718, 222.926, 193.285, 90, 99.2, 90
R / Rfree (%) 24.9 / 29.1

Other elements in 9n5e:

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Ampcpp in E-Site 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, Ampcpp in E-Site (pdb code 9n5e). 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, Ampcpp in E-Site, PDB code: 9n5e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:282.5
occ:1.00
 SG A:CYS110 2.3 290.5 1.0
CB A:CYS110 2.3 302.5 1.0
CB A:CYS167 2.4 260.0 1.0
N A:CYS110 2.5 295.0 1.0
CA A:CYS110 2.8 301.4 1.0
CA A:CYS167 2.8 261.9 1.0
O A:MET108 2.8 252.5 1.0
C A:HIS109 3.3 270.5 1.0
O A:CYS110 3.3 276.1 1.0
C A:CYS110 3.3 284.1 1.0
C A:MET108 3.5 236.8 1.0
CB A:CYS107 3.7 248.7 1.0
N A:CYS167 3.7 264.8 1.0
C A:CYS167 3.9 262.5 1.0
O A:HIS109 3.9 271.1 1.0
N A:HIS109 4.0 249.3 1.0
CA A:HIS109 4.0 260.7 1.0
SG A:CYS167 4.1 264.3 1.0
O A:CYS167 4.1 260.3 1.0
N A:MET108 4.1 218.2 1.0
C A:CYS107 4.2 236.5 1.0
N A:GLY111 4.4 236.0 1.0
CB A:HIS109 4.4 264.8 1.0
CA A:MET108 4.4 213.4 1.0
CA A:CYS107 4.6 234.2 1.0
O A:CYS107 4.6 245.8 1.0
C A:GLY166 4.6 276.6 1.0
NE2 A:GLN171 4.7 208.8 1.0
O A:GLY166 4.8 276.4 1.0

Zinc binding site 2 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:187.3
occ:1.00
 NE2 A:HIS80 2.2 200.5 1.0
SG A:CYS77 2.3 133.9 1.0
SG A:CYS70 2.3 189.8 1.0
SG A:CYS67 2.3 147.1 1.0
CB A:CYS70 2.6 122.6 1.0
CD2 A:HIS80 3.0 189.9 1.0
CE1 A:HIS80 3.0 201.3 1.0
CB A:CYS67 3.4 166.7 1.0
N A:CYS70 3.6 140.7 1.0
CA A:CYS70 3.7 151.2 1.0
N A:GLY79 3.8 163.9 1.0
CA A:GLY79 3.8 156.1 1.0
CB A:CYS77 3.9 156.3 1.0
ND1 A:HIS80 4.0 191.4 1.0
CG A:HIS80 4.0 182.9 1.0
C A:GLY79 4.4 146.8 1.0
N A:GLY59 4.6 224.7 1.0
CA A:CYS77 4.6 143.1 1.0
CA A:GLY59 4.6 221.7 1.0
C A:CYS77 4.7 150.0 1.0
C A:CYS70 4.7 192.1 1.0
C A:THR69 4.8 150.6 1.0
CA A:CYS67 4.9 175.3 1.0
N A:HIS80 4.9 162.6 1.0
N A:PRO78 4.9 178.1 1.0
O A:GLY79 4.9 138.7 1.0

Zinc binding site 3 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:230.4
occ:1.00
 CB B:CYS1166 1.7 185.3 1.0
SG B:CYS1182 2.3 265.8 1.0
SG B:CYS1185 2.3 135.1 1.0
SG B:CYS1163 2.3 204.2 1.0
SG B:CYS1166 2.3 194.0 1.0
CA B:CYS1166 2.9 151.2 1.0
CB B:CYS1185 3.0 154.4 1.0
N B:CYS1166 3.4 141.0 1.0
CB B:CYS1182 3.6 254.1 1.0
CB B:CYS1163 3.8 207.9 1.0
C B:CYS1166 4.2 152.4 1.0
CA B:CYS1185 4.4 168.0 1.0
C B:ILE1165 4.5 136.0 1.0
O B:LYS1183 4.6 176.0 1.0
N B:CYS1185 4.6 168.2 1.0
O B:CYS1163 4.7 189.0 1.0
N B:GLY1167 4.8 158.0 1.0
CD1 A:ILE30 4.8 171.3 1.0
CA B:CYS1163 4.9 203.6 1.0
CA B:CYS1182 4.9 258.9 1.0
O B:CYS1166 4.9 155.8 1.0
C B:CYS1163 5.0 189.2 1.0

Zinc binding site 4 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:200.2
occ:1.00
 SG C:CYS88 2.3 111.7 1.0
CB C:CYS92 2.3 113.1 1.0
SG C:CYS95 2.3 155.6 1.0
SG C:CYS86 2.3 114.2 1.0
CB C:CYS95 2.6 133.7 1.0
N C:CYS92 2.8 110.6 1.0
CB C:CYS86 2.9 136.9 1.0
CA C:CYS92 3.1 111.5 1.0
CB C:CYS88 3.5 114.2 1.0
SG C:CYS92 3.7 246.6 1.0
N C:CYS95 3.8 127.4 1.0
CA C:CYS95 3.8 118.1 1.0
C C:HIS91 3.9 122.2 1.0
C C:CYS92 3.9 110.4 1.0
O C:CYS92 3.9 115.8 1.0
CA C:HIS91 4.3 129.8 1.0
N C:CYS88 4.4 116.7 1.0
CA C:CYS86 4.4 121.3 1.0
CA C:CYS88 4.6 116.3 1.0
C C:CYS95 4.6 104.7 1.0
O C:HIS91 4.7 122.0 1.0
N C:SER96 4.8 128.1 1.0
C C:LYS94 4.9 132.1 1.0
C C:CYS86 4.9 130.2 1.0
O C:SER83 4.9 108.5 1.0
N C:ASP93 5.0 111.9 1.0

Zinc binding site 5 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:121.7
occ:1.00
 SG I:CYS32 2.3 151.8 1.0
SG I:CYS29 2.3 163.2 1.0
SG I:CYS10 2.3 218.9 1.0
CB I:CYS32 3.0 150.8 1.0
O I:ASP9 3.1 142.2 1.0
N I:CYS32 3.2 136.0 1.0
CB I:CYS29 3.2 133.4 1.0
O I:CYS10 3.5 195.0 1.0
CA I:CYS32 3.7 136.7 1.0
SG I:CYS7 3.8 107.8 1.0
CB I:CYS7 3.8 104.8 1.0
CB I:CYS10 3.9 212.2 1.0
CB I:THR31 4.0 144.5 1.0
C I:THR31 4.0 138.7 1.0
C I:ASP9 4.1 142.0 1.0
C I:CYS10 4.2 189.7 1.0
O I:CYS32 4.3 176.7 1.0
C I:CYS32 4.4 154.4 1.0
CA I:THR31 4.4 145.7 1.0
CA I:CYS10 4.5 199.7 1.0
N I:THR31 4.5 130.3 1.0
N I:CYS10 4.7 211.3 1.0
CA I:CYS29 4.7 146.5 1.0
CG2 I:THR31 4.8 150.1 1.0
OG1 I:THR31 4.8 153.8 1.0
CB I:ASN12 4.9 116.0 1.0
O I:THR31 4.9 139.9 1.0

Zinc binding site 6 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:163.8
occ:1.00
 CB I:CYS78 2.2 134.4 1.0
SG I:CYS78 2.3 181.8 1.0
SG I:CYS106 2.3 143.4 1.0
SG I:CYS103 2.3 224.4 1.0
N I:CYS106 2.5 187.6 1.0
CB I:CYS106 2.5 151.6 1.0
CB I:CYS103 3.0 146.6 1.0
CA I:CYS106 3.0 154.7 1.0
C I:SER105 3.5 262.6 1.0
CA I:CYS78 3.6 149.5 1.0
OG I:SER80 3.7 224.3 1.0
N I:SER105 3.9 274.0 1.0
CB I:SER105 3.9 293.0 1.0
N I:CYS78 4.0 190.3 1.0
CA I:SER105 4.0 277.4 1.0
CB I:CYS75 4.0 159.7 1.0
O I:CYS103 4.0 172.9 1.0
C I:CYS103 4.1 142.7 1.0
CA I:CYS103 4.1 129.5 1.0
C I:CYS106 4.2 165.3 1.0
SG I:CYS75 4.3 183.9 1.0
N I:SER107 4.4 192.8 1.0
O I:SER105 4.5 273.1 1.0
C I:CYS78 4.6 162.5 1.0
N I:LEU104 4.7 148.9 1.0
C I:LEU104 4.7 194.5 1.0
O I:SER80 4.9 190.0 1.0
N I:CYS103 4.9 128.0 1.0

Zinc binding site 7 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:82.5
occ:1.00
 CB J:CYS10 2.1 62.9 1.0
SG J:CYS7 2.3 150.1 1.0
SG J:CYS45 2.3 177.8 1.0
N J:CYS10 2.6 62.1 1.0
N J:CYS46 2.7 152.8 1.0
CB J:CYS45 2.7 114.6 1.0
CA J:CYS10 2.8 70.0 1.0
C J:CYS45 2.9 130.3 1.0
CB J:CYS7 3.1 117.5 1.0
CA J:CYS46 3.3 145.5 1.0
CA J:CYS45 3.3 104.1 1.0
SG J:CYS10 3.4 92.3 1.0
O J:CYS45 3.5 106.8 1.0
CB J:CYS46 3.6 139.7 1.0
C J:SER9 3.9 74.6 1.0
C J:CYS10 4.1 97.1 1.0
CB J:SER9 4.2 83.3 1.0
N J:CYS45 4.2 72.5 1.0
SG J:CYS46 4.4 151.2 1.0
CA J:SER9 4.4 67.3 1.0
CA J:CYS7 4.5 110.6 1.0
N J:GLY11 4.5 104.0 1.0
N J:SER9 4.5 64.2 1.0
C J:CYS46 4.7 131.9 1.0
C J:CYS7 4.8 108.7 1.0
O J:SER9 4.8 87.6 1.0
NH2 J:ARG48 4.9 74.8 1.0
O J:CYS7 4.9 115.5 1.0

Zinc binding site 8 out of 8 in 9n5e

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


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, Ampcpp in E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:306.8
occ:1.00
 SG L:CYS48 2.3 305.2 1.0
SG L:CYS34 2.3 322.8 1.0
CB L:CYS51 2.4 279.7 1.0
CB L:CYS34 2.6 304.1 1.0
CB L:CYS48 3.0 261.5 1.0
SG L:CYS51 3.2 269.5 1.0
CB L:CYS31 3.3 246.2 1.0
N L:CYS51 3.3 288.3 1.0
CA L:CYS51 3.4 285.0 1.0
CA L:CYS34 3.8 302.0 1.0
N L:CYS34 3.8 312.2 1.0
SG L:CYS31 4.0 239.2 1.0
CD2 L:LEU38 4.0 217.1 1.0
C L:ASP50 4.2 315.8 1.0
CA L:CYS48 4.4 256.6 1.0
CD1 L:LEU38 4.4 228.7 1.0
CA L:CYS31 4.5 223.1 1.0
O L:CYS48 4.5 265.9 1.0
CB L:ASP50 4.6 324.5 1.0
C L:CYS48 4.7 262.3 1.0
CG L:LEU38 4.7 225.0 1.0
C L:CYS51 4.7 285.6 1.0
N L:CYS31 4.7 176.0 1.0
OG L:SER36 4.8 279.5 1.0
CA L:ASP50 4.8 318.5 1.0
C L:CYS34 4.8 292.8 1.0
C L:CYS31 4.9 254.1 1.0
O L:CYS31 4.9 244.7 1.0
N L:ASP50 4.9 310.3 1.0
C L:GLU33 5.0 288.9 1.0
O L:ASP50 5.0 330.2 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 18:47:00 2025

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