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Zinc in PDB 9n5g: Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and E-Site

Enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and E-Site

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and E-Site, PDB code: 9n5g 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) 48.06 / 3.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.784, 222.488, 192.287, 90, 98.1, 90
R / Rfree (%) 22 / 25.4

Other elements in 9n5g:

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site (pdb code 9n5g). 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, Atp in Both A- and E-Site, PDB code: 9n5g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9n5g

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:214.4
occ:1.00
 CB A:CYS167 2.2 272.5 1.0
SG A:CYS107 2.3 187.7 1.0
SG A:CYS148 2.3 208.7 1.0
SG A:CYS167 2.3 269.8 1.0
N A:CYS167 2.8 272.8 1.0
CB A:CYS110 3.0 197.8 1.0
CA A:CYS167 3.0 277.5 1.0
CB A:CYS107 3.4 192.0 1.0
N A:CYS110 3.6 201.9 1.0
CA A:CYS110 3.9 200.8 1.0
C A:CYS167 4.0 274.9 1.0
N A:GLY168 4.0 223.3 1.0
CB A:CYS148 4.1 190.1 1.0
C A:GLY166 4.1 221.8 1.0
C A:HIS109 4.2 194.9 1.0
CB A:HIS109 4.2 190.9 1.0
SG A:CYS110 4.2 149.9 1.0
CA A:GLY166 4.6 203.5 1.0
CA A:HIS109 4.7 188.9 1.0
O A:CYS148 4.7 205.0 1.0
NE2 A:GLN171 4.8 178.8 1.0
N A:HIS109 4.8 176.0 1.0
CA A:CYS107 4.8 171.8 1.0
O A:HIS109 4.9 195.6 1.0
C A:CYS110 5.0 181.2 1.0

Zinc binding site 2 out of 8 in 9n5g

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:137.9
occ:1.00
 NE2 A:HIS80 2.2 161.0 1.0
SG A:CYS77 2.3 146.9 1.0
SG A:CYS67 2.3 142.5 1.0
SG A:CYS70 2.4 148.8 1.0
CB A:CYS70 2.6 152.5 1.0
CD2 A:HIS80 3.0 147.7 1.0
NE2 A:GLN68 3.2 165.4 1.0
CE1 A:HIS80 3.2 144.0 1.0
CB A:CYS77 3.3 126.0 1.0
CB A:CYS67 3.8 156.0 1.0
CA A:CYS77 4.1 136.4 1.0
O A:CYS67 4.1 185.9 1.0
CA A:CYS70 4.1 178.3 1.0
CG A:HIS80 4.2 126.9 1.0
ND1 A:HIS80 4.3 125.3 1.0
CD A:GLN68 4.4 163.1 1.0
N A:GLY79 4.4 129.3 1.0
CD A:PRO78 4.5 121.2 1.0
C A:CYS77 4.6 132.9 1.0
N A:PRO78 4.7 122.9 1.0
C A:CYS67 4.8 167.3 1.0
N A:CYS70 4.8 194.8 1.0
CG A:GLN68 4.9 158.3 1.0
CA A:GLY79 4.9 127.2 1.0
C A:CYS70 4.9 177.0 1.0
CA A:CYS67 4.9 137.6 1.0

Zinc binding site 3 out of 8 in 9n5g

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:157.9
occ:1.00
 CB B:CYS1166 1.6 126.9 1.0
SG B:CYS1182 2.3 151.8 1.0
SG B:CYS1185 2.3 151.8 1.0
SG B:CYS1166 2.3 144.5 1.0
CA B:CYS1166 2.8 135.1 1.0
N B:CYS1166 3.3 133.9 1.0
SG B:CYS1163 3.3 116.6 1.0
CB B:CYS1163 3.5 133.3 1.0
CB B:CYS1185 3.5 167.7 1.0
CB B:CYS1182 3.9 157.7 1.0
CG2 B:THR1170 4.1 121.7 1.0
C B:CYS1166 4.1 124.8 1.0
O B:LYS1183 4.5 163.2 1.0
C B:ILE1165 4.5 129.4 1.0
N B:GLY1167 4.7 125.1 1.0
CA B:CYS1185 4.8 181.0 1.0
N B:CYS1185 4.8 173.9 1.0
O B:CYS1166 4.8 112.8 1.0
CA B:CYS1163 4.9 126.1 1.0

Zinc binding site 4 out of 8 in 9n5g

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:105.5
occ:1.00
 SG C:CYS92 2.3 86.3 1.0
SG C:CYS88 2.3 70.1 1.0
SG C:CYS86 2.3 115.9 1.0
SG C:CYS95 2.3 95.1 1.0
CB C:CYS86 3.2 77.7 1.0
CB C:CYS92 3.2 88.5 1.0
CB C:CYS95 3.2 75.7 1.0
N C:CYS92 3.3 81.0 1.0
CB C:CYS88 3.5 72.5 1.0
CA C:CYS92 3.8 75.6 1.0
N C:CYS95 3.9 79.1 1.0
C C:HIS91 4.1 85.5 1.0
O C:CYS86 4.1 77.8 1.0
N C:CYS88 4.1 74.9 1.0
CA C:CYS95 4.2 66.5 1.0
C C:CYS86 4.2 83.3 1.0
CA C:CYS86 4.3 89.7 1.0
CA C:HIS91 4.3 67.2 1.0
C C:CYS92 4.4 68.1 1.0
CA C:CYS88 4.5 74.4 1.0
O C:CYS92 4.6 69.5 1.0
C C:LYS94 4.8 80.4 1.0
N C:PHE87 4.8 90.5 1.0
N C:LYS94 4.9 71.0 1.0
CB C:LYS94 4.9 73.8 1.0
O C:HIS91 5.0 83.2 1.0
C C:CYS95 5.0 71.5 1.0

Zinc binding site 5 out of 8 in 9n5g

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:114.4
occ:1.00
 SG I:CYS29 2.3 96.1 1.0
SG I:CYS10 2.3 117.1 1.0
SG I:CYS7 2.3 97.2 1.0
SG I:CYS32 2.3 171.4 1.0
CB I:CYS7 3.1 96.1 1.0
CB I:CYS29 3.3 97.6 1.0
CB I:CYS32 3.6 140.4 1.0
N I:CYS32 3.7 118.3 1.0
O I:CYS10 3.9 133.7 1.0
CB I:CYS10 4.0 119.0 1.0
N I:CYS10 4.0 117.7 1.0
CA I:CYS32 4.2 124.2 1.0
CB I:THR31 4.3 101.1 1.0
CB I:TYR34 4.3 100.6 1.0
CA I:CYS10 4.4 115.5 1.0
C I:THR31 4.5 115.9 1.0
CA I:CYS7 4.5 95.7 1.0
C I:CYS10 4.6 117.2 1.0
C I:CYS32 4.7 120.4 1.0
CA I:CYS29 4.8 99.6 1.0
CA I:THR31 4.8 97.3 1.0
N I:THR31 4.8 96.8 1.0
CB I:ASP9 4.8 113.1 1.0
O I:CYS32 4.9 116.4 1.0
OG1 I:THR31 4.9 116.2 1.0
C I:CYS7 5.0 96.2 1.0

Zinc binding site 6 out of 8 in 9n5g

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:97.5
occ:1.00
 CB I:CYS78 2.2 61.6 1.0
SG I:CYS106 2.3 81.2 1.0
SG I:CYS103 2.3 107.7 1.0
SG I:CYS75 2.3 85.4 1.0
CB I:CYS75 2.5 80.4 1.0
CB I:CYS103 3.1 93.0 1.0
CA I:CYS78 3.3 88.0 1.0
N I:CYS78 3.3 93.8 1.0
SG I:CYS78 3.4 90.2 1.0
CB I:CYS106 3.7 84.8 1.0
OG I:SER80 3.8 83.8 1.0
CA I:CYS75 4.0 75.9 1.0
C I:CYS78 4.1 83.7 1.0
N I:CYS106 4.2 80.7 1.0
N I:HIS79 4.2 92.5 1.0
CB I:SER80 4.3 83.3 1.0
N I:SER80 4.3 81.8 1.0
CA I:CYS106 4.5 84.0 1.0
CA I:CYS103 4.6 77.3 1.0
C I:LYS77 4.6 78.9 1.0
N I:CYS75 4.8 72.9 1.0
C I:CYS75 4.8 88.8 1.0
CA I:SER80 4.9 82.1 1.0
O I:SER80 5.0 80.4 1.0
O I:CYS78 5.0 79.8 1.0
CB I:HIS108 5.0 82.9 1.0
CB I:SER105 5.0 83.6 1.0

Zinc binding site 7 out of 8 in 9n5g

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:69.1
occ:1.00
 SG J:CYS46 2.3 55.7 1.0
SG J:CYS7 2.3 74.2 1.0
SG J:CYS45 2.3 103.2 1.0
SG J:CYS10 2.3 117.0 1.0
CB J:CYS10 3.0 61.3 1.0
N J:CYS46 3.2 84.8 1.0
CB J:CYS7 3.3 75.3 1.0
CB J:CYS46 3.5 80.4 1.0
CA J:CYS46 3.6 82.4 1.0
CB J:CYS45 3.6 81.7 1.0
C J:CYS45 3.6 83.6 1.0
N J:CYS10 3.7 76.4 1.0
OG J:SER9 3.8 73.1 1.0
CA J:CYS10 3.9 70.4 1.0
O J:CYS45 4.1 70.9 1.0
CA J:CYS45 4.2 57.2 1.0
NH2 J:ARG43 4.2 67.2 1.0
NE J:ARG43 4.2 93.8 1.0
CZ J:ARG43 4.7 79.0 1.0
C J:SER9 4.7 61.3 1.0
CA J:CYS7 4.8 59.4 1.0
N J:CYS45 4.9 40.7 1.0
CB J:SER9 4.9 68.3 1.0
CB J:ARG43 4.9 65.1 1.0
CB J:LYS12 4.9 34.2 1.0

Zinc binding site 8 out of 8 in 9n5g

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Atp in Both A- and 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, Atp in Both A- and E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:182.7
occ:1.00
 CB L:CYS51 1.6 183.9 1.0
SG L:CYS34 2.3 219.6 1.0
SG L:CYS51 2.3 201.9 1.0
SG L:CYS48 2.3 220.6 1.0
CB L:CYS34 2.7 168.7 1.0
CA L:CYS51 2.9 187.9 1.0
CB L:CYS48 2.9 163.1 1.0
N L:CYS51 3.3 201.4 1.0
SG L:CYS31 3.7 195.9 1.0
CB L:CYS31 3.8 160.3 1.0
CA L:CYS34 3.9 169.3 1.0
N L:CYS34 4.0 179.6 1.0
C L:CYS51 4.1 184.5 1.0
C L:ASP50 4.1 200.0 1.0
CA L:CYS48 4.2 159.0 1.0
O L:CYS48 4.4 184.4 1.0
C L:CYS48 4.5 181.9 1.0
N L:GLY52 4.6 176.8 1.0
O L:ASP50 4.7 200.1 1.0
CA L:ASP50 4.9 183.7 1.0
O L:CYS51 4.9 183.5 1.0
OG L:SER36 4.9 188.8 1.0
C L:CYS34 4.9 173.5 1.0
N L:CYS48 4.9 159.8 1.0
N L:ASP50 4.9 176.8 1.0
CB L:ASP50 5.0 154.7 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 18:47:35 2025

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