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Zinc in PDB 9n5b: Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form

Enzymatic activity of Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form

All present enzymatic activity of Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form, PDB code: 9n5b 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) 46.28 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.839, 221.722, 190.842, 90, 97.41, 90
R / Rfree (%) 21.3 / 25.6

Other elements in 9n5b:

The structure of Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form 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 Containing 8-Oxog at +1 Site, Apo Form (pdb code 9n5b). 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 Containing 8-Oxog at +1 Site, Apo Form, PDB code: 9n5b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9n5b

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:217.2
occ:1.00
 SG A:CYS110 2.3 169.5 1.0
SG A:CYS107 2.4 178.2 1.0
CB A:CYS148 2.5 197.7 1.0
SG A:CYS148 2.6 199.3 1.0
SG A:CYS167 2.7 253.2 1.0
CB A:CYS107 2.7 187.5 1.0
CB A:CYS167 3.6 246.5 1.0
CA A:CYS148 4.0 190.0 1.0
CB A:CYS110 4.1 144.4 1.0
O A:MET108 4.1 171.4 1.0
CA A:CYS107 4.2 171.8 1.0
O A:CYS110 4.4 159.0 1.0
N A:CYS167 4.4 237.5 1.0
O A:CYS148 4.5 195.4 1.0
CA A:CYS167 4.5 244.2 1.0
N A:CYS148 4.6 185.8 1.0
CD A:LYS112 4.6 143.1 1.0
CB A:LYS112 4.6 151.8 1.0
C A:CYS107 4.7 160.0 1.0
C A:CYS148 4.7 189.1 1.0
N A:CYS110 4.8 158.9 1.0
CA A:CYS110 4.9 148.8 1.0
C A:CYS110 4.9 158.6 1.0
O A:ASN169 4.9 186.7 1.0

Zinc binding site 2 out of 8 in 9n5b

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:108.3
occ:1.00
 NE2 A:HIS80 2.0 104.7 1.0
SG A:CYS67 2.4 137.2 1.0
CB A:CYS70 2.4 136.7 1.0
SG A:CYS77 2.4 102.1 1.0
SG A:CYS70 2.5 118.7 1.0
CE1 A:HIS80 2.9 99.5 1.0
CD2 A:HIS80 3.0 105.6 1.0
CB A:CYS77 3.4 98.5 1.0
NE2 A:GLN68 3.5 121.8 1.0
CB A:CYS67 3.6 130.4 1.0
CA A:CYS70 3.9 155.3 1.0
O A:CYS67 4.0 164.3 1.0
ND1 A:HIS80 4.0 84.4 1.0
CG A:HIS80 4.1 89.8 1.0
CA A:CYS77 4.2 102.4 1.0
CD A:GLN68 4.5 117.2 1.0
C A:CYS70 4.5 156.5 1.0
N A:CYS70 4.5 174.4 1.0
CG A:GLN68 4.6 120.3 1.0
C A:CYS67 4.6 146.3 1.0
CA A:CYS67 4.7 126.5 1.0
O A:CYS70 4.9 147.7 1.0
CA A:GLY59 4.9 111.6 1.0
CD A:PRO78 5.0 101.5 1.0
C A:CYS77 5.0 109.7 1.0

Zinc binding site 3 out of 8 in 9n5b

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:121.2
occ:1.00
 CB B:CYS1166 2.3 112.9 1.0
SG B:CYS1166 2.3 130.2 1.0
SG B:CYS1182 2.4 137.4 1.0
SG B:CYS1163 2.5 101.8 1.0
N B:CYS1166 2.9 119.6 1.0
CB B:CYS1163 3.0 111.1 1.0
CA B:CYS1166 3.1 113.4 1.0
CB B:CYS1185 3.7 159.6 1.0
CB B:CYS1182 3.7 122.5 1.0
SG B:CYS1185 4.0 156.3 1.0
C B:ILE1165 4.2 103.8 1.0
C B:CYS1166 4.3 112.3 1.0
CA B:CYS1163 4.5 107.6 1.0
N B:GLY1167 4.5 126.1 1.0
CB B:ILE1165 4.6 107.8 1.0
O B:LYS1183 4.6 151.3 1.0
N B:ILE1165 4.7 106.2 1.0
CA B:ILE1165 4.7 99.9 1.0
CA B:CYS1185 4.9 165.7 1.0
N B:CYS1185 5.0 155.6 1.0

Zinc binding site 4 out of 8 in 9n5b

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:82.7
occ:1.00
 SG C:CYS88 2.1 66.9 1.0
SG C:CYS92 2.2 68.8 1.0
SG C:CYS86 2.4 62.9 1.0
SG C:CYS95 2.6 68.5 1.0
CB C:CYS92 2.7 49.2 1.0
N C:CYS92 3.1 69.2 1.0
CB C:CYS86 3.2 54.7 1.0
CB C:CYS88 3.2 51.8 1.0
CB C:CYS95 3.4 64.3 1.0
CA C:CYS92 3.5 49.5 1.0
C C:HIS91 4.0 73.2 1.0
N C:CYS88 4.0 59.2 1.0
N C:CYS95 4.2 63.6 1.0
C C:CYS92 4.2 56.4 1.0
CA C:CYS88 4.3 55.5 1.0
CA C:CYS95 4.4 59.0 1.0
CA C:HIS91 4.4 64.2 1.0
CA C:CYS86 4.5 58.3 1.0
O C:CYS92 4.6 59.5 1.0
N C:PHE87 4.7 65.4 1.0
O C:HIS91 4.8 66.2 1.0
C C:CYS86 4.8 60.5 1.0
C C:LYS94 4.8 69.8 1.0
N C:LYS94 4.9 49.2 1.0
N C:ASP93 4.9 66.3 1.0

Zinc binding site 5 out of 8 in 9n5b

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:93.6
occ:1.00
 SG I:CYS29 2.3 107.7 1.0
SG I:CYS10 2.4 98.7 1.0
SG I:CYS7 2.4 84.3 1.0
SG I:CYS32 2.4 109.4 1.0
CB I:CYS7 2.8 69.0 1.0
CB I:CYS29 2.9 76.6 1.0
O I:ASP9 3.4 100.2 1.0
CB I:CYS32 3.5 97.0 1.0
O I:CYS10 3.8 103.5 1.0
N I:CYS32 3.9 100.2 1.0
CB I:CYS10 4.0 120.8 1.0
C I:ASP9 4.2 95.0 1.0
CA I:CYS7 4.3 80.8 1.0
CA I:CYS32 4.3 98.2 1.0
CA I:CYS29 4.4 85.6 1.0
CB I:TYR34 4.5 65.2 1.0
C I:CYS10 4.6 101.0 1.0
CA I:CYS10 4.7 122.6 1.0
CB I:THR31 4.7 95.9 1.0
N I:CYS10 4.9 117.7 1.0
C I:CYS7 4.9 90.7 1.0
C I:CYS32 4.9 91.6 1.0

Zinc binding site 6 out of 8 in 9n5b

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:139.2
occ:1.00
 SG I:CYS106 2.1 56.5 1.0
SG I:CYS78 2.1 52.4 1.0
SG I:CYS75 2.1 59.6 1.0
SG I:CYS103 2.3 111.3 1.0
CB I:CYS75 2.7 79.9 1.0
CB I:CYS103 2.9 73.0 1.0
OG I:SER80 3.4 122.5 1.0
CB I:CYS106 3.5 78.0 1.0
CB I:CYS78 3.6 75.3 1.0
N I:CYS78 3.9 67.4 1.0
N I:CYS106 4.0 67.0 1.0
CA I:CYS75 4.3 72.7 1.0
CA I:CYS78 4.3 57.6 1.0
CA I:CYS106 4.3 61.5 1.0
CA I:CYS103 4.4 66.5 1.0
CB I:HIS108 4.5 56.3 1.0
CB I:LYS77 4.8 57.7 1.0
CB I:SER105 4.8 79.2 1.0
CB I:SER80 4.8 97.9 1.0
C I:CYS78 4.8 71.0 1.0
C I:SER105 4.8 75.7 1.0
N I:HIS79 4.9 80.4 1.0
C I:CYS106 4.9 60.3 1.0
C I:CYS75 4.9 75.2 1.0
N I:SER80 4.9 86.2 1.0
C I:CYS103 4.9 74.4 1.0
N I:HIS108 4.9 56.7 1.0

Zinc binding site 7 out of 8 in 9n5b

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:69.2
occ:1.00
 SG J:CYS10 2.2 53.7 1.0
SG J:CYS7 2.4 54.9 1.0
SG J:CYS46 2.4 48.4 1.0
SG J:CYS45 2.4 65.2 1.0
CB J:CYS7 3.0 62.2 1.0
N J:CYS46 3.0 67.2 1.0
CA J:CYS46 3.2 54.1 1.0
CB J:CYS46 3.3 53.4 1.0
C J:CYS45 3.5 61.2 1.0
CB J:CYS10 3.6 47.5 1.0
CB J:CYS45 3.8 54.2 1.0
N J:CYS10 3.9 43.6 1.0
O J:CYS45 4.0 51.0 1.0
CA J:CYS45 4.3 50.9 1.0
CA J:CYS10 4.3 59.1 1.0
NE J:ARG43 4.4 69.4 1.0
NH2 J:ARG43 4.5 52.3 1.0
CA J:CYS7 4.5 51.2 1.0
CB J:LYS12 4.6 49.1 1.0
N J:GLY11 4.6 54.0 1.0
N J:LYS12 4.7 55.6 1.0
C J:CYS46 4.8 55.5 1.0
CB J:SER9 4.8 54.8 1.0
C J:CYS10 4.9 64.2 1.0
CZ J:ARG43 4.9 61.5 1.0
C J:CYS7 5.0 47.9 1.0

Zinc binding site 8 out of 8 in 9n5b

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Containing 8-Oxog at +1 Site, Apo Form


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 Containing 8-Oxog at +1 Site, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:200.9
occ:1.00
 SG L:CYS48 2.3 147.6 1.0
SG L:CYS51 2.4 226.2 1.0
SG L:CYS31 2.4 183.9 1.0
CB L:CYS31 2.5 138.1 1.0
SG L:CYS34 2.5 174.1 1.0
CB L:CYS48 3.1 147.0 1.0
OG L:SER36 3.6 164.8 1.0
CB L:CYS51 3.7 211.8 1.0
CA L:CYS31 4.0 125.8 1.0
CB L:CYS34 4.3 164.6 1.0
N L:CYS51 4.4 219.2 1.0
CA L:CYS48 4.5 153.1 1.0
N L:CYS34 4.5 167.4 1.0
CA L:CYS51 4.5 216.0 1.0
CB L:HIS53 4.6 154.5 1.0
C L:CYS31 4.7 150.4 1.0
CB L:SER36 4.7 156.4 1.0
N L:CYS31 4.8 122.4 1.0
CD1 L:LEU38 4.9 130.2 1.0
N L:HIS53 4.9 173.1 1.0
CA L:CYS34 5.0 170.1 1.0
N L:ALA32 5.0 157.9 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 18:45:20 2025

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