Zinc in PDB 8ukq: Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State

Enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State

All present enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State, PDB code: 8ukq was solved by P.Hou, J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.44 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.54, 223.485, 191.472, 90, 98.38, 90
R / Rfree (%) 26.8 / 30.2

Other elements in 8ukq:

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State 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 Fapy-Dg Lesion in Apo State (pdb code 8ukq). 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 Fapy-Dg Lesion in Apo State, PDB code: 8ukq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8ukq

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:301.0
occ:1.00
 ND1 A:HIS109 2.1 270.1 1.0
SG A:CYS167 2.3 269.6 1.0
SG A:CYS107 2.3 221.5 1.0
SG A:CYS110 2.3 261.8 1.0
NZ A:LYS112 2.9 210.2 1.0
OD1 A:ASN169 3.0 262.8 1.0
CE1 A:HIS109 3.0 266.8 1.0
CG A:HIS109 3.2 258.7 1.0
CB A:CYS167 3.3 249.7 1.0
N A:CYS110 3.3 237.3 1.0
CB A:HIS109 3.6 234.7 1.0
CB A:CYS107 3.7 193.7 1.0
CB A:CYS110 3.7 242.9 1.0
CG A:ASN169 3.8 240.2 1.0
O A:CYS110 3.9 203.8 1.0
C A:HIS109 3.9 235.4 1.0
N A:HIS109 4.0 222.3 1.0
CA A:CYS110 4.0 229.9 1.0
CA A:HIS109 4.0 228.2 1.0
CB A:ASN169 4.0 229.2 1.0
NE2 A:HIS109 4.2 265.4 1.0
CD2 A:HIS109 4.3 260.0 1.0
CE A:LYS112 4.3 189.3 1.0
C A:CYS110 4.4 211.1 1.0
C A:CYS107 4.7 187.8 1.0
CA A:CYS167 4.7 228.9 1.0
N A:ASN169 4.7 228.8 1.0
CA A:CYS107 4.8 179.1 1.0
O A:HIS109 4.9 233.3 1.0
O A:CYS107 4.9 194.3 1.0
N A:MET108 5.0 194.7 1.0
CA A:ASN169 5.0 218.6 1.0
C A:CYS167 5.0 226.9 1.0

Zinc binding site 2 out of 8 in 8ukq

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:167.2
occ:1.00
 SG A:CYS70 2.3 117.3 1.0
SG A:CYS67 2.3 180.9 1.0
SG A:CYS77 2.3 135.8 1.0
CB A:CYS67 2.9 180.6 1.0
CB A:CYS70 3.1 146.0 1.0
CB A:CYS77 3.1 135.0 1.0
CA A:GLY59 4.1 153.8 1.0
N A:GLY59 4.3 176.3 1.0
CA A:CYS77 4.3 144.6 1.0
CA A:CYS67 4.3 165.0 1.0
O A:ARG57 4.5 170.3 1.0
N A:GLY79 4.5 140.4 1.0
NE2 A:HIS80 4.5 189.5 1.0
CA A:CYS70 4.5 171.1 1.0
CA A:GLY79 4.8 123.5 1.0
C A:CYS77 4.8 156.1 1.0
C A:CYS67 4.9 189.1 1.0
CD2 A:HIS80 4.9 176.8 1.0
C A:ARG57 4.9 158.5 1.0
C A:LEU58 4.9 163.8 1.0

Zinc binding site 3 out of 8 in 8ukq

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:204.8
occ:1.00
 SG B:CYS1185 2.3 165.9 1.0
SG B:CYS1163 2.3 195.6 1.0
SG B:CYS1166 2.3 146.0 1.0
SG B:CYS1182 2.3 194.6 1.0
OG1 B:THR1170 2.8 184.4 1.0
CB B:CYS1185 2.8 165.0 1.0
CB B:CYS1166 3.2 165.8 1.0
CB B:CYS1163 3.3 165.7 1.0
N B:CYS1166 3.6 169.9 1.0
O B:CYS1166 3.8 170.8 1.0
CB B:CYS1182 3.8 179.4 1.0
CA B:CYS1166 3.9 161.8 1.0
OD1 B:ASN1187 4.0 204.9 1.0
CB B:THR1170 4.0 177.3 1.0
O B:LYS1183 4.2 151.0 1.0
CA B:CYS1185 4.2 162.5 1.0
C B:CYS1166 4.3 157.2 1.0
CG2 B:THR1170 4.4 174.2 1.0
N B:CYS1185 4.4 142.2 1.0
C B:ILE1165 4.7 170.8 1.0
CA B:CYS1163 4.7 153.0 1.0
CB B:ILE1165 4.8 176.2 1.0
C B:CYS1185 4.9 178.1 1.0
O B:LEU1168 5.0 139.3 1.0
N B:ILE1165 5.0 172.3 1.0

Zinc binding site 4 out of 8 in 8ukq

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:120.5
occ:1.00
 SG C:CYS92 2.3 68.8 1.0
SG C:CYS86 2.3 103.1 1.0
SG C:CYS88 2.3 68.5 1.0
SG C:CYS95 2.3 98.7 1.0
N C:CYS92 2.6 100.6 1.0
CB C:CYS92 3.1 104.5 1.0
CB C:CYS95 3.2 95.7 1.0
CB C:CYS88 3.4 38.8 1.0
CA C:CYS92 3.4 95.5 1.0
CB C:CYS86 3.4 84.5 1.0
C C:HIS91 3.6 115.0 1.0
CA C:HIS91 3.8 106.0 1.0
O C:CYS92 4.1 75.7 1.0
C C:CYS92 4.1 73.4 1.0
N C:CYS88 4.4 82.9 1.0
CA C:CYS95 4.4 100.1 1.0
N C:CYS95 4.5 102.5 1.0
CA C:CYS88 4.5 77.7 1.0
O C:HIS91 4.6 119.4 1.0
N C:HIS91 4.7 119.9 1.0
CA C:CYS86 4.7 85.2 1.0
OG C:SER83 4.8 63.2 1.0
CA C:SER83 4.8 44.1 1.0
CB C:HIS91 4.8 91.8 1.0
C C:CYS86 4.9 99.2 1.0
O C:SER83 4.9 92.2 1.0

Zinc binding site 5 out of 8 in 8ukq

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:113.7
occ:1.00
 SG I:CYS10 2.3 156.8 1.0
SG I:CYS7 2.3 86.2 1.0
SG I:CYS32 2.3 174.2 1.0
SG I:CYS29 2.3 99.8 1.0
CB I:CYS32 2.9 133.2 1.0
N I:CYS32 3.2 111.0 1.0
CB I:CYS7 3.2 87.0 1.0
O I:CYS32 3.4 137.5 1.0
CA I:CYS32 3.4 120.5 1.0
CB I:CYS29 3.6 89.8 1.0
CB I:CYS10 3.6 94.8 1.0
C I:CYS32 3.7 123.4 1.0
N I:CYS10 3.9 96.5 1.0
C I:THR31 4.2 116.4 1.0
CA I:CYS10 4.3 105.5 1.0
CA I:CYS7 4.6 87.0 1.0
CB I:THR31 4.7 131.2 1.0
CB I:ASP9 4.7 142.6 1.0
CA I:THR31 4.8 123.8 1.0
N I:SER33 4.8 114.3 1.0
N I:THR31 4.9 121.1 1.0
C I:CYS7 4.9 102.1 1.0
CA I:CYS29 4.9 116.7 1.0
N I:TYR34 4.9 87.5 1.0
N I:ASP9 4.9 97.6 1.0
C I:ASP9 4.9 126.2 1.0
C I:CYS10 4.9 114.1 1.0
CB I:TYR34 5.0 87.0 1.0

Zinc binding site 6 out of 8 in 8ukq

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:273.3
occ:1.00
 SG I:CYS106 2.3 124.5 1.0
SG I:CYS75 2.3 210.9 1.0
SG I:CYS103 2.3 179.7 1.0
SG I:CYS78 2.3 209.4 1.0
CB I:CYS78 2.9 125.5 1.0
CB I:CYS75 3.0 197.7 1.0
CB I:CYS103 3.0 131.7 1.0
CE1 I:PHE110 3.5 158.0 1.0
CB I:CYS106 3.7 127.2 1.0
N I:CYS75 3.9 159.2 1.0
CD1 I:PHE110 3.9 120.8 1.0
CA I:CYS75 4.0 182.0 1.0
N I:CYS78 4.0 162.8 1.0
CA I:CYS78 4.1 128.0 1.0
CA I:CYS103 4.1 134.4 1.0
O I:HIS108 4.2 122.4 1.0
N I:CYS103 4.2 119.5 1.0
CZ I:PHE110 4.3 166.1 1.0
O I:CYS103 4.4 164.4 1.0
C I:CYS103 4.5 152.5 1.0
N I:CYS106 4.5 148.1 1.0
O I:SER80 4.6 159.0 1.0
O I:CYS75 4.7 181.6 1.0
C I:CYS75 4.7 173.9 1.0
CA I:CYS106 4.7 127.5 1.0
CG I:PHE110 5.0 121.7 1.0

Zinc binding site 7 out of 8 in 8ukq

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:133.6
occ:1.00
 SG J:CYS10 2.3 73.5 1.0
SG J:CYS45 2.3 119.9 1.0
SG J:CYS7 2.3 23.2 1.0
SG J:CYS46 2.3 44.8 1.0
N J:CYS46 3.2 106.2 1.0
CB J:CYS45 3.4 73.0 1.0
CB J:CYS10 3.4 66.6 1.0
C J:CYS45 3.5 91.0 1.0
CB J:CYS7 3.6 76.5 1.0
CB J:CYS46 3.6 104.5 1.0
CA J:CYS46 3.7 99.7 1.0
NE J:ARG43 3.9 93.3 1.0
N J:CYS10 3.9 53.3 1.0
CA J:CYS45 4.0 70.6 1.0
O J:CYS45 4.1 83.8 1.0
NH2 J:ARG43 4.2 111.8 1.0
CA J:CYS10 4.2 81.9 1.0
N J:GLY11 4.4 78.7 1.0
CZ J:ARG43 4.5 91.5 1.0
CB J:ARG43 4.5 104.0 1.0
N J:CYS45 4.7 71.0 1.0
C J:CYS10 4.7 70.0 1.0
N J:LYS12 4.8 65.0 1.0
CD J:ARG43 4.9 119.7 1.0
CB J:SER9 4.9 71.9 1.0
CB J:LYS12 4.9 61.4 1.0
CA J:CYS7 4.9 108.1 1.0

Zinc binding site 8 out of 8 in 8ukq

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State


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 Fapy-Dg Lesion in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:363.1
occ:1.00
 SG L:CYS34 2.3 317.9 1.0
SG L:CYS48 2.3 236.3 1.0
SG L:CYS51 2.3 232.3 1.0
SG L:CYS31 2.3 312.9 1.0
CB L:CYS31 2.9 216.2 1.0
CB L:CYS51 3.0 220.8 1.0
CB L:CYS48 3.3 238.1 1.0
CB L:CYS34 3.6 257.6 1.0
N L:CYS48 3.8 214.2 1.0
CD1 L:LEU38 4.1 172.7 1.0
CA L:CYS48 4.1 236.3 1.0
CA L:CYS31 4.2 200.2 1.0
CA L:CYS51 4.3 221.6 1.0
N L:CYS34 4.3 254.1 1.0
N L:CYS51 4.4 231.1 1.0
O L:CYS48 4.5 242.8 1.0
O L:HIS53 4.5 179.1 1.0
CA L:CYS34 4.6 256.2 1.0
N L:CYS31 4.6 194.9 1.0
C L:CYS31 4.7 230.1 1.0
O L:CYS31 4.7 238.8 1.0
C L:CYS48 4.7 241.9 1.0
CD2 L:LEU56 4.8 111.5 1.0
C L:ARG47 5.0 212.6 1.0

Reference:

S.Gao, P.Hou, J.Oh, D.Wang, M.M.Greenberg. Molecular Mechanism of Rna Polymerase II Transcriptional Mutagenesis By the Epimerizable Dna Lesion, Fapy·Dg. J.Am.Chem.Soc. V. 146 6274 2024.
ISSN: ESSN 1520-5126
PubMed: 38393762
DOI: 10.1021/JACS.3C14476
Page generated: Thu Oct 31 12:18:13 2024

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