Zinc in PDB 8uku: Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Cmp Added

Enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Cmp Added

All present enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Cmp Added:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Cmp Added, PDB code: 8uku 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) 49.24 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.103, 224.009, 192.541, 90, 99.98, 90
R / Rfree (%) 25.8 / 30.2

Other elements in 8uku:

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

Zinc binding site 1 out of 8 in 8uku

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:348.8
occ:1.00
 SG A:CYS110 2.3 200.6 1.0
SG A:CYS148 2.3 335.9 1.0
SG A:CYS167 2.3 284.9 1.0
SG A:CYS107 2.3 230.9 1.0
CB A:CYS107 3.2 214.8 1.0
CB A:CYS167 3.3 258.4 1.0
CB A:CYS110 3.3 195.9 1.0
CB A:CYS148 3.4 279.7 1.0
N A:CYS110 3.9 212.0 1.0
N A:GLY168 3.9 236.0 1.0
CA A:CYS167 4.1 262.7 1.0
N A:CYS148 4.2 271.6 1.0
CA A:CYS110 4.2 208.1 1.0
O A:ASN169 4.3 203.8 1.0
CA A:CYS148 4.4 274.3 1.0
C A:CYS167 4.4 270.2 1.0
CB A:HIS109 4.6 227.0 1.0
CA A:CYS107 4.7 199.8 1.0
C A:HIS109 4.7 207.5 1.0
N A:ASN169 4.8 212.6 1.0
CD2 A:HIS109 4.8 229.2 1.0
O A:CYS148 4.9 271.7 1.0
CA A:GLY168 5.0 205.9 1.0

Zinc binding site 2 out of 8 in 8uku

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:195.3
occ:1.00
 NE2 A:HIS80 2.1 265.7 1.0
SG A:CYS77 2.3 190.5 1.0
SG A:CYS67 2.3 212.6 1.0
SG A:CYS70 2.3 211.8 1.0
CE1 A:HIS80 2.8 260.4 1.0
CB A:CYS70 3.1 200.2 1.0
CD2 A:HIS80 3.1 261.0 1.0
CB A:CYS77 3.2 149.1 1.0
CB A:CYS67 3.5 206.6 1.0
ND1 A:HIS80 3.9 257.3 1.0
N A:GLY79 4.1 173.4 1.0
CG A:HIS80 4.1 253.2 1.0
CA A:CYS77 4.2 166.0 1.0
CA A:GLY79 4.4 176.3 1.0
CA A:CYS70 4.5 214.0 1.0
O A:ARG57 4.5 219.1 1.0
N A:GLN68 4.5 240.2 1.0
O A:LEU58 4.6 229.2 1.0
C A:CYS77 4.6 174.1 1.0
CA A:CYS67 4.7 204.3 1.0
CD A:PRO78 4.7 192.2 1.0
N A:PRO78 4.7 194.1 1.0
N A:CYS70 4.8 218.3 1.0
C A:GLY79 4.9 162.5 1.0

Zinc binding site 3 out of 8 in 8uku

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:293.9
occ:1.00
 SG B:CYS1166 2.3 168.1 1.0
SG B:CYS1182 2.3 288.0 1.0
SG B:CYS1185 2.3 160.4 1.0
SG B:CYS1163 2.3 270.0 1.0
N B:CYS1166 2.9 204.2 1.0
CB B:CYS1185 3.0 195.0 1.0
CB B:CYS1182 3.3 274.9 1.0
CB B:CYS1163 3.4 228.5 1.0
CB B:CYS1166 3.4 151.3 1.0
CA B:CYS1166 3.5 171.7 1.0
CB B:ILE1165 3.6 241.2 1.0
C B:ILE1165 3.7 222.6 1.0
CA B:ILE1165 4.0 231.6 1.0
CA B:CYS1185 4.3 184.5 1.0
N B:ILE1165 4.3 238.6 1.0
CG1 B:ILE1165 4.3 227.1 1.0
N B:CYS1185 4.3 181.2 1.0
O B:LYS1183 4.4 194.2 1.0
CA B:CYS1182 4.4 266.9 1.0
O B:ILE1165 4.5 211.1 1.0
CG2 B:ILE1165 4.6 227.5 1.0
C B:CYS1182 4.6 269.1 1.0
N B:LYS1183 4.8 230.0 1.0
CA B:CYS1163 4.8 220.7 1.0
O B:ASN1187 4.9 226.8 1.0
C B:CYS1166 5.0 176.1 1.0

Zinc binding site 4 out of 8 in 8uku

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:253.6
occ:1.00
 SG C:CYS92 2.3 100.0 1.0
SG C:CYS95 2.3 116.4 1.0
SG C:CYS88 2.3 68.6 1.0
SG C:CYS86 2.3 105.8 1.0
CB C:CYS92 3.0 123.4 1.0
CB C:CYS86 3.2 131.6 1.0
CB C:CYS95 3.2 124.3 1.0
N C:CYS92 3.3 120.2 1.0
CB C:CYS88 3.5 73.6 1.0
CA C:CYS92 3.6 113.1 1.0
N C:CYS95 4.0 122.5 1.0
N C:CYS88 4.0 111.5 1.0
CA C:CYS95 4.2 111.4 1.0
C C:CYS92 4.2 87.7 1.0
C C:HIS91 4.3 135.6 1.0
CA C:CYS88 4.4 97.0 1.0
O C:CYS92 4.4 96.2 1.0
CA C:CYS86 4.5 144.2 1.0
N C:PHE87 4.5 121.7 1.0
CA C:HIS91 4.8 97.5 1.0
C C:CYS86 4.8 144.5 1.0

Zinc binding site 5 out of 8 in 8uku

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:124.3
occ:1.00
 SG I:CYS10 2.3 206.4 1.0
SG I:CYS7 2.3 117.9 1.0
SG I:CYS32 2.3 182.6 1.0
SG I:CYS29 2.3 155.5 1.0
CB I:CYS32 2.9 157.7 1.0
N I:CYS32 3.1 121.2 1.0
CB I:CYS10 3.3 160.3 1.0
CB I:CYS7 3.4 132.0 1.0
CA I:CYS32 3.5 125.9 1.0
CB I:CYS29 3.5 134.5 1.0
O I:CYS32 3.6 159.6 1.0
N I:CYS10 3.9 162.9 1.0
C I:CYS32 4.0 141.7 1.0
C I:THR31 4.0 116.5 1.0
CB I:THR31 4.0 134.1 1.0
CA I:CYS10 4.2 165.7 1.0
CG2 I:THR31 4.3 94.6 1.0
CA I:THR31 4.4 132.7 1.0
O I:CYS7 4.5 146.9 1.0
N I:THR31 4.6 137.3 1.0
CA I:CYS7 4.6 118.8 1.0
C I:CYS7 4.7 122.8 1.0
CB I:ASP9 4.7 155.3 1.0
C I:ASP9 4.8 160.0 1.0
CA I:CYS29 4.9 127.1 1.0
N I:ASP9 4.9 120.5 1.0
O I:THR31 5.0 134.9 1.0

Zinc binding site 6 out of 8 in 8uku

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:228.8
occ:1.00
 SG I:CYS78 2.3 143.3 1.0
SG I:CYS103 2.3 244.2 1.0
SG I:CYS75 2.3 282.4 1.0
SG I:CYS106 2.3 196.9 1.0
CB I:CYS78 3.2 147.0 1.0
CB I:CYS75 3.2 212.8 1.0
CB I:HIS108 3.2 154.7 1.0
O I:SER105 3.2 202.0 1.0
N I:CYS78 3.3 216.4 1.0
CB I:CYS103 3.5 147.7 1.0
CB I:CYS106 3.5 156.0 1.0
N I:HIS108 3.8 157.9 1.0
CA I:CYS78 3.8 151.5 1.0
CA I:HIS108 4.0 153.3 1.0
CG I:HIS108 4.1 145.6 1.0
O I:HIS108 4.3 137.1 1.0
C I:CYS106 4.3 143.5 1.0
ND1 I:HIS108 4.3 177.8 1.0
C I:SER105 4.3 196.4 1.0
C I:LYS77 4.3 225.1 1.0
CA I:CYS106 4.3 159.9 1.0
O I:CYS75 4.4 213.7 1.0
N I:SER107 4.4 145.1 1.0
CB I:LYS77 4.5 174.2 1.0
CA I:CYS75 4.5 197.7 1.0
C I:CYS75 4.6 218.8 1.0
N I:LYS77 4.6 190.9 1.0
C I:HIS108 4.6 142.2 1.0
O I:CYS106 4.7 186.5 1.0
CA I:LYS77 4.7 191.7 1.0
N I:CYS106 4.8 177.3 1.0
CA I:CYS103 4.8 130.5 1.0
C I:SER107 4.9 144.0 1.0
CG I:LYS77 4.9 157.8 1.0

Zinc binding site 7 out of 8 in 8uku

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:110.5
occ:1.00
 SG J:CYS10 2.3 98.2 1.0
SG J:CYS7 2.3 46.5 1.0
SG J:CYS45 2.3 158.3 1.0
SG J:CYS46 2.3 84.7 1.0
CB J:CYS10 2.9 64.0 1.0
N J:CYS46 3.2 140.7 1.0
CB J:CYS7 3.4 81.8 1.0
CB J:CYS45 3.5 90.4 1.0
OG J:SER9 3.5 77.3 1.0
N J:CYS10 3.7 86.5 1.0
CB J:CYS46 3.7 145.6 1.0
C J:CYS45 3.9 124.0 1.0
CA J:CYS10 3.9 82.5 1.0
CA J:CYS46 3.9 127.6 1.0
NE J:ARG43 4.0 110.3 1.0
CB J:ARG43 4.0 120.1 1.0
CA J:CYS45 4.2 93.1 1.0
NH2 J:ARG43 4.2 121.3 1.0
N J:CYS45 4.6 84.6 1.0
CZ J:ARG43 4.6 116.7 1.0
CG J:ARG43 4.7 149.2 1.0
O J:CYS45 4.7 96.3 1.0
CA J:CYS7 4.8 109.0 1.0
CB J:SER9 4.8 88.0 1.0
C J:SER9 4.8 96.1 1.0
CD J:ARG43 5.0 132.6 1.0

Zinc binding site 8 out of 8 in 8uku

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with 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 Fapy-Dg Lesion with Cmp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:341.0
occ:1.00
 SG L:CYS34 2.3 420.9 1.0
SG L:CYS51 2.3 414.4 1.0
SG L:CYS31 2.3 339.6 1.0
SG L:CYS48 2.3 267.6 1.0
CB L:CYS51 3.0 394.2 1.0
CB L:CYS48 3.1 253.7 1.0
CB L:CYS34 3.3 401.3 1.0
CB L:CYS31 3.5 309.9 1.0
O L:CYS51 3.5 375.2 1.0
N L:CYS34 3.7 408.8 1.0
CA L:CYS51 3.7 386.0 1.0
C L:CYS51 3.7 381.1 1.0
N L:CYS51 3.8 380.0 1.0
O L:HIS53 4.0 253.2 1.0
CA L:CYS34 4.1 404.9 1.0
CA L:CYS48 4.3 248.4 1.0
N L:CYS48 4.4 250.1 1.0
N L:HIS53 4.4 262.7 1.0
N L:GLY52 4.6 287.6 1.0
CB L:HIS53 4.7 268.7 1.0
C L:GLU33 4.7 271.9 1.0
CA L:CYS31 4.7 306.5 1.0
O L:CYS48 4.7 260.0 1.0
C L:ASP50 4.8 316.6 1.0
C L:CYS48 4.8 253.4 1.0
C L:CYS31 4.8 314.3 1.0
CB L:GLU33 4.8 264.2 1.0
C L:HIS53 4.9 254.8 1.0
CA L:HIS53 4.9 261.8 1.0
O L:CYS31 4.9 317.7 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 12:22:35 2024

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