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

Go back to Zinc Binding Sites List in 8uku
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

Go back to Zinc Binding Sites List in 8uku
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

Go back to Zinc Binding Sites List in 8uku
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

Go back to Zinc Binding Sites List in 8uku
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

Go back to Zinc Binding Sites List in 8uku
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

Go back to Zinc Binding Sites List in 8uku
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

Go back to Zinc Binding Sites List in 8uku
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

Go back to Zinc Binding Sites List in 8uku
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy