Atomistry » Zinc » PDB 8ucm-8uq9 » 8ukt
Atomistry »
  Zinc »
    PDB 8ucm-8uq9 »
      8ukt »

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

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added, PDB code: 8ukt 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) 47.75 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.681, 221.393, 190.539, 90, 97.67, 90
R / Rfree (%) 25.1 / 29

Other elements in 8ukt:

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

Zinc binding site 1 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:358.2
occ:1.00
 OD1 A:ASN169 2.2 315.8 1.0
SG A:CYS110 2.3 218.5 1.0
SG A:CYS167 2.3 337.2 1.0
SG A:CYS107 2.3 293.1 1.0
CB A:CYS167 2.9 319.6 1.0
CB A:CYS110 3.0 199.2 1.0
CG A:ASN169 3.1 294.7 1.0
N A:CYS110 3.3 245.9 1.0
CB A:ASN169 3.4 278.4 1.0
O A:CYS167 3.4 343.9 1.0
CB A:CYS107 3.5 255.0 1.0
CA A:CYS167 3.6 325.0 1.0
C A:CYS167 3.6 324.9 1.0
CB A:HIS109 3.7 308.6 1.0
CA A:CYS110 3.7 219.6 1.0
C A:HIS109 4.0 288.6 1.0
N A:ASN169 4.2 261.8 1.0
ND1 A:HIS109 4.3 311.2 1.0
CA A:HIS109 4.3 298.9 1.0
CG A:HIS109 4.3 317.5 1.0
ND2 A:ASN169 4.4 293.2 1.0
CA A:ASN169 4.4 263.9 1.0
N A:GLY168 4.5 232.4 1.0
O A:CYS110 4.6 223.6 1.0
N A:HIS109 4.6 295.3 1.0
NE2 A:GLN171 4.6 253.8 1.0
C A:CYS110 4.7 229.7 1.0
CA A:CYS107 4.9 238.2 1.0
C A:GLY168 4.9 220.7 1.0
O A:HIS109 4.9 288.7 1.0
N A:CYS167 5.0 319.0 1.0

Zinc binding site 2 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:185.5
occ:1.00
 NE2 A:HIS80 2.1 186.7 1.0
SG A:CYS77 2.3 170.7 1.0
SG A:CYS70 2.3 149.5 1.0
SG A:CYS67 2.3 153.3 1.0
CE1 A:HIS80 2.6 176.5 1.0
CD2 A:HIS80 2.9 176.8 1.0
CB A:CYS70 3.3 126.0 1.0
CB A:CYS67 3.3 146.9 1.0
CB A:CYS77 3.4 157.0 1.0
ND1 A:HIS80 3.5 157.2 1.0
CG A:HIS80 3.7 161.0 1.0
N A:GLY79 3.9 127.7 1.0
CA A:CYS77 4.2 154.0 1.0
CA A:GLY79 4.3 127.5 1.0
CD A:PRO78 4.4 155.6 1.0
C A:CYS77 4.5 159.7 1.0
N A:PRO78 4.5 157.8 1.0
C A:GLY79 4.6 130.4 1.0
CA A:CYS70 4.7 150.3 1.0
CA A:CYS67 4.7 158.0 1.0
N A:HIS80 4.8 142.7 1.0
N A:GLY59 4.9 171.7 1.0
CG A:PRO78 4.9 130.8 1.0
O A:LEU58 4.9 181.1 1.0
CA A:GLY59 4.9 159.6 1.0
C A:LEU58 5.0 165.0 1.0
CB A:HIS80 5.0 149.5 1.0

Zinc binding site 3 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:172.1
occ:1.00
 SG B:CYS1185 2.3 164.9 1.0
SG B:CYS1166 2.3 174.2 1.0
SG B:CYS1163 2.3 176.8 1.0
SG B:CYS1182 2.3 185.5 1.0
CB B:CYS1166 3.1 140.1 1.0
CB B:CYS1185 3.1 164.2 1.0
CB B:CYS1163 3.3 148.1 1.0
N B:CYS1166 3.4 177.4 1.0
CA B:CYS1166 3.7 152.4 1.0
CB B:CYS1182 3.8 174.7 1.0
O B:CYS1166 3.8 166.4 1.0
OG1 B:THR1170 4.0 156.2 1.0
C B:CYS1166 4.2 152.4 1.0
O B:LYS1183 4.3 168.2 1.0
CA B:CYS1185 4.4 181.5 1.0
C B:ILE1165 4.4 170.3 1.0
ND2 B:ASN1187 4.5 182.5 1.0
CB B:ILE1165 4.5 168.1 1.0
N B:CYS1185 4.5 182.4 1.0
CA B:CYS1163 4.7 145.1 1.0
CA B:ILE1165 4.8 163.0 1.0
N B:ILE1165 4.9 145.0 1.0
O B:LEU1168 4.9 136.0 1.0
C B:CYS1163 5.0 162.5 1.0

Zinc binding site 4 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:100.7
occ:1.00
 CB C:CYS92 1.1 105.8 1.0
SG C:CYS86 2.3 88.0 1.0
SG C:CYS88 2.3 69.1 1.0
SG C:CYS92 2.3 132.2 1.0
CA C:CYS92 2.4 98.3 1.0
CB C:CYS95 2.7 64.5 1.0
N C:CYS92 2.8 106.2 1.0
C C:CYS92 3.2 76.5 1.0
CB C:CYS88 3.3 68.9 1.0
CB C:CYS86 3.6 89.8 1.0
N C:CYS95 3.6 101.6 1.0
O C:CYS92 3.7 97.0 1.0
CA C:CYS95 3.8 83.2 1.0
C C:HIS91 3.8 109.0 1.0
SG C:CYS95 4.0 123.6 1.0
N C:ASP93 4.1 68.1 1.0
O C:HIS91 4.4 114.2 1.0
N C:CYS88 4.4 96.2 1.0
CA C:CYS88 4.5 75.6 1.0
C C:LYS94 4.7 98.7 1.0
N C:LYS94 4.8 77.4 1.0
CA C:HIS91 4.8 85.7 1.0
C C:CYS95 4.9 98.2 1.0
N C:SER96 5.0 108.2 1.0
CA C:CYS86 5.0 104.8 1.0

Zinc binding site 5 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:126.5
occ:1.00
 SG I:CYS7 2.3 113.9 1.0
SG I:CYS29 2.3 140.7 1.0
SG I:CYS10 2.3 163.8 1.0
SG I:CYS32 2.3 181.0 1.0
CB I:CYS7 3.2 113.4 1.0
CB I:CYS29 3.4 116.8 1.0
N I:CYS32 3.4 125.8 1.0
CB I:CYS32 3.6 174.4 1.0
CB I:CYS10 3.8 126.2 1.0
CA I:CYS32 4.0 149.9 1.0
CB I:THR31 4.0 134.7 1.0
O I:CYS32 4.2 140.1 1.0
N I:CYS10 4.2 123.6 1.0
C I:THR31 4.3 122.5 1.0
C I:CYS32 4.5 137.9 1.0
CA I:THR31 4.5 133.7 1.0
N I:THR31 4.5 147.7 1.0
CA I:CYS7 4.6 112.9 1.0
CA I:CYS10 4.6 129.0 1.0
OG1 I:THR31 4.6 149.7 1.0
CB I:ASP9 4.7 156.6 1.0
CA I:CYS29 4.8 125.4 1.0
C I:CYS7 4.9 122.6 1.0
CG2 I:THR31 5.0 124.4 1.0
C I:ASP9 5.0 132.2 1.0
N I:ASP9 5.0 112.9 1.0

Zinc binding site 6 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:277.3
occ:1.00
 SG I:CYS78 2.3 152.4 1.0
SG I:CYS106 2.3 159.2 1.0
SG I:CYS75 2.3 207.6 1.0
SG I:CYS103 2.3 231.1 1.0
CB I:CYS103 2.7 153.9 1.0
CB I:CYS75 2.9 172.3 1.0
CB I:CYS78 3.1 130.3 1.0
CB I:CYS106 3.5 131.3 1.0
CE1 I:PHE110 3.6 133.4 1.0
N I:CYS75 3.8 145.9 1.0
CA I:CYS75 3.9 161.6 1.0
CD1 I:PHE110 3.9 108.9 1.0
CA I:CYS103 4.0 126.9 1.0
N I:CYS78 4.2 197.6 1.0
CA I:CYS78 4.2 134.3 1.0
O I:HIS108 4.3 117.2 1.0
N I:CYS106 4.3 155.0 1.0
N I:CYS103 4.3 114.7 1.0
CZ I:PHE110 4.4 150.2 1.0
OG I:SER80 4.4 174.4 1.0
O I:CYS75 4.4 170.8 1.0
CA I:CYS106 4.5 135.7 1.0
C I:CYS103 4.5 135.0 1.0
C I:CYS75 4.5 162.5 1.0
O I:CYS103 4.6 146.2 1.0
O I:SER80 4.7 162.6 1.0
CG I:PHE110 5.0 107.4 1.0

Zinc binding site 7 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:165.2
occ:1.00
 SG J:CYS46 2.3 47.5 1.0
SG J:CYS10 2.3 76.5 1.0
SG J:CYS45 2.3 110.0 1.0
SG J:CYS7 2.3 48.5 1.0
N J:CYS46 3.1 94.9 1.0
CB J:CYS10 3.4 69.4 1.0
CB J:CYS45 3.4 89.3 1.0
CB J:CYS46 3.5 95.1 1.0
C J:CYS45 3.5 81.2 1.0
CB J:CYS7 3.5 72.6 1.0
CA J:CYS46 3.6 94.2 1.0
NH2 J:ARG43 3.8 107.7 1.0
N J:CYS10 3.8 73.8 1.0
CA J:CYS45 4.0 73.1 1.0
NE J:ARG43 4.1 105.0 1.0
O J:CYS45 4.1 61.8 1.0
CA J:CYS10 4.1 70.4 1.0
CZ J:ARG43 4.4 97.5 1.0
N J:GLY11 4.5 65.5 1.0
N J:CYS45 4.7 71.9 1.0
CB J:SER9 4.7 66.2 1.0
C J:CYS10 4.8 56.7 1.0
CB J:ARG43 4.9 92.0 1.0
N J:LYS12 4.9 59.1 1.0
CA J:CYS7 4.9 88.6 1.0
C J:SER9 4.9 69.4 1.0
CB J:LYS12 5.0 52.9 1.0

Zinc binding site 8 out of 8 in 8ukt

Go back to Zinc Binding Sites List in 8ukt
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp 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 Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:364.5
occ:1.00
 SG L:CYS51 2.3 257.3 1.0
SG L:CYS48 2.3 326.6 1.0
SG L:CYS31 2.3 306.7 1.0
SG L:CYS34 2.3 402.4 1.0
CD1 L:LEU38 2.7 274.4 1.0
CB L:CYS31 2.9 245.5 1.0
CB L:CYS48 3.1 295.6 1.0
CB L:CYS51 3.3 248.2 1.0
CB L:CYS34 3.3 408.5 1.0
CG L:LEU38 3.9 258.1 1.0
CA L:CYS31 4.1 234.3 1.0
N L:CYS51 4.2 256.3 1.0
CA L:CYS48 4.2 280.8 1.0
N L:CYS48 4.3 267.6 1.0
N L:CYS34 4.3 415.0 1.0
CD2 L:LEU38 4.3 272.7 1.0
CA L:CYS51 4.4 240.0 1.0
N L:CYS31 4.4 219.6 1.0
CA L:CYS34 4.4 413.3 1.0
O L:CYS31 4.5 284.5 1.0
C L:CYS31 4.5 277.9 1.0
O L:CYS48 4.8 290.5 1.0
C L:CYS48 4.8 289.8 1.0
O L:SER36 4.9 226.3 1.0
CD2 L:LEU56 4.9 171.7 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: Fri Aug 22 14:18:45 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy