Atomistry » Zinc » PDB 6uo4-6v65 » 6upy
Atomistry »
  Zinc »
    PDB 6uo4-6v65 »
      6upy »

Zinc in PDB 6upy: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E, PDB code: 6upy 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) 49.22 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.536, 223.125, 193.062, 90.00, 100.92, 90.00
R / Rfree (%) 22.7 / 28.2

Other elements in 6upy:

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

Zinc binding site 1 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.9
occ:1.00
 SG A:CYS110 2.5 0.5 1.0
SG A:CYS148 2.5 0.3 1.0
SG A:CYS107 2.6 1.0 1.0
SG A:CYS167 2.7 0.6 1.0
CB A:CYS167 2.8 0.1 1.0
O A:MET108 2.9 0.8 1.0
CB A:CYS110 3.1 0.5 1.0
N A:CYS167 3.1 0.5 1.0
CB A:CYS107 3.2 0.4 1.0
CB A:CYS148 3.3 0.1 1.0
CA A:CYS167 3.5 1.0 1.0
N A:CYS110 3.8 0.8 1.0
C A:MET108 4.0 0.6 1.0
C A:CYS107 4.0 0.5 1.0
CA A:CYS110 4.1 0.3 1.0
N A:GLY168 4.2 0.8 1.0
CA A:CYS107 4.2 0.5 1.0
O A:CYS107 4.3 0.5 1.0
N A:MET108 4.3 0.8 1.0
C A:GLY166 4.3 0.4 1.0
C A:CYS167 4.4 0.2 1.0
C A:HIS109 4.6 0.6 1.0
CA A:GLY166 4.6 0.7 1.0
CA A:CYS148 4.7 0.1 1.0
CA A:MET108 4.8 0.5 1.0
N A:HIS109 4.9 0.8 1.0

Zinc binding site 2 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.7
occ:1.00
 NE2 A:HIS80 2.0 0.0 1.0
CE1 A:HIS80 2.5 0.9 1.0
SG A:CYS70 2.5 1.0 1.0
SG A:CYS67 2.7 0.8 1.0
SG A:CYS77 2.8 98.0 1.0
CB A:CYS77 3.1 0.1 1.0
CD2 A:HIS80 3.2 0.2 1.0
CA A:CYS77 3.7 0.8 1.0
ND1 A:HIS80 3.7 0.2 1.0
CB A:GLU72 3.8 0.2 1.0
CB A:CYS67 4.0 0.1 1.0
CG A:HIS80 4.1 0.6 1.0
CB A:CYS70 4.1 0.9 1.0
CG A:GLU72 4.3 0.8 1.0
O A:CYS67 4.3 0.8 1.0
CD A:PRO78 4.6 0.7 1.0
C A:CYS77 4.7 0.1 1.0
N A:CYS77 4.7 0.5 1.0
O A:GLU72 4.8 99.7 1.0
C A:CYS67 4.8 0.3 1.0
CA A:GLU72 4.9 0.3 1.0
N A:PRO78 5.0 0.5 1.0

Zinc binding site 3 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:0.9
occ:1.00
 SG B:CYS1166 2.3 0.4 1.0
SG B:CYS1163 2.4 0.8 1.0
SG B:CYS1182 2.4 0.9 1.0
SG B:CYS1185 2.4 0.0 1.0
CB B:CYS1163 3.0 0.1 1.0
CB B:CYS1166 3.2 0.2 1.0
CB B:CYS1185 3.2 0.4 1.0
N B:CYS1166 3.2 0.5 1.0
O B:CYS1166 3.4 0.9 1.0
CB B:CYS1182 3.4 0.4 1.0
CA B:CYS1166 3.6 0.4 1.0
C B:CYS1166 4.0 0.8 1.0
C B:ILE1165 4.4 0.7 1.0
CB B:ILE1165 4.4 0.5 1.0
CA B:CYS1163 4.5 0.5 1.0
CA B:CYS1185 4.6 0.1 1.0
N B:ILE1165 4.7 0.7 1.0
N B:CYS1185 4.7 0.6 1.0
CA B:ILE1165 4.7 0.8 1.0
CA B:CYS1182 4.8 0.3 1.0
C B:CYS1163 4.8 0.8 1.0
O B:CYS1182 4.8 0.8 1.0
O B:LYS1183 5.0 0.8 1.0

Zinc binding site 4 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.8
occ:1.00
 SG C:CYS88 2.3 73.9 1.0
SG C:CYS92 2.4 99.5 1.0
CB C:CYS92 2.5 89.7 1.0
SG C:CYS86 2.5 0.6 1.0
SG C:CYS95 2.5 92.4 1.0
N C:CYS92 2.6 99.3 1.0
CB C:CYS86 3.1 85.8 1.0
CA C:CYS92 3.1 78.9 1.0
CB C:CYS88 3.2 76.2 1.0
CB C:CYS95 3.5 75.7 1.0
C C:HIS91 3.8 0.1 1.0
C C:CYS92 3.9 77.8 1.0
CA C:HIS91 4.1 94.9 1.0
N C:CYS88 4.2 78.4 1.0
N C:CYS95 4.2 0.6 1.0
CA C:CYS88 4.4 78.2 1.0
O C:CYS92 4.4 75.8 1.0
CA C:CYS95 4.5 74.8 1.0
CA C:CYS86 4.5 95.9 1.0
N C:ASP93 4.7 79.2 1.0
O C:HIS91 4.8 0.8 1.0
C C:CYS86 4.9 0.3 1.0
N C:PHE87 4.9 93.6 1.0
N C:LYS94 5.0 0.9 1.0

Zinc binding site 5 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.6
occ:1.00
 SG I:CYS32 2.2 0.3 1.0
SG I:CYS7 2.3 0.4 1.0
SG I:CYS10 2.5 1.0 1.0
SG I:CYS29 2.6 0.9 1.0
N I:CYS32 3.0 0.2 1.0
CB I:CYS32 3.2 0.5 1.0
CB I:CYS10 3.3 0.5 1.0
CB I:CYS29 3.4 0.7 1.0
CB I:CYS7 3.6 0.2 1.0
CA I:CYS32 3.7 0.0 1.0
CB I:THR31 3.8 0.7 1.0
N I:CYS10 3.9 0.1 1.0
C I:THR31 4.0 0.0 1.0
CA I:THR31 4.2 0.4 1.0
CA I:CYS10 4.3 0.3 1.0
N I:THR31 4.4 99.2 1.0
CB I:ASP9 4.4 1.0 1.0
N I:SER33 4.5 0.4 1.0
CG2 I:THR31 4.5 0.7 1.0
CB I:TYR34 4.6 87.7 1.0
C I:CYS32 4.6 0.5 1.0
OG1 I:THR31 4.7 0.4 1.0
N I:TYR34 4.7 89.2 1.0
CA I:CYS29 4.9 0.9 1.0
C I:ASP9 4.9 0.1 1.0
CA I:CYS7 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:80.3
occ:1.00
 SG I:CYS106 2.2 95.6 1.0
SG I:CYS78 2.3 75.9 1.0
SG I:CYS75 2.4 97.0 1.0
SG I:CYS103 2.5 0.3 1.0
CB I:CYS75 2.9 0.3 1.0
CB I:CYS78 3.1 83.5 1.0
CB I:CYS103 3.2 0.4 1.0
OG I:SER80 3.3 0.9 1.0
N I:CYS78 3.5 0.8 1.0
CB I:CYS106 3.7 97.8 1.0
CA I:CYS78 3.7 95.4 1.0
N I:CYS106 4.1 0.2 1.0
C I:CYS78 4.1 95.8 1.0
N I:HIS79 4.2 0.7 1.0
CB I:HIS108 4.3 0.6 1.0
CA I:CYS75 4.3 95.7 1.0
N I:SER80 4.4 98.2 1.0
CA I:CYS106 4.4 97.8 1.0
CB I:SER80 4.5 0.8 1.0
C I:LYS77 4.7 77.8 1.0
CB I:LYS77 4.7 83.3 1.0
CA I:CYS103 4.7 97.5 1.0
O I:CYS78 4.8 88.3 1.0
CB I:SER105 4.9 0.2 1.0
C I:CYS75 4.9 0.7 1.0
C I:CYS106 5.0 0.9 1.0
ND1 I:HIS108 5.0 0.6 1.0

Zinc binding site 7 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:79.1
occ:1.00
 SG J:CYS7 2.3 60.8 1.0
CB J:CYS10 2.4 60.6 1.0
SG J:CYS46 2.5 48.9 1.0
SG J:CYS45 2.7 0.9 1.0
CB J:CYS7 2.7 65.1 1.0
SG J:CYS10 3.1 87.8 1.0
N J:CYS46 3.1 84.7 1.0
CA J:CYS46 3.2 73.8 1.0
N J:CYS10 3.2 47.1 1.0
CB J:CYS46 3.2 55.1 1.0
CA J:CYS10 3.4 56.2 1.0
C J:CYS45 3.6 72.7 1.0
O J:CYS45 4.0 59.4 1.0
CB J:CYS45 4.1 74.1 1.0
CA J:CYS7 4.3 66.6 1.0
N J:GLY11 4.4 68.8 1.0
C J:CYS10 4.4 63.1 1.0
C J:SER9 4.5 53.0 1.0
CA J:CYS45 4.5 45.4 1.0
C J:CYS46 4.7 73.4 1.0
C J:CYS7 4.8 62.7 1.0
CB J:SER9 4.9 58.1 1.0
N J:LYS12 4.9 56.7 1.0
N J:SER9 4.9 35.1 1.0
CB J:LYS12 5.0 46.6 1.0
CA J:SER9 5.0 49.8 1.0

Zinc binding site 8 out of 8 in 6upy

Go back to Zinc Binding Sites List in 6upy
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E


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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.6
occ:1.00
 SG L:CYS51 2.3 0.4 1.0
SG L:CYS48 2.3 0.7 1.0
SG L:CYS31 2.3 0.4 1.0
SG L:CYS34 2.5 0.0 1.0
OG L:SER36 2.8 0.7 1.0
CB L:CYS51 3.0 0.3 1.0
CB L:CYS48 3.1 0.5 1.0
CB L:CYS31 3.2 0.2 1.0
CB L:CYS34 3.7 0.3 1.0
CB L:SER36 3.8 0.7 1.0
N L:CYS51 3.8 0.2 1.0
CA L:CYS51 4.0 0.7 1.0
N L:CYS34 4.2 0.7 1.0
CA L:CYS34 4.4 0.9 1.0
N L:SER36 4.5 0.6 1.0
CA L:CYS48 4.5 0.7 1.0
C L:CYS34 4.6 0.7 1.0
N L:SER35 4.7 0.2 1.0
CA L:CYS31 4.7 0.4 1.0
C L:ASP50 4.7 0.5 1.0
O L:CYS48 4.8 0.3 1.0
CA L:SER36 4.8 0.1 1.0
C L:CYS51 4.8 0.7 1.0
CB L:ASP50 4.9 0.8 1.0
N L:GLY52 4.9 0.2 1.0
C L:CYS48 4.9 0.1 1.0

Reference:

J.Oh, A.M.Fleming, J.Xu, J.Chong, C.J.Burrows, D.Wang. Rna Polymerase II Stalls on Oxidative Dna Damage Via A Torsion-Latch Mechanism Involving Lone Pair-Pi and Ch-Pi Interactions. Proc.Natl.Acad.Sci.Usa V. 117 9338 2020.
ISSN: ESSN 1091-6490
PubMed: 32284409
DOI: 10.1073/PNAS.1919904117
Page generated: Tue Oct 29 08:42:39 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy