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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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 12:59:35 2020

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