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Zinc in PDB 6upz: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3, PDB code: 6upz 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) 49.04 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.664, 222.901, 193.486, 90.00, 100.85, 90.00
R / Rfree (%) 22.4 / 26.9

Other elements in 6upz:

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

Zinc binding site 1 out of 8 in 6upz

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.5
occ:1.00
 SG A:CYS107 2.5 0.7 1.0
SG A:CYS167 2.5 0.6 1.0
SG A:CYS110 2.5 0.8 1.0
CB A:CYS167 2.8 0.9 1.0
CB A:CYS107 3.0 0.3 1.0
SG A:CYS148 3.1 0.3 1.0
CB A:CYS148 3.8 0.0 1.0
N A:CYS167 3.9 0.6 1.0
CA A:CYS167 3.9 0.7 1.0
CB A:CYS110 3.9 0.4 1.0
O A:MET108 4.3 0.8 1.0
CB A:LYS112 4.3 0.1 1.0
CA A:CYS107 4.5 0.3 1.0
C A:GLY166 4.6 0.8 1.0
C A:CYS107 4.9 0.4 1.0
O A:CYS148 5.0 0.3 1.0

Zinc binding site 2 out of 8 in 6upz

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.4
occ:1.00
 NE2 A:HIS80 2.0 0.3 1.0
SG A:CYS70 2.4 0.9 1.0
CE1 A:HIS80 2.5 0.8 1.0
SG A:CYS77 2.6 0.8 1.0
SG A:CYS67 2.8 0.8 1.0
CB A:CYS77 2.9 0.1 1.0
CD2 A:HIS80 3.3 0.5 1.0
CB A:CYS70 3.7 0.1 1.0
ND1 A:HIS80 3.7 0.5 1.0
CA A:CYS77 3.8 0.3 1.0
OE1 A:GLN68 4.1 0.6 1.0
CG A:HIS80 4.2 0.2 1.0
CB A:CYS67 4.2 0.7 1.0
O A:CYS67 4.2 0.9 1.0
C A:CYS77 4.6 0.8 1.0
CD A:PRO78 4.7 99.1 1.0
CB A:GLN68 4.8 0.2 1.0
C A:CYS67 4.8 0.5 1.0
CB A:GLU72 4.9 0.8 1.0
N A:CYS77 4.9 0.1 1.0
N A:PRO78 5.0 0.5 1.0
CD A:GLN68 5.0 0.4 1.0

Zinc binding site 3 out of 8 in 6upz

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:0.5
occ:1.00
 SG B:CYS1166 2.4 0.4 1.0
SG B:CYS1185 2.5 1.0 1.0
SG B:CYS1163 2.6 0.9 1.0
SG B:CYS1182 2.6 0.3 1.0
CB B:CYS1163 3.1 0.6 1.0
CB B:CYS1185 3.3 0.9 1.0
N B:CYS1166 3.6 0.8 1.0
CB B:CYS1166 3.7 0.0 1.0
CB B:CYS1182 3.9 0.8 1.0
O B:CYS1166 4.1 0.4 1.0
CA B:CYS1166 4.1 0.7 1.0
CB B:ILE1165 4.3 0.2 1.0
C B:CYS1166 4.6 0.5 1.0
CA B:CYS1163 4.6 0.7 1.0
C B:ILE1165 4.7 0.1 1.0
CA B:CYS1185 4.7 0.5 1.0
N B:ILE1165 4.7 1.0 1.0
CG1 B:ILE1165 4.8 0.9 1.0
CA B:ILE1165 4.8 0.3 1.0
OG1 B:THR1170 4.9 0.4 1.0

Zinc binding site 4 out of 8 in 6upz

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.2
occ:1.00
 SG C:CYS95 2.3 68.1 1.0
SG C:CYS86 2.3 96.8 1.0
SG C:CYS92 2.3 74.5 1.0
SG C:CYS88 2.3 40.0 1.0
CB C:CYS95 2.7 65.9 1.0
CB C:CYS86 2.7 87.7 1.0
CB C:CYS92 3.7 75.8 1.0
N C:CYS95 3.7 79.7 1.0
CB C:CYS88 3.8 40.0 1.0
CA C:CYS95 3.8 58.5 1.0
N C:CYS92 4.0 50.0 1.0
CA C:CYS86 4.1 84.9 1.0
CA C:CYS92 4.3 59.7 1.0
C C:LYS94 4.4 85.4 1.0
N C:CYS88 4.5 41.1 1.0
CB C:LYS94 4.5 50.8 1.0
C C:CYS86 4.6 82.1 1.0
C C:HIS91 4.6 51.7 1.0
CA C:HIS91 4.7 48.7 1.0
N C:LYS94 4.8 45.0 1.0
C C:CYS92 4.8 65.7 1.0
CA C:LYS94 4.8 60.8 1.0
C C:CYS95 4.8 57.8 1.0
CA C:CYS88 4.8 40.3 1.0
N C:PHE87 4.8 66.5 1.0
N C:CYS86 5.0 84.8 1.0

Zinc binding site 5 out of 8 in 6upz

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:56.7
occ:1.00
 SG I:CYS29 2.4 96.8 1.0
SG I:CYS7 2.4 80.5 1.0
SG I:CYS32 2.5 83.3 1.0
SG I:CYS10 2.7 86.5 1.0
CB I:CYS7 2.7 80.1 1.0
CB I:CYS29 3.0 90.5 1.0
CB I:CYS10 3.1 80.5 1.0
N I:CYS32 3.7 92.0 1.0
CB I:CYS32 3.7 84.4 1.0
N I:CYS10 4.0 79.5 1.0
CA I:CYS10 4.1 79.6 1.0
CA I:CYS32 4.2 86.8 1.0
CA I:CYS7 4.3 79.2 1.0
CB I:TYR34 4.4 82.8 1.0
CB I:THR31 4.5 92.2 1.0
CA I:CYS29 4.5 84.2 1.0
C I:THR31 4.6 93.0 1.0
C I:CYS32 4.6 97.6 1.0
O I:CYS32 4.8 0.6 1.0
N I:THR31 4.8 84.7 1.0
OG1 I:THR31 4.9 93.9 1.0
CA I:THR31 4.9 84.9 1.0
C I:ASP9 4.9 85.7 1.0
C I:CYS7 4.9 79.2 1.0

Zinc binding site 6 out of 8 in 6upz

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:55.1
occ:1.00
 SG I:CYS78 2.3 61.6 1.0
CB I:CYS106 2.3 62.0 1.0
SG I:CYS103 2.6 68.7 1.0
SG I:CYS75 2.8 66.1 1.0
SG I:CYS106 3.1 0.4 1.0
CB I:CYS78 3.2 63.4 1.0
CB I:CYS75 3.3 67.5 1.0
CB I:CYS103 3.3 55.0 1.0
CA I:CYS106 3.7 57.8 1.0
N I:CYS78 3.7 70.7 1.0
N I:CYS106 3.9 74.1 1.0
CA I:CYS78 4.0 66.7 1.0
CB I:HIS108 4.2 58.8 1.0
OG I:SER80 4.3 77.6 1.0
C I:CYS106 4.5 59.4 1.0
C I:CYS78 4.6 77.5 1.0
CB I:LYS77 4.6 63.6 1.0
C I:SER105 4.7 87.1 1.0
N I:HIS79 4.8 84.3 1.0
CA I:CYS75 4.8 73.1 1.0
CA I:CYS103 4.8 53.3 1.0
C I:LYS77 4.8 67.8 1.0
OG I:SER105 4.8 93.9 1.0
N I:HIS108 4.9 56.3 1.0

Zinc binding site 7 out of 8 in 6upz

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.1
occ:1.00
 SG J:CYS46 2.2 47.5 1.0
SG J:CYS7 2.3 44.9 1.0
SG J:CYS45 2.4 79.7 1.0
SG J:CYS10 2.4 53.5 1.0
N J:CYS46 2.9 94.7 1.0
CB J:CYS7 3.1 44.9 1.0
CB J:CYS46 3.1 63.5 1.0
CA J:CYS46 3.1 75.3 1.0
C J:CYS45 3.4 80.4 1.0
CB J:CYS45 3.7 65.5 1.0
CB J:CYS10 3.8 51.3 1.0
O J:CYS45 3.9 68.0 1.0
N J:CYS10 4.0 57.0 1.0
NH2 J:ARG43 4.1 42.6 1.0
CA J:CYS45 4.1 56.6 1.0
NE J:ARG43 4.5 52.7 1.0
CA J:CYS10 4.5 55.4 1.0
CA J:CYS7 4.5 31.9 1.0
C J:CYS46 4.7 64.2 1.0
CB J:LYS12 4.7 28.4 1.0
CZ J:ARG43 4.7 43.0 1.0
CB J:SER9 4.8 40.2 1.0
N J:GLY11 4.8 40.4 1.0
N J:CYS45 4.8 52.0 1.0
N J:LYS12 4.9 31.3 1.0

Zinc binding site 8 out of 8 in 6upz

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.4
occ:1.00
 SG L:CYS48 2.4 0.5 1.0
SG L:CYS34 2.4 99.3 1.0
SG L:CYS31 2.4 1.0 1.0
SG L:CYS51 2.5 0.9 1.0
CB L:CYS48 2.7 0.3 1.0
CB L:CYS31 2.9 0.0 1.0
CB L:CYS34 3.6 0.5 1.0
CB L:CYS51 4.0 0.8 1.0
OG L:SER36 4.0 0.7 1.0
N L:CYS34 4.2 1.0 1.0
CA L:CYS48 4.2 0.1 1.0
N L:CYS51 4.4 0.5 1.0
CA L:CYS31 4.4 0.7 1.0
CA L:CYS34 4.4 0.5 1.0
CB L:HIS53 4.5 0.7 1.0
CA L:CYS51 4.7 0.1 1.0
N L:HIS53 4.8 0.3 1.0
O L:HIS53 4.8 0.4 1.0
N L:GLY52 4.8 0.5 1.0
C L:CYS34 4.9 0.1 1.0
CD1 L:LEU38 5.0 0.0 1.0
N L:SER35 5.0 1.0 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

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