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Zinc in PDB 6upx: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1, PDB code: 6upx 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) 49.30 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.988, 223.314, 193.102, 90.00, 101.03, 90.00
R / Rfree (%) 22 / 26.6

Other elements in 6upx:

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

Zinc binding site 1 out of 8 in 6upx

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


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

b:0.1
occ:1.00
 N A:CYS110 2.2 0.4 1.0
SG A:CYS107 2.5 0.0 1.0
SG A:CYS110 2.5 0.1 1.0
CB A:CYS110 2.5 0.0 1.0
SG A:CYS167 2.6 0.6 1.0
CA A:CYS110 2.7 0.5 1.0
C A:HIS109 3.0 0.9 1.0
CB A:CYS167 3.0 0.1 1.0
CB A:HIS109 3.5 0.0 1.0
CA A:HIS109 3.6 0.6 1.0
CB A:CYS107 3.7 0.9 1.0
N A:HIS109 3.8 0.1 1.0
O A:HIS109 3.9 0.2 1.0
N A:CYS167 3.9 0.0 1.0
SG A:CYS148 4.0 0.8 1.0
CA A:CYS167 4.1 0.6 1.0
C A:CYS110 4.2 0.2 1.0
CB A:CYS148 4.4 0.8 1.0
N A:GLY111 4.6 0.0 1.0
C A:CYS107 4.7 0.5 1.0
C A:CYS167 4.8 0.7 1.0
CA A:CYS107 4.8 0.2 1.0
O A:CYS107 4.9 0.3 1.0
CG A:HIS109 4.9 0.0 1.0

Zinc binding site 2 out of 8 in 6upx

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1


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

b:0.9
occ:1.00
 NE2 A:HIS80 2.0 0.3 1.0
CE1 A:HIS80 2.3 0.3 1.0
SG A:CYS67 2.5 0.4 1.0
SG A:CYS70 2.6 0.5 1.0
SG A:CYS77 2.6 0.9 1.0
CB A:CYS70 2.6 0.2 1.0
CB A:CYS77 3.2 0.1 1.0
CD2 A:HIS80 3.4 0.9 1.0
ND1 A:HIS80 3.6 0.9 1.0
CG A:HIS80 4.1 0.1 1.0
CA A:CYS70 4.1 0.7 1.0
CA A:CYS77 4.2 0.2 1.0
CB A:CYS67 4.2 1.0 1.0
N A:GLN68 4.5 0.2 1.0
CB A:GLN68 4.6 0.8 1.0
C A:CYS70 4.7 0.8 1.0
N A:CYS70 4.8 1.0 1.0
O A:GLU72 4.9 0.4 1.0
C A:CYS77 5.0 0.5 1.0

Zinc binding site 3 out of 8 in 6upx

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.9
occ:1.00
 SG B:CYS1163 2.4 0.9 1.0
SG B:CYS1182 2.5 0.6 1.0
CB B:CYS1166 2.5 0.2 1.0
SG B:CYS1185 2.6 0.2 1.0
N B:CYS1166 2.6 0.4 1.0
SG B:CYS1166 3.0 0.5 1.0
CA B:CYS1166 3.1 0.5 1.0
CB B:CYS1185 3.5 0.0 1.0
C B:ILE1165 3.7 0.1 1.0
CB B:CYS1182 3.7 0.5 1.0
CB B:ILE1165 3.8 0.8 1.0
CB B:CYS1163 3.9 0.2 1.0
CA B:ILE1165 4.1 0.7 1.0
C B:CYS1166 4.3 0.2 1.0
N B:ILE1165 4.4 0.2 1.0
CG2 B:ILE1165 4.5 0.6 1.0
N B:GLY1167 4.5 0.2 1.0
O B:ILE1165 4.7 0.7 1.0
CG1 B:ILE1165 4.8 0.4 1.0
CA B:CYS1185 4.9 1.0 1.0
CD1 A:ILE30 4.9 0.5 1.0

Zinc binding site 4 out of 8 in 6upx

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1


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

b:0.6
occ:1.00
 SG C:CYS92 2.4 0.7 1.0
SG C:CYS88 2.4 71.6 1.0
SG C:CYS86 2.4 0.6 1.0
SG C:CYS95 2.4 77.5 1.0
CB C:CYS92 2.7 0.2 1.0
CB C:CYS88 2.9 45.6 1.0
N C:CYS92 3.1 0.4 1.0
CB C:CYS86 3.3 0.8 1.0
CA C:CYS92 3.4 91.7 1.0
CB C:CYS95 3.5 73.6 1.0
C C:HIS91 3.9 0.7 1.0
N C:CYS95 4.1 93.5 1.0
N C:CYS88 4.1 87.5 1.0
CA C:CYS88 4.1 69.2 1.0
C C:CYS92 4.1 78.0 1.0
CA C:HIS91 4.3 88.6 1.0
CA C:CYS95 4.4 72.8 1.0
O C:CYS92 4.6 71.3 1.0
CA C:CYS86 4.7 0.5 1.0
O C:HIS91 4.8 1.0 1.0
N C:ASP93 4.8 76.2 1.0
C C:LYS94 4.8 0.4 1.0
N C:LYS94 4.9 82.7 1.0
C C:CYS86 4.9 0.6 1.0
N C:PHE87 5.0 95.3 1.0

Zinc binding site 5 out of 8 in 6upx

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


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

b:0.0
occ:1.00
 SG I:CYS32 2.4 1.0 1.0
SG I:CYS29 2.4 0.6 1.0
SG I:CYS10 2.5 99.7 1.0
SG I:CYS7 2.5 0.8 1.0
CB I:CYS7 2.7 0.2 1.0
CB I:CYS29 2.8 0.6 1.0
CB I:CYS32 3.7 0.7 1.0
N I:CYS32 3.8 0.6 1.0
CB I:TYR34 4.1 84.9 1.0
CA I:CYS7 4.2 0.8 1.0
CA I:CYS32 4.2 0.4 1.0
CB I:CYS10 4.2 0.9 1.0
N I:CYS10 4.3 0.4 1.0
CA I:CYS29 4.3 0.9 1.0
C I:CYS32 4.5 1.0 1.0
N I:TYR34 4.7 0.5 1.0
O I:CYS32 4.7 0.2 1.0
CA I:CYS10 4.8 0.0 1.0
C I:CYS7 4.8 0.2 1.0
CB I:ASP9 4.8 0.1 1.0
CB I:THR31 4.8 0.3 1.0
N I:CYS7 4.9 0.9 1.0
C I:THR31 5.0 0.2 1.0
N I:ASP9 5.0 0.1 1.0
C I:CYS29 5.0 1.0 1.0
CG I:TYR34 5.0 84.1 1.0
N I:THR31 5.0 0.5 1.0
CD2 I:LEU14 5.0 83.8 1.0

Zinc binding site 6 out of 8 in 6upx

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1


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

b:0.5
occ:1.00
 SG I:CYS75 2.4 0.8 1.0
SG I:CYS106 2.4 81.9 1.0
SG I:CYS78 2.4 68.0 1.0
SG I:CYS103 2.5 88.8 1.0
CB I:CYS75 2.6 0.5 1.0
CB I:CYS103 2.9 93.5 1.0
CB I:CYS78 3.6 84.0 1.0
CB I:CYS106 3.7 0.6 1.0
N I:CYS78 3.8 0.3 1.0
CA I:CYS75 4.1 0.5 1.0
CA I:CYS78 4.2 96.5 1.0
N I:CYS106 4.2 0.4 1.0
CA I:CYS103 4.4 91.8 1.0
N I:HIS79 4.5 0.9 1.0
CA I:CYS106 4.5 0.1 1.0
C I:CYS78 4.5 0.6 1.0
N I:SER80 4.6 0.3 1.0
CB I:SER80 4.7 92.8 1.0
CB I:LYS77 4.8 85.2 1.0
CB I:HIS108 4.8 88.5 1.0
O I:SER80 4.8 87.1 1.0
N I:CYS75 4.9 0.1 1.0
C I:CYS75 4.9 0.8 1.0
C I:LYS77 4.9 0.5 1.0

Zinc binding site 7 out of 8 in 6upx

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1


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

b:0.0
occ:1.00
 SG J:CYS7 2.2 58.6 1.0
SG J:CYS46 2.2 54.0 1.0
SG J:CYS45 2.4 97.0 1.0
CB J:CYS10 2.4 45.3 1.0
N J:CYS46 2.7 0.1 1.0
CA J:CYS46 3.0 0.0 1.0
CB J:CYS7 3.1 36.5 1.0
CB J:CYS46 3.1 0.4 1.0
C J:CYS45 3.2 0.1 1.0
N J:CYS10 3.3 85.0 1.0
CA J:CYS10 3.5 61.6 1.0
CB J:CYS45 3.5 98.5 1.0
SG J:CYS10 3.6 57.1 1.0
O J:CYS45 3.6 0.1 1.0
CA J:CYS45 4.0 81.2 1.0
C J:SER9 4.5 84.4 1.0
C J:CYS46 4.5 0.5 1.0
C J:CYS10 4.5 35.2 1.0
CA J:CYS7 4.6 69.7 1.0
N J:GLY11 4.6 53.6 1.0
N J:CYS45 4.7 55.7 1.0
CB J:SER9 4.7 82.1 1.0
NE J:ARG43 4.8 71.2 1.0
N J:SER9 5.0 74.0 1.0
CA J:SER9 5.0 75.6 1.0

Zinc binding site 8 out of 8 in 6upx

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


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

b:0.6
occ:1.00
 SG L:CYS31 2.4 0.6 1.0
SG L:CYS48 2.4 0.5 1.0
SG L:CYS51 2.5 0.9 1.0
CB L:CYS34 2.5 0.8 1.0
CB L:CYS31 3.0 0.2 1.0
SG L:CYS34 3.2 0.8 1.0
OG L:SER36 3.4 0.4 1.0
CB L:CYS48 3.6 0.8 1.0
CA L:CYS34 3.7 0.6 1.0
N L:CYS34 3.7 0.8 1.0
CB L:CYS51 3.8 1.0 1.0
N L:CYS51 4.1 1.0 1.0
CB L:ASP50 4.4 0.1 1.0
CA L:CYS31 4.5 0.3 1.0
C L:CYS34 4.5 0.4 1.0
CB L:SER36 4.5 0.5 1.0
CA L:CYS51 4.6 0.6 1.0
N L:SER35 4.8 0.6 1.0
C L:ASP50 4.9 0.6 1.0
C L:GLU33 4.9 0.9 1.0
CA L:CYS48 5.0 0.8 1.0
N L:SER36 5.0 0.9 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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