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Zinc in PDB 6uq0: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4, PDB code: 6uq0 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) 49.70 / 3.56
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.897, 223.273, 193.139, 90.00, 100.94, 90.00
R / Rfree (%) 23.6 / 27.8

Other elements in 6uq0:

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4 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 4 (pdb code 6uq0). 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 4, PDB code: 6uq0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6uq0

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


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

b:0.7
occ:1.00
 SG A:CYS107 2.3 0.4 1.0
SG A:CYS167 2.3 0.8 1.0
CB A:CYS148 2.6 0.6 1.0
SG A:CYS148 2.9 0.8 1.0
O A:MET108 3.1 0.5 1.0
CB A:CYS167 3.4 0.9 1.0
CB A:CYS107 3.6 0.5 1.0
N A:MET108 3.8 0.9 1.0
CA A:CYS107 4.0 0.5 1.0
SG A:CYS110 4.0 0.7 1.0
CA A:CYS148 4.0 0.3 1.0
C A:CYS107 4.0 0.3 1.0
C A:MET108 4.1 0.5 1.0
NE2 A:GLN171 4.3 0.9 1.0
N A:CYS167 4.3 0.1 1.0
O A:CYS110 4.3 0.8 1.0
CA A:CYS167 4.3 0.7 1.0
SD A:MET108 4.4 0.2 1.0
N A:CYS148 4.4 0.3 1.0
N A:GLY168 4.4 0.7 1.0
CA A:MET108 4.6 0.3 1.0
O A:CYS148 4.7 0.4 1.0
O A:ASN169 4.7 0.4 1.0
O A:CYS107 4.8 1.0 1.0
C A:CYS167 4.8 0.3 1.0
C A:CYS148 4.9 0.5 1.0
N A:ASN169 4.9 0.6 1.0
N A:CYS110 5.0 0.1 1.0

Zinc binding site 2 out of 8 in 6uq0

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4


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

b:0.6
occ:1.00
 NE2 A:HIS80 2.2 0.4 1.0
SG A:CYS77 2.4 75.8 1.0
SG A:CYS70 2.7 0.4 1.0
CB A:CYS70 2.7 0.8 1.0
CE1 A:HIS80 3.1 0.5 1.0
SG A:CYS67 3.2 0.5 1.0
CB A:CYS77 3.2 93.9 1.0
CD2 A:HIS80 3.3 1.0 1.0
O A:CYS67 3.8 0.3 1.0
CB A:CYS67 4.2 0.7 1.0
CA A:CYS70 4.2 0.1 1.0
ND1 A:HIS80 4.2 0.4 1.0
CG A:HIS80 4.4 0.9 1.0
CA A:CYS77 4.4 0.7 1.0
CG A:GLN68 4.5 0.1 1.0
C A:CYS67 4.7 0.3 1.0
N A:CYS70 4.8 0.1 1.0
NE2 A:GLN68 4.9 0.3 1.0
C A:CYS70 4.9 0.2 1.0
O A:CYS70 4.9 0.8 1.0

Zinc binding site 3 out of 8 in 6uq0

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


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

b:0.4
occ:1.00
 SG B:CYS1182 2.4 0.3 1.0
CB B:CYS1166 2.4 0.5 1.0
SG B:CYS1185 2.5 0.7 1.0
SG B:CYS1166 2.8 0.6 1.0
SG B:CYS1163 2.8 0.6 1.0
CB B:CYS1185 3.2 0.7 1.0
N B:CYS1166 3.2 0.6 1.0
CA B:CYS1166 3.3 0.4 1.0
CB B:CYS1163 3.6 0.8 1.0
CB B:CYS1182 3.7 0.9 1.0
C B:ILE1165 4.4 0.2 1.0
CA B:CYS1185 4.4 0.8 1.0
O B:LYS1183 4.4 0.7 1.0
N B:CYS1185 4.4 0.2 1.0
C B:CYS1166 4.5 0.0 1.0
CB B:THR1170 4.6 85.0 1.0
O B:CYS1163 4.6 0.2 1.0
OG1 B:THR1170 4.6 0.5 1.0
N B:GLY1167 4.8 0.6 1.0
CG2 B:ILE1165 4.9 0.2 1.0
CB B:ILE1165 4.9 0.3 1.0
CA B:CYS1163 4.9 0.1 1.0
C B:CYS1163 4.9 0.8 1.0
CG2 B:THR1170 5.0 71.0 1.0

Zinc binding site 4 out of 8 in 6uq0

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


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

b:92.5
occ:1.00
 SG C:CYS88 2.3 57.5 1.0
SG C:CYS92 2.3 95.2 1.0
SG C:CYS95 2.3 73.8 1.0
SG C:CYS86 2.8 90.8 1.0
CB C:CYS92 2.9 78.5 1.0
CB C:CYS88 2.9 48.1 1.0
N C:CYS92 3.1 64.8 1.0
CA C:CYS92 3.5 53.4 1.0
C C:HIS91 3.8 90.6 1.0
CB C:CYS86 3.9 86.8 1.0
CB C:CYS95 4.0 70.7 1.0
CA C:HIS91 4.1 96.5 1.0
N C:CYS88 4.1 53.0 1.0
C C:CYS92 4.1 48.8 1.0
CA C:CYS88 4.1 54.8 1.0
O C:CYS92 4.3 65.3 1.0
N C:CYS95 4.4 72.0 1.0
O C:HIS91 4.6 90.4 1.0
CA C:CYS95 4.8 62.0 1.0
N C:LYS94 4.9 64.3 1.0
N C:ASP93 5.0 48.4 1.0
CB C:LYS94 5.0 80.0 1.0
C C:LYS94 5.0 80.8 1.0

Zinc binding site 5 out of 8 in 6uq0

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


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

b:72.3
occ:1.00
 SG I:CYS10 2.3 86.8 1.0
SG I:CYS29 2.3 92.0 1.0
SG I:CYS32 2.4 0.2 1.0
SG I:CYS7 2.5 64.7 1.0
CB I:CYS7 3.1 69.7 1.0
CB I:CYS29 3.1 88.5 1.0
CB I:CYS32 3.3 0.7 1.0
N I:CYS32 3.4 1.0 1.0
CA I:CYS32 3.8 1.0 1.0
CB I:CYS10 4.0 95.3 1.0
N I:CYS10 4.2 0.9 1.0
C I:CYS32 4.4 0.6 1.0
C I:THR31 4.4 0.8 1.0
CB I:TYR34 4.5 55.4 1.0
CB I:THR31 4.5 90.3 1.0
CA I:CYS7 4.5 84.6 1.0
CA I:CYS29 4.6 90.5 1.0
N I:SER33 4.6 0.0 1.0
CA I:CYS10 4.6 99.6 1.0
N I:THR31 4.7 0.5 1.0
N I:TYR34 4.8 68.0 1.0
CA I:THR31 4.8 0.5 1.0
CB I:ASN12 4.9 76.3 1.0
CB I:ASP9 4.9 0.1 1.0

Zinc binding site 6 out of 8 in 6uq0

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4


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

b:0.2
occ:1.00
 SG I:CYS106 2.4 78.6 1.0
SG I:CYS75 2.4 0.7 1.0
SG I:CYS103 2.4 0.9 1.0
SG I:CYS78 2.4 48.7 1.0
CB I:CYS75 3.1 0.7 1.0
CB I:CYS78 3.4 74.9 1.0
OG I:SER80 3.4 0.5 1.0
CB I:CYS103 3.4 90.1 1.0
N I:CYS78 3.5 74.5 1.0
CB I:CYS106 3.5 74.2 1.0
CA I:CYS78 3.9 73.8 1.0
N I:CYS106 4.0 71.1 1.0
CB I:LYS77 4.1 63.5 1.0
CA I:CYS106 4.3 76.8 1.0
N I:HIS79 4.3 86.4 1.0
C I:CYS78 4.4 72.1 1.0
C I:LYS77 4.5 60.7 1.0
CA I:CYS75 4.6 91.1 1.0
CB I:HIS108 4.6 88.2 1.0
CA I:LYS77 4.7 57.7 1.0
N I:SER80 4.7 97.8 1.0
N I:LYS77 4.7 58.2 1.0
CB I:SER80 4.7 1.0 1.0
C I:CYS106 4.8 90.0 1.0
CA I:CYS103 4.9 72.6 1.0
C I:CYS75 4.9 90.8 1.0
N I:HIS108 5.0 53.5 1.0

Zinc binding site 7 out of 8 in 6uq0

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 4


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

b:74.6
occ:1.00
 SG J:CYS10 2.4 0.6 1.0
SG J:CYS45 2.4 0.6 1.0
N J:CYS46 2.4 1.0 1.0
CB J:CYS46 2.5 92.0 1.0
SG J:CYS7 2.5 86.7 1.0
CA J:CYS46 2.7 0.7 1.0
SG J:CYS46 2.9 62.6 1.0
CB J:CYS7 3.0 62.2 1.0
C J:CYS45 3.3 66.4 1.0
CB J:CYS10 3.6 75.9 1.0
CB J:CYS45 3.6 67.2 1.0
N J:CYS10 4.0 61.9 1.0
O J:CYS45 4.0 28.9 1.0
CA J:CYS45 4.0 45.9 1.0
C J:CYS46 4.2 82.6 1.0
NH2 J:ARG43 4.3 48.6 1.0
CA J:CYS10 4.3 71.9 1.0
N J:GLY11 4.4 86.9 1.0
CA J:CYS7 4.4 72.0 1.0
N J:CYS45 4.7 29.4 1.0
N J:ARG47 4.8 68.8 1.0
O J:CYS7 4.8 79.0 1.0
C J:CYS7 4.8 66.3 1.0
CB J:SER9 4.9 42.8 1.0
C J:CYS10 4.9 75.8 1.0
CZ J:ARG43 4.9 51.4 1.0
N J:LYS12 5.0 62.2 1.0
O J:ARG43 5.0 60.0 1.0

Zinc binding site 8 out of 8 in 6uq0

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


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

b:0.1
occ:1.00
 SG L:CYS51 2.4 0.8 1.0
OG L:SER36 2.4 0.3 1.0
SG L:CYS34 2.5 0.3 1.0
SG L:CYS48 2.5 79.7 1.0
SG L:CYS31 2.6 0.1 1.0
CB L:CYS51 3.3 0.9 1.0
CB L:SER36 3.5 0.8 1.0
CB L:CYS31 3.5 0.6 1.0
CB L:CYS48 3.6 91.3 1.0
CB L:CYS34 4.0 0.8 1.0
N L:CYS51 4.2 0.8 1.0
CA L:CYS51 4.3 0.0 1.0
N L:CYS34 4.4 0.2 1.0
N L:SER36 4.6 0.6 1.0
CA L:CYS34 4.7 0.3 1.0
CA L:SER36 4.7 0.5 1.0
CB L:HIS53 4.7 0.1 1.0
C L:CYS51 4.8 0.9 1.0
CA L:CYS31 4.9 0.7 1.0
C L:CYS34 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 08:43:13 2024

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