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Zinc in PDB 6uq3: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5, PDB code: 6uq3 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) 49.27 / 3.47
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.189, 222.584, 194.612, 90.00, 101.34, 90.00
R / Rfree (%) 23.4 / 28.6

Other elements in 6uq3:

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5 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 5 (pdb code 6uq3). 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 5, PDB code: 6uq3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6uq3

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


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

b:1.0
occ:1.00
 SG A:CYS167 2.4 0.5 1.0
SG A:CYS110 2.5 0.2 1.0
SG A:CYS107 2.5 0.6 1.0
CB A:CYS167 2.7 0.6 1.0
CB A:CYS148 3.1 0.1 1.0
CB A:CYS107 3.1 0.0 1.0
O A:MET108 3.3 0.1 1.0
SG A:CYS148 3.5 0.9 1.0
N A:CYS167 3.6 0.8 1.0
CA A:CYS167 3.8 0.1 1.0
CB A:CYS110 3.9 0.3 1.0
O A:CYS148 4.1 0.0 1.0
CA A:CYS148 4.3 0.5 1.0
CA A:CYS107 4.4 0.5 1.0
N A:CYS110 4.4 0.5 1.0
C A:CYS107 4.4 0.3 1.0
C A:MET108 4.5 0.6 1.0
N A:GLY168 4.6 0.2 1.0
O A:CYS110 4.6 0.4 1.0
C A:CYS148 4.7 0.8 1.0
N A:MET108 4.7 0.7 1.0
N A:CYS148 4.7 0.1 1.0
CA A:CYS110 4.7 0.5 1.0
C A:CYS167 4.7 0.3 1.0
O A:CYS107 4.7 0.3 1.0
C A:GLY166 4.9 0.9 1.0

Zinc binding site 2 out of 8 in 6uq3

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


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

b:0.1
occ:1.00
 NE2 A:HIS80 2.2 0.7 1.0
SG A:CYS70 2.5 0.8 1.0
SG A:CYS77 2.5 0.2 1.0
SG A:CYS67 2.5 0.6 1.0
CB A:CYS70 2.6 0.4 1.0
CB A:CYS77 2.8 0.8 1.0
CE1 A:HIS80 2.9 0.5 1.0
CD2 A:HIS80 3.2 0.4 1.0
NE2 A:GLN68 3.5 0.7 1.0
CB A:CYS67 3.7 0.5 1.0
CA A:CYS77 3.8 0.8 1.0
O A:CYS67 3.9 0.6 1.0
CA A:CYS70 4.0 0.7 1.0
ND1 A:HIS80 4.1 0.1 1.0
CG A:HIS80 4.2 0.2 1.0
N A:CYS70 4.6 0.4 1.0
C A:CYS67 4.6 0.7 1.0
CD A:GLN68 4.6 0.7 1.0
C A:CYS77 4.7 0.7 1.0
CA A:CYS67 4.8 0.0 1.0
N A:CYS77 4.8 0.8 1.0
CG A:GLN68 4.9 0.6 1.0

Zinc binding site 3 out of 8 in 6uq3

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1402

b:0.5
occ:1.00
 SG B:CYS1185 2.4 0.7 1.0
SG B:CYS1163 2.4 0.7 1.0
SG B:CYS1166 2.4 0.5 1.0
SG B:CYS1182 2.5 0.9 1.0
N B:CYS1166 2.9 0.6 1.0
CB B:CYS1166 3.0 0.2 1.0
CB B:CYS1185 3.2 0.6 1.0
CB B:CYS1163 3.3 0.4 1.0
CA B:CYS1166 3.4 0.3 1.0
O B:CYS1166 3.7 0.7 1.0
CB B:CYS1182 3.8 0.9 1.0
CB B:ILE1165 4.0 0.5 1.0
C B:CYS1166 4.0 0.5 1.0
C B:ILE1165 4.1 0.0 1.0
CA B:ILE1165 4.4 0.4 1.0
N B:ILE1165 4.4 0.8 1.0
CA B:CYS1185 4.5 0.8 1.0
CA B:CYS1163 4.7 0.2 1.0
CG1 B:ILE1165 4.8 0.1 1.0
N B:CYS1185 4.8 0.7 1.0
CG2 B:ILE1165 4.8 0.5 1.0
C B:CYS1163 5.0 0.0 1.0

Zinc binding site 4 out of 8 in 6uq3

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


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

b:94.6
occ:1.00
 SG C:CYS92 2.5 76.3 1.0
SG C:CYS95 2.5 80.1 1.0
SG C:CYS86 2.5 0.1 1.0
SG C:CYS88 2.5 55.0 1.0
CB C:CYS95 2.6 68.3 1.0
CB C:CYS86 2.8 0.2 1.0
N C:CYS95 3.5 70.7 1.0
CB C:CYS92 3.6 80.2 1.0
CA C:CYS95 3.7 55.7 1.0
CB C:CYS88 3.8 35.5 1.0
N C:CYS92 3.8 89.3 1.0
CA C:CYS92 4.2 72.9 1.0
CA C:CYS86 4.2 96.3 1.0
C C:LYS94 4.3 86.0 1.0
N C:CYS88 4.5 57.5 1.0
C C:HIS91 4.5 88.1 1.0
C C:CYS92 4.5 47.9 1.0
CB C:LYS94 4.6 74.4 1.0
O C:CYS92 4.6 62.6 1.0
C C:CYS86 4.7 83.0 1.0
CA C:HIS91 4.7 85.2 1.0
C C:CYS95 4.8 56.9 1.0
CA C:CYS88 4.8 50.4 1.0
N C:PHE87 4.8 58.6 1.0
N C:LYS94 4.8 53.8 1.0
CA C:LYS94 4.8 70.1 1.0
N C:SER96 4.9 64.6 1.0

Zinc binding site 5 out of 8 in 6uq3

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


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

b:0.5
occ:1.00
 SG I:CYS32 2.4 0.3 1.0
SG I:CYS29 2.5 0.9 1.0
SG I:CYS10 2.8 1.0 1.0
SG I:CYS7 2.8 67.5 1.0
CB I:CYS32 2.8 0.0 1.0
CB I:CYS10 3.0 0.6 1.0
N I:CYS32 3.3 94.7 1.0
CB I:CYS29 3.3 0.2 1.0
CB I:CYS7 3.4 82.1 1.0
CA I:CYS32 3.6 0.8 1.0
N I:CYS10 3.7 0.3 1.0
CA I:CYS10 3.9 0.7 1.0
C I:CYS32 4.3 0.5 1.0
C I:THR31 4.4 0.3 1.0
CB I:ASP9 4.6 99.9 1.0
C I:ASP9 4.7 0.4 1.0
CB I:THR31 4.7 0.7 1.0
N I:THR31 4.8 97.9 1.0
O I:CYS32 4.8 0.0 1.0
CA I:CYS29 4.8 94.2 1.0
CA I:THR31 4.9 0.5 1.0
CA I:CYS7 4.9 95.0 1.0
C I:CYS10 4.9 0.5 1.0
N I:SER33 4.9 0.3 1.0
CB I:ASN12 4.9 66.3 1.0

Zinc binding site 6 out of 8 in 6uq3

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


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

b:92.9
occ:1.00
 SG I:CYS75 2.4 0.4 1.0
SG I:CYS103 2.5 88.9 1.0
CB I:CYS106 2.5 0.5 1.0
SG I:CYS78 2.5 58.2 1.0
CB I:CYS103 3.0 91.5 1.0
CB I:CYS75 3.1 96.7 1.0
OG I:SER80 3.4 0.4 1.0
CA I:CYS106 3.5 1.0 1.0
N I:CYS106 3.6 0.4 1.0
CB I:CYS78 3.6 77.3 1.0
SG I:CYS106 3.7 0.9 1.0
N I:CYS78 3.9 0.9 1.0
CB I:HIS108 3.9 95.4 1.0
C I:CYS106 4.3 0.5 1.0
CA I:CYS78 4.3 97.3 1.0
N I:HIS108 4.4 67.8 1.0
CA I:CYS103 4.5 81.3 1.0
CB I:LYS77 4.6 63.8 1.0
N I:SER107 4.6 1.0 1.0
CA I:CYS75 4.6 0.8 1.0
C I:SER105 4.6 0.2 1.0
CB I:SER80 4.8 0.9 1.0
CA I:HIS108 4.8 89.3 1.0
C I:CYS78 4.8 89.8 1.0
N I:HIS79 4.9 88.6 1.0
CG I:HIS108 5.0 0.4 1.0
C I:LYS77 5.0 0.2 1.0
ND1 I:HIS108 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 6uq3

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


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

b:0.5
occ:1.00
 SG J:CYS7 2.4 29.8 1.0
SG J:CYS46 2.5 73.8 1.0
SG J:CYS10 2.5 78.2 1.0
SG J:CYS45 2.5 83.5 1.0
N J:CYS46 2.7 0.3 1.0
CA J:CYS46 2.8 1.0 1.0
CB J:CYS7 3.0 56.8 1.0
CB J:CYS46 3.1 98.2 1.0
C J:CYS45 3.2 0.5 1.0
O J:CYS45 3.5 0.3 1.0
CB J:CYS10 3.7 75.8 1.0
CB J:CYS45 3.7 87.8 1.0
CA J:CYS45 4.0 79.0 1.0
N J:CYS10 4.1 64.9 1.0
NH2 J:ARG43 4.2 85.9 1.0
C J:CYS46 4.3 86.8 1.0
CA J:CYS10 4.5 65.5 1.0
CA J:CYS7 4.5 72.2 1.0
NE J:ARG43 4.6 76.5 1.0
CB J:LYS12 4.7 11.9 1.0
CZ J:ARG43 4.8 78.8 1.0
N J:CYS45 4.8 61.9 1.0
N J:GLY11 4.9 54.7 1.0
O J:CYS46 4.9 68.3 1.0
N J:LYS12 5.0 48.6 1.0

Zinc binding site 8 out of 8 in 6uq3

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


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

b:0.6
occ:1.00
 SG L:CYS48 2.4 69.0 1.0
SG L:CYS31 2.4 0.6 1.0
SG L:CYS34 2.4 0.1 1.0
SG L:CYS51 2.4 0.2 1.0
CB L:CYS31 2.9 0.5 1.0
CB L:CYS48 3.2 67.9 1.0
CB L:CYS51 3.3 0.1 1.0
CB L:CYS34 3.7 0.5 1.0
OG L:SER36 4.0 0.9 1.0
N L:CYS51 4.0 0.6 1.0
CA L:CYS51 4.2 0.4 1.0
N L:CYS34 4.3 0.4 1.0
CB L:SER36 4.3 0.5 1.0
CA L:CYS31 4.4 0.8 1.0
CA L:CYS34 4.5 0.2 1.0
CB L:HIS53 4.5 0.0 1.0
CA L:CYS48 4.6 82.9 1.0
C L:CYS51 4.7 0.7 1.0
C L:CYS34 4.9 0.5 1.0
C L:CYS31 4.9 0.2 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 08:44:30 2024

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