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Zinc in PDB 6blo: Pol II Elongation Complex with An Abasic Lesion at I+1 Position

Enzymatic activity of Pol II Elongation Complex with An Abasic Lesion at I+1 Position

All present enzymatic activity of Pol II Elongation Complex with An Abasic Lesion at I+1 Position:
2.7.7.6;

Protein crystallography data

The structure of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, PDB code: 6blo was solved by W.Wang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.48 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.550, 222.280, 193.770, 90.00, 100.62, 90.00
R / Rfree (%) 20.3 / 22.7

Other elements in 6blo:

The structure of Pol II Elongation Complex with An Abasic Lesion at I+1 Position also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position (pdb code 6blo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position, PDB code: 6blo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6blo

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Zinc binding site 1 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.0
occ:1.00
 SG A:CYS110 2.5 0.1 1.0
O A:CYS167 2.5 0.1 1.0
CB A:CYS110 2.9 0.0 1.0
SG A:CYS167 3.2 0.1 1.0
SG A:CYS148 3.3 0.6 1.0
CB A:CYS167 3.4 0.2 1.0
O A:MET108 3.5 0.6 1.0
C A:CYS167 3.6 0.2 1.0
SG A:CYS107 3.7 0.9 1.0
CB A:CYS107 4.0 0.2 1.0
N A:CYS110 4.1 0.7 1.0
CA A:CYS110 4.1 0.2 1.0
CA A:CYS167 4.1 0.5 1.0
O A:GLY166 4.2 0.6 1.0
N A:ASN169 4.6 0.3 1.0
CB A:ASN169 4.6 0.9 1.0
CB A:CYS148 4.7 0.2 1.0
C A:MET108 4.7 0.5 1.0
N A:GLY168 4.8 0.5 1.0
N A:MET108 5.0 0.8 1.0
C A:CYS107 5.0 0.9 1.0

Zinc binding site 2 out of 8 in 6blo

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Zinc binding site 2 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:97.9
occ:1.00
 NE2 A:HIS80 2.2 0.1 1.0
SG A:CYS77 2.3 90.0 1.0
SG A:CYS70 2.6 0.6 1.0
SG A:CYS67 2.8 0.8 1.0
CD2 A:HIS80 2.8 0.5 1.0
O A:CYS67 3.0 0.1 1.0
CE1 A:HIS80 3.4 0.1 1.0
CB A:CYS77 3.7 0.3 1.0
CB A:CYS67 3.7 0.8 1.0
C A:CYS67 3.8 0.8 1.0
CG A:HIS80 4.0 99.9 1.0
CB A:CYS70 4.1 0.2 1.0
CB A:GLN68 4.2 0.1 1.0
OE1 A:GLN68 4.3 0.8 1.0
ND1 A:HIS80 4.3 0.8 1.0
CA A:CYS67 4.4 0.3 1.0
O A:GLN71 4.5 0.1 1.0
N A:GLN68 4.6 0.5 1.0
CA A:GLN68 4.9 0.1 1.0
CA A:CYS77 4.9 91.5 1.0

Zinc binding site 3 out of 8 in 6blo

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Zinc binding site 3 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:100.0
occ:1.00
 SG B:CYS1166 2.4 95.3 1.0
SG B:CYS1163 2.5 91.5 1.0
SG B:CYS1185 2.7 0.6 1.0
SG B:CYS1182 2.8 0.9 1.0
CB B:CYS1163 3.1 91.0 1.0
CB B:CYS1185 3.4 0.9 1.0
CB B:CYS1166 3.8 92.5 1.0
N B:CYS1166 4.0 98.6 1.0
CA B:CYS1166 4.5 98.3 1.0
CB B:CYS1182 4.5 99.7 1.0
CB B:ILE1165 4.5 0.6 1.0
CA B:CYS1163 4.6 85.8 1.0
CB B:THR1170 4.7 0.8 1.0
CA B:CYS1185 4.7 0.4 1.0
N B:CYS1185 4.7 0.3 1.0
OG1 B:THR1170 4.8 0.9 1.0
N B:GLY1167 5.0 0.4 1.0

Zinc binding site 4 out of 8 in 6blo

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Zinc binding site 4 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:53.9
occ:1.00
 SG C:CYS88 2.4 45.0 1.0
SG C:CYS92 2.4 51.7 1.0
SG C:CYS86 2.4 68.2 1.0
SG C:CYS95 2.5 64.3 1.0
CB C:CYS86 2.9 52.6 1.0
CB C:CYS95 3.2 57.1 1.0
N C:CYS92 3.4 49.8 1.0
CB C:CYS92 3.5 54.8 1.0
CB C:CYS88 3.5 44.2 1.0
CA C:CYS92 4.0 56.9 1.0
N C:CYS95 4.0 69.4 1.0
C C:HIS91 4.2 64.9 1.0
CA C:CYS95 4.3 59.1 1.0
CA C:HIS91 4.4 61.4 1.0
CA C:CYS86 4.4 55.9 1.0
C C:CYS92 4.5 58.5 1.0
N C:CYS88 4.6 44.4 1.0
C C:LYS94 4.7 66.2 1.0
CA C:CYS88 4.7 44.3 1.0
O C:CYS92 4.8 58.3 1.0
N C:LYS94 4.8 60.1 1.0
C C:CYS86 4.8 61.5 1.0
CB C:LYS94 4.8 67.6 1.0

Zinc binding site 5 out of 8 in 6blo

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Zinc binding site 5 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:72.0
occ:1.00
 SG I:CYS32 2.4 96.4 1.0
SG I:CYS29 2.4 88.7 1.0
SG I:CYS10 2.5 97.8 1.0
SG I:CYS7 2.7 67.0 1.0
CB I:CYS10 2.8 82.7 1.0
CB I:CYS7 3.4 68.0 1.0
CB I:CYS32 3.4 0.2 1.0
CB I:CYS29 3.6 95.7 1.0
N I:CYS32 3.6 0.8 1.0
CB I:THR31 3.7 98.0 1.0
N I:CYS10 3.8 87.3 1.0
CA I:CYS10 3.9 84.7 1.0
C I:THR31 4.1 90.5 1.0
CA I:CYS32 4.1 0.6 1.0
CA I:THR31 4.3 89.8 1.0
OG1 I:THR31 4.4 0.7 1.0
N I:THR31 4.5 90.2 1.0
CG2 I:THR31 4.6 0.1 1.0
CB I:TYR34 4.7 67.3 1.0
C I:ASP9 4.8 87.3 1.0
C I:CYS10 4.9 78.7 1.0
O I:THR31 4.9 91.0 1.0
CA I:CYS7 4.9 70.6 1.0
N I:SER33 4.9 0.0 1.0
CA I:CYS29 5.0 91.1 1.0

Zinc binding site 6 out of 8 in 6blo

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Zinc binding site 6 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:55.9
occ:1.00
 SG I:CYS78 2.3 65.8 1.0
SG I:CYS106 2.4 63.5 1.0
SG I:CYS75 2.4 48.8 1.0
SG I:CYS103 2.5 61.0 1.0
CB I:CYS103 3.3 44.0 1.0
CB I:CYS75 3.3 49.8 1.0
CB I:CYS78 3.4 65.6 1.0
N I:CYS78 3.5 67.2 1.0
CB I:CYS106 3.7 64.2 1.0
N I:CYS106 3.9 64.6 1.0
CA I:CYS78 4.0 65.0 1.0
CB I:HIS108 4.1 52.8 1.0
CB I:LYS77 4.3 46.3 1.0
CA I:CYS106 4.3 64.6 1.0
N I:HIS79 4.5 60.8 1.0
C I:CYS78 4.5 69.1 1.0
CB I:SER105 4.6 61.4 1.0
CB I:SER80 4.6 67.9 1.0
C I:LYS77 4.7 49.7 1.0
N I:SER80 4.7 69.7 1.0
N I:HIS108 4.7 56.8 1.0
CA I:CYS103 4.8 43.5 1.0
CA I:CYS75 4.8 48.7 1.0
C I:CYS106 4.8 64.7 1.0
CA I:LYS77 4.9 43.7 1.0
N I:LYS77 5.0 47.7 1.0
C I:SER105 5.0 69.2 1.0

Zinc binding site 7 out of 8 in 6blo

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Zinc binding site 7 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:42.8
occ:1.00
 SG J:CYS45 2.3 48.9 1.0
SG J:CYS46 2.4 27.1 1.0
SG J:CYS10 2.4 45.8 1.0
SG J:CYS7 2.4 41.9 1.0
N J:CYS46 3.4 26.4 1.0
CB J:CYS45 3.4 38.2 1.0
CB J:CYS7 3.5 39.5 1.0
CB J:CYS10 3.5 51.5 1.0
N J:CYS10 3.6 45.8 1.0
CB J:CYS46 3.7 26.7 1.0
CA J:CYS46 3.9 26.2 1.0
C J:CYS45 3.9 44.9 1.0
NE J:ARG43 4.0 64.7 1.0
CB J:SER9 4.1 49.4 1.0
CA J:CYS10 4.1 49.1 1.0
CA J:CYS45 4.3 40.3 1.0
NH2 J:ARG43 4.4 72.1 1.0
N J:GLY11 4.6 28.2 1.0
C J:SER9 4.6 49.6 1.0
O J:CYS45 4.7 51.8 1.0
CA J:SER9 4.7 49.1 1.0
OG J:SER9 4.7 49.6 1.0
CZ J:ARG43 4.7 66.7 1.0
N J:SER9 4.8 48.6 1.0
CA J:CYS7 4.9 39.3 1.0
N J:CYS45 4.9 37.5 1.0
CB J:ARG43 4.9 65.0 1.0
C J:CYS10 5.0 50.1 1.0
CD J:ARG43 5.0 68.3 1.0

Zinc binding site 8 out of 8 in 6blo

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Zinc binding site 8 out of 8 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.2
occ:1.00
 SG L:CYS34 2.4 0.6 1.0
CB L:CYS51 2.4 0.8 1.0
SG L:CYS51 2.5 0.9 1.0
SG L:CYS48 2.5 0.2 1.0
SG L:CYS31 2.9 0.8 1.0
CB L:CYS48 3.3 0.1 1.0
CB L:CYS31 3.5 0.6 1.0
CB L:CYS34 3.8 0.5 1.0
CA L:CYS51 3.9 0.4 1.0
N L:CYS51 4.6 0.9 1.0
O L:LYS49 4.7 0.7 1.0
O L:ASP50 4.7 0.3 1.0
OG L:SER36 4.7 0.8 1.0
CA L:CYS48 4.8 0.9 1.0
CA L:CYS34 4.8 0.6 1.0
C L:CYS51 4.9 0.4 1.0
C L:ASP50 4.9 1.0 1.0
N L:CYS34 4.9 0.5 1.0
N L:LYS49 4.9 1.0 1.0
N L:GLY52 4.9 1.0 1.0

Reference:

W.Wang, C.Walmacq, J.Chong, M.Kashlev, D.Wang. Structural Basis of Transcriptional Stalling and Bypass of Abasic Dna Lesion By Rna Polymerase II. Proc. Natl. Acad. Sci. V. 115 E2538 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29487211
DOI: 10.1073/PNAS.1722050115
Page generated: Mon Oct 28 18:01:05 2024

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