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Zinc in PDB 6bqf: Pol II Elongation Complex with 'Dt-Ap' at I+1, I-1 Position

Enzymatic activity of Pol II Elongation Complex with 'Dt-Ap' at I+1, I-1 Position

All present enzymatic activity of Pol II Elongation Complex with 'Dt-Ap' at I+1, I-1 Position:
2.7.7.6;

Protein crystallography data

The structure of Pol II Elongation Complex with 'Dt-Ap' at I+1, I-1 Position, PDB code: 6bqf 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) 82.76 / 3.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.400, 221.350, 193.700, 90.00, 100.60, 90.00
R / Rfree (%) 21.7 / 24.5

Other elements in 6bqf:

The structure of Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position (pdb code 6bqf). 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 'Dt-Ap' at I+1, I-1 Position, PDB code: 6bqf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6bqf

Go back to Zinc Binding Sites List in 6bqf
Zinc binding site 1 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.3
occ:1.00
 SG A:CYS110 2.5 0.8 1.0
O A:CYS167 2.8 0.0 1.0
SG A:CYS107 3.1 0.8 1.0
CB A:CYS110 3.2 0.0 1.0
SG A:CYS148 3.2 0.3 1.0
O A:MET108 3.2 1.0 1.0
SG A:CYS167 3.4 0.8 1.0
CB A:CYS107 3.5 0.5 1.0
CB A:CYS167 3.8 0.1 1.0
C A:CYS167 3.9 0.6 1.0
N A:CYS110 4.0 0.2 1.0
CB A:ASN169 4.2 0.1 1.0
N A:ASN169 4.2 0.7 1.0
CA A:CYS110 4.2 0.6 1.0
C A:MET108 4.4 0.0 1.0
C A:CYS107 4.5 0.5 1.0
CA A:CYS167 4.5 0.7 1.0
CB A:CYS148 4.6 0.5 1.0
N A:MET108 4.6 0.8 1.0
O A:GLY166 4.6 0.6 1.0
CA A:CYS107 4.6 1.0 1.0
O A:ASN169 4.8 0.2 1.0
CA A:ASN169 4.8 0.7 1.0
O A:CYS107 4.9 0.3 1.0
N A:GLY168 5.0 98.7 1.0

Zinc binding site 2 out of 8 in 6bqf

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Zinc binding site 2 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:83.0
occ:1.00
 NE2 A:HIS80 2.2 86.6 1.0
SG A:CYS77 2.8 80.6 1.0
SG A:CYS70 2.8 0.2 1.0
SG A:CYS67 3.0 0.2 1.0
CE1 A:HIS80 3.1 85.1 1.0
O A:CYS67 3.1 0.7 1.0
CD2 A:HIS80 3.1 88.4 1.0
CB A:CYS77 3.4 92.7 1.0
CB A:CYS67 3.8 0.7 1.0
C A:CYS67 4.1 0.5 1.0
O A:GLN71 4.1 0.7 1.0
ND1 A:HIS80 4.2 82.2 1.0
CG A:HIS80 4.3 85.2 1.0
OE1 A:GLN68 4.5 0.4 1.0
CA A:CYS77 4.5 78.8 1.0
CB A:CYS70 4.5 1.0 1.0
CA A:CYS67 4.6 0.1 1.0
CB A:GLN68 4.7 0.2 1.0
O A:GLN68 5.0 0.3 1.0

Zinc binding site 3 out of 8 in 6bqf

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Zinc binding site 3 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:95.9
occ:1.00
 SG B:CYS1166 2.4 0.3 1.0
SG B:CYS1163 2.5 74.8 1.0
SG B:CYS1182 3.0 0.8 1.0
CB B:CYS1163 3.1 71.6 1.0
SG B:CYS1185 3.3 0.5 1.0
CB B:CYS1166 3.7 98.1 1.0
CB B:CYS1185 3.8 0.3 1.0
N B:CYS1166 3.9 97.6 1.0
CA B:CYS1166 4.4 0.7 1.0
CB B:ILE1165 4.5 0.2 1.0
CA B:CYS1163 4.6 73.4 1.0
CB B:CYS1182 4.6 0.0 1.0
N B:GLY1167 4.8 0.9 1.0
CB B:THR1170 4.8 0.1 1.0
OG1 B:THR1170 4.9 1.0 1.0
N B:CYS1185 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 6bqf

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Zinc binding site 4 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:37.8
occ:1.00
 SG C:CYS92 2.4 37.1 1.0
SG C:CYS88 2.4 43.1 1.0
SG C:CYS86 2.4 47.9 1.0
SG C:CYS95 2.5 63.3 1.0
CB C:CYS86 3.1 33.1 1.0
CB C:CYS95 3.2 54.5 1.0
N C:CYS92 3.3 42.5 1.0
CB C:CYS92 3.3 46.3 1.0
CB C:CYS88 3.5 47.4 1.0
CA C:CYS92 3.8 43.0 1.0
C C:HIS91 3.9 37.5 1.0
N C:CYS95 4.0 61.1 1.0
CA C:HIS91 4.2 34.8 1.0
CA C:CYS95 4.3 52.6 1.0
C C:CYS92 4.4 45.7 1.0
CA C:CYS86 4.5 38.9 1.0
N C:CYS88 4.6 37.9 1.0
CA C:CYS88 4.6 38.8 1.0
C C:LYS94 4.7 53.1 1.0
N C:LYS94 4.7 47.2 1.0
O C:HIS91 4.8 38.9 1.0
CB C:LYS94 4.8 51.1 1.0
O C:CYS92 4.8 50.5 1.0
C C:CYS86 4.9 38.7 1.0
N C:ASP93 4.9 36.3 1.0

Zinc binding site 5 out of 8 in 6bqf

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Zinc binding site 5 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:53.0
occ:1.00
 SG I:CYS29 2.4 92.8 1.0
SG I:CYS10 2.5 74.2 1.0
SG I:CYS7 2.6 63.2 1.0
SG I:CYS32 2.6 81.8 1.0
CB I:CYS10 2.9 61.8 1.0
CB I:CYS7 3.2 65.6 1.0
CB I:CYS29 3.4 91.1 1.0
CB I:CYS32 3.7 88.0 1.0
N I:CYS10 3.8 71.5 1.0
N I:CYS32 3.8 88.0 1.0
CA I:CYS10 3.9 66.7 1.0
CB I:THR31 4.1 70.4 1.0
CB I:TYR34 4.3 57.0 1.0
CA I:CYS32 4.4 89.9 1.0
C I:THR31 4.6 78.8 1.0
CA I:CYS7 4.7 65.7 1.0
CA I:THR31 4.7 70.1 1.0
CA I:CYS29 4.8 86.1 1.0
OG1 I:THR31 4.8 76.9 1.0
N I:THR31 4.8 72.2 1.0
C I:ASP9 4.8 80.7 1.0
CG2 I:THR31 4.8 70.6 1.0
C I:CYS10 4.9 64.1 1.0
N I:TYR34 5.0 69.0 1.0
CB I:ASP9 5.0 88.8 1.0
O I:CYS29 5.0 95.0 1.0
C I:CYS29 5.0 90.2 1.0

Zinc binding site 6 out of 8 in 6bqf

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Zinc binding site 6 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:33.4
occ:1.00
 SG I:CYS78 2.4 48.8 1.0
SG I:CYS106 2.4 31.4 1.0
SG I:CYS75 2.4 31.1 1.0
SG I:CYS103 2.4 38.2 1.0
CB I:CYS103 3.1 32.7 1.0
CB I:CYS75 3.2 32.9 1.0
CB I:CYS78 3.5 52.5 1.0
N I:CYS78 3.6 48.3 1.0
CB I:CYS106 3.8 40.5 1.0
N I:CYS106 4.0 31.3 1.0
CA I:CYS78 4.0 47.1 1.0
CB I:HIS108 4.1 29.8 1.0
CB I:LYS77 4.3 40.9 1.0
CA I:CYS106 4.4 39.6 1.0
C I:CYS78 4.5 50.0 1.0
N I:HIS79 4.6 50.0 1.0
CB I:SER105 4.6 50.6 1.0
CA I:CYS103 4.6 31.0 1.0
C I:LYS77 4.7 42.6 1.0
CB I:SER80 4.7 43.2 1.0
N I:SER80 4.7 47.8 1.0
CA I:CYS75 4.7 37.7 1.0
N I:HIS108 4.8 36.5 1.0
CA I:LYS77 4.9 38.1 1.0
C I:CYS106 4.9 42.3 1.0
N I:LYS77 5.0 36.6 1.0
C I:SER105 5.0 50.9 1.0
CG I:HIS108 5.0 30.0 1.0

Zinc binding site 7 out of 8 in 6bqf

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Zinc binding site 7 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:34.7
occ:1.00
 SG J:CYS46 2.4 27.3 1.0
SG J:CYS45 2.4 31.3 1.0
SG J:CYS10 2.4 49.7 1.0
SG J:CYS7 2.4 35.0 1.0
N J:CYS46 3.3 27.1 1.0
CB J:CYS7 3.4 27.3 1.0
CB J:CYS10 3.4 46.8 1.0
CB J:CYS45 3.4 26.5 1.0
N J:CYS10 3.6 42.5 1.0
CB J:CYS46 3.6 27.2 1.0
CA J:CYS46 3.8 27.1 1.0
C J:CYS45 3.8 32.8 1.0
CA J:CYS10 4.1 51.1 1.0
CA J:CYS45 4.2 26.6 1.0
CB J:SER9 4.2 41.4 1.0
NE J:ARG43 4.3 56.5 1.0
O J:CYS45 4.5 40.4 1.0
N J:GLY11 4.5 27.5 1.0
C J:SER9 4.7 43.0 1.0
NH2 J:ARG43 4.8 69.8 1.0
CA J:CYS7 4.8 27.2 1.0
N J:CYS45 4.8 27.0 1.0
CA J:SER9 4.8 40.7 1.0
C J:CYS10 4.9 45.3 1.0
N J:SER9 4.9 41.0 1.0
CB J:ARG43 4.9 50.2 1.0
OG J:SER9 5.0 40.2 1.0

Zinc binding site 8 out of 8 in 6bqf

Go back to Zinc Binding Sites List in 6bqf
Zinc binding site 8 out of 8 in the Pol II Elongation Complex with 'Dt-Ap' at I+1, 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 'Dt-Ap' at I+1, I-1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:73.3
occ:1.00
 SG L:CYS34 2.4 66.6 1.0
CB L:CYS51 2.4 0.2 1.0
SG L:CYS51 2.5 1.0 1.0
SG L:CYS48 2.6 83.0 1.0
SG L:CYS31 3.0 92.0 1.0
CB L:CYS34 3.5 76.3 1.0
CB L:CYS48 3.5 83.2 1.0
CB L:CYS31 3.7 72.3 1.0
CA L:CYS51 3.9 0.1 1.0
OG L:SER36 4.4 0.5 1.0
O L:ASP50 4.5 0.5 1.0
N L:CYS51 4.6 0.2 1.0
O L:LYS49 4.6 0.7 1.0
CA L:CYS34 4.7 77.3 1.0
C L:ASP50 4.8 0.8 1.0
N L:CYS34 4.8 77.4 1.0
C L:CYS51 4.9 0.1 1.0
N L:GLY52 4.9 0.2 1.0
CA L:CYS48 4.9 80.0 1.0
CB L:SER36 5.0 0.9 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 18:12:22 2024

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