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Zinc in PDB 6blp: Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp

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

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

Protein crystallography data

The structure of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp, PDB code: 6blp 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) 82.88 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.060, 222.180, 193.200, 90.00, 101.34, 90.00
R / Rfree (%) 21.4 / 25.7

Other elements in 6blp:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position, Soaking Ampcpp (pdb code 6blp). 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, Soaking Ampcpp, PDB code: 6blp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.6
occ:1.00
 O A:CYS167 2.4 0.2 1.0
SG A:CYS110 2.5 0.4 1.0
CB A:CYS110 2.9 0.3 1.0
SG A:CYS148 3.0 0.9 1.0
CB A:CYS167 3.2 0.8 1.0
C A:CYS167 3.5 0.7 1.0
SG A:CYS167 3.5 0.2 1.0
O A:GLY166 3.6 0.1 1.0
SG A:CYS107 3.9 0.1 1.0
CA A:CYS167 3.9 0.6 1.0
O A:MET108 4.0 0.2 1.0
CB A:CYS107 4.1 0.1 1.0
CA A:CYS110 4.2 0.8 1.0
CB A:CYS148 4.3 0.1 1.0
N A:CYS110 4.4 0.9 1.0
C A:GLY166 4.5 0.4 1.0
N A:ASN169 4.6 0.6 1.0
N A:GLY168 4.6 0.7 1.0
N A:CYS167 4.7 0.5 1.0
CB A:ASN169 4.9 0.7 1.0

Zinc binding site 2 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:91.8
occ:1.00
 NE2 A:HIS80 2.1 73.0 1.0
SG A:CYS77 2.4 73.2 1.0
CD2 A:HIS80 2.7 74.6 1.0
SG A:CYS67 2.8 0.8 1.0
SG A:CYS70 2.9 88.8 1.0
O A:CYS67 3.1 0.7 1.0
CE1 A:HIS80 3.3 70.9 1.0
CB A:CYS77 3.6 97.7 1.0
CB A:CYS67 3.8 0.6 1.0
C A:CYS67 3.9 0.2 1.0
CG A:HIS80 4.0 68.4 1.0
CB A:GLN68 4.2 0.1 1.0
ND1 A:HIS80 4.2 64.5 1.0
OE1 A:GLN68 4.3 70.7 1.0
CA A:CYS67 4.5 0.6 1.0
O A:GLN71 4.5 0.3 1.0
CB A:CYS70 4.6 0.1 1.0
N A:GLN68 4.7 0.0 1.0
CA A:CYS77 4.9 76.7 1.0
CA A:GLN68 5.0 0.3 1.0

Zinc binding site 3 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:82.8
occ:1.00
 SG B:CYS1166 2.4 91.5 1.0
SG B:CYS1163 2.4 86.6 1.0
SG B:CYS1185 2.7 0.7 1.0
SG B:CYS1182 3.1 81.2 1.0
CB B:CYS1163 3.2 92.4 1.0
CB B:CYS1185 3.3 0.2 1.0
CB B:CYS1166 3.5 80.0 1.0
N B:CYS1166 3.6 78.6 1.0
CB B:ILE1165 4.1 0.9 1.0
CA B:CYS1166 4.2 88.5 1.0
CA B:CYS1185 4.6 0.2 1.0
CA B:CYS1163 4.7 0.7 1.0
C B:ILE1165 4.7 96.4 1.0
CB B:CYS1182 4.7 82.5 1.0
N B:GLY1167 4.7 0.2 1.0
N B:CYS1185 4.8 0.4 1.0
CA B:ILE1165 4.8 93.6 1.0
N B:ILE1165 4.8 89.1 1.0
CG1 B:ILE1165 4.8 93.0 1.0
C B:CYS1166 4.9 98.9 1.0
CG2 B:ILE1165 4.9 0.1 1.0

Zinc binding site 4 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:47.6
occ:1.00
 SG C:CYS88 2.4 43.3 1.0
SG C:CYS92 2.4 33.2 1.0
SG C:CYS86 2.4 61.2 1.0
SG C:CYS95 2.4 69.0 1.0
CB C:CYS86 2.9 37.4 1.0
CB C:CYS95 3.1 53.2 1.0
CB C:CYS88 3.5 48.1 1.0
CB C:CYS92 3.5 49.5 1.0
N C:CYS92 3.5 47.0 1.0
N C:CYS95 4.0 61.8 1.0
CA C:CYS92 4.0 45.5 1.0
C C:HIS91 4.2 48.1 1.0
CA C:CYS95 4.2 48.8 1.0
CA C:CYS86 4.4 47.2 1.0
CA C:HIS91 4.4 45.5 1.0
N C:CYS88 4.5 30.1 1.0
CA C:CYS88 4.6 32.5 1.0
C C:CYS92 4.6 50.1 1.0
C C:LYS94 4.6 55.5 1.0
C C:CYS86 4.8 46.2 1.0
CB C:LYS94 4.8 48.0 1.0
N C:LYS94 4.8 42.7 1.0
O C:CYS92 5.0 60.3 1.0
O C:HIS91 5.0 49.3 1.0

Zinc binding site 5 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:53.7
occ:1.00
 SG I:CYS29 2.4 95.0 1.0
SG I:CYS32 2.5 82.2 1.0
SG I:CYS7 2.6 54.3 1.0
SG I:CYS10 2.7 77.5 1.0
CB I:CYS10 2.8 54.1 1.0
CB I:CYS7 3.2 59.5 1.0
CB I:CYS29 3.4 90.8 1.0
CB I:CYS32 3.6 92.0 1.0
N I:CYS32 3.7 92.1 1.0
N I:CYS10 3.8 75.5 1.0
CA I:CYS10 3.9 67.4 1.0
CB I:THR31 3.9 69.5 1.0
CA I:CYS32 4.3 94.3 1.0
C I:THR31 4.3 81.3 1.0
CB I:TYR34 4.4 56.6 1.0
CA I:THR31 4.5 66.9 1.0
OG1 I:THR31 4.6 81.8 1.0
N I:THR31 4.6 70.2 1.0
CA I:CYS7 4.7 60.2 1.0
C I:CYS10 4.8 64.1 1.0
CG2 I:THR31 4.8 70.3 1.0
C I:ASP9 4.8 67.1 1.0
CA I:CYS29 4.8 80.8 1.0
N I:SER33 4.9 0.8 1.0
N I:TYR34 4.9 75.0 1.0
N I:ASN11 5.0 47.7 1.0

Zinc binding site 6 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:45.8
occ:1.00
 SG I:CYS78 2.4 56.1 1.0
SG I:CYS103 2.4 57.6 1.0
SG I:CYS75 2.4 41.0 1.0
SG I:CYS106 2.4 43.6 1.0
CB I:CYS103 3.1 48.8 1.0
CB I:CYS75 3.2 44.3 1.0
CB I:CYS78 3.5 61.2 1.0
N I:CYS78 3.6 54.0 1.0
CB I:CYS106 3.9 58.8 1.0
N I:CYS106 4.0 43.5 1.0
CA I:CYS78 4.0 51.1 1.0
CB I:HIS108 4.1 34.6 1.0
CB I:LYS77 4.4 51.5 1.0
CA I:CYS106 4.4 57.8 1.0
CB I:SER105 4.5 61.0 1.0
C I:CYS78 4.5 55.9 1.0
N I:HIS79 4.6 52.4 1.0
CA I:CYS103 4.6 46.3 1.0
CB I:SER80 4.7 35.9 1.0
CA I:CYS75 4.7 52.5 1.0
C I:LYS77 4.7 53.0 1.0
N I:HIS108 4.7 47.2 1.0
N I:SER80 4.7 51.6 1.0
C I:CYS106 4.9 63.3 1.0
CA I:LYS77 5.0 45.6 1.0

Zinc binding site 7 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:38.9
occ:1.00
 SG J:CYS45 2.4 34.5 1.0
SG J:CYS10 2.4 56.8 1.0
SG J:CYS7 2.4 46.6 1.0
SG J:CYS46 2.4 28.3 1.0
N J:CYS46 3.3 27.4 1.0
CB J:CYS10 3.4 50.7 1.0
CB J:CYS45 3.4 25.8 1.0
CB J:CYS7 3.5 31.6 1.0
N J:CYS10 3.6 44.6 1.0
CB J:CYS46 3.7 34.4 1.0
CA J:CYS46 3.8 34.3 1.0
C J:CYS45 3.8 37.9 1.0
CA J:CYS10 4.1 58.5 1.0
CA J:CYS45 4.2 26.1 1.0
CB J:SER9 4.2 31.8 1.0
NE J:ARG43 4.2 54.1 1.0
NH2 J:ARG43 4.4 78.8 1.0
O J:CYS45 4.5 51.7 1.0
N J:GLY11 4.6 27.9 1.0
C J:SER9 4.7 33.2 1.0
N J:CYS45 4.8 23.5 1.0
CA J:SER9 4.8 29.2 1.0
CZ J:ARG43 4.8 57.0 1.0
N J:SER9 4.8 31.2 1.0
CA J:CYS7 4.9 31.3 1.0
OG J:SER9 4.9 24.7 1.0
C J:CYS10 4.9 47.7 1.0
CB J:ARG43 5.0 42.9 1.0

Zinc binding site 8 out of 8 in 6blp

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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, Soaking Ampcpp


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, Soaking Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.6
occ:1.00
 SG L:CYS48 2.4 78.9 1.0
SG L:CYS34 2.4 79.8 1.0
CB L:CYS51 2.4 0.6 1.0
SG L:CYS51 2.5 0.8 1.0
SG L:CYS31 2.8 0.2 1.0
CB L:CYS48 3.2 79.7 1.0
CB L:CYS31 3.4 89.8 1.0
CB L:CYS34 3.7 91.3 1.0
CA L:CYS51 3.9 0.8 1.0
OG L:SER36 4.5 0.5 1.0
N L:CYS51 4.6 0.6 1.0
O L:LYS49 4.6 0.4 1.0
CA L:CYS48 4.7 72.8 1.0
O L:ASP50 4.7 0.3 1.0
CA L:CYS34 4.8 92.6 1.0
N L:CYS34 4.9 96.5 1.0
CA L:CYS31 4.9 77.2 1.0
C L:CYS51 4.9 0.8 1.0
C L:ASP50 4.9 0.5 1.0
N L:LYS49 4.9 0.0 1.0
N L:GLY52 5.0 0.1 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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