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Zinc in PDB 6bm4: Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp

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

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

Protein crystallography data

The structure of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp, PDB code: 6bm4 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) 55.61 / 2.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.720, 220.430, 193.150, 90.00, 100.97, 90.00
R / Rfree (%) 23.4 / 26

Other elements in 6bm4:

The structure of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp 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 Umpnpp (pdb code 6bm4). 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 Umpnpp, PDB code: 6bm4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6bm4

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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 Umpnpp


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

b:0.1
occ:1.00
 SG A:CYS107 2.8 0.2 1.0
SG A:CYS110 2.8 0.2 1.0
O A:CYS167 2.8 0.9 1.0
SG A:CYS148 3.0 0.7 1.0
O A:MET108 3.3 0.4 1.0
CB A:CYS107 3.3 0.7 1.0
SG A:CYS167 3.5 0.5 1.0
CB A:CYS110 3.8 0.8 1.0
CB A:ASN169 3.9 0.7 1.0
C A:CYS167 4.0 0.4 1.0
N A:ASN169 4.0 0.4 1.0
CB A:CYS167 4.0 0.7 1.0
O A:ASN169 4.4 0.1 1.0
N A:MET108 4.4 0.6 1.0
N A:CYS110 4.4 0.6 1.0
CB A:CYS148 4.4 0.4 1.0
CA A:ASN169 4.5 0.7 1.0
C A:MET108 4.5 0.6 1.0
C A:CYS107 4.5 0.1 1.0
CA A:CYS107 4.5 0.2 1.0
CA A:CYS167 4.7 0.8 1.0
CA A:CYS110 4.7 0.1 1.0
O A:GLY166 4.8 0.8 1.0
C A:ASN169 4.9 0.7 1.0

Zinc binding site 2 out of 8 in 6bm4

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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 Umpnpp


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

b:80.9
occ:1.00
 NE2 A:HIS80 2.1 83.3 1.0
SG A:CYS77 2.4 0.5 1.0
CD2 A:HIS80 2.6 85.2 1.0
SG A:CYS67 2.9 0.9 1.0
CE1 A:HIS80 3.3 82.6 1.0
CB A:CYS77 3.4 0.6 1.0
SG A:CYS70 3.4 0.6 1.0
O A:CYS67 3.5 1.0 1.0
CG A:HIS80 3.9 84.7 1.0
CB A:CYS67 4.0 0.0 1.0
ND1 A:HIS80 4.2 83.5 1.0
OE1 A:GLN68 4.2 0.2 1.0
C A:CYS67 4.3 0.4 1.0
CA A:CYS77 4.6 97.2 1.0
CB A:GLN68 4.6 0.7 1.0
O A:GLN71 4.7 0.6 1.0
CA A:CYS67 4.8 0.2 1.0

Zinc binding site 3 out of 8 in 6bm4

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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 Umpnpp


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

b:93.4
occ:1.00
 SG B:CYS1166 2.4 84.1 1.0
SG B:CYS1163 2.5 76.0 1.0
SG B:CYS1185 3.1 0.4 1.0
SG B:CYS1182 3.1 0.9 1.0
CB B:CYS1163 3.2 72.9 1.0
CB B:CYS1166 3.7 82.4 1.0
CB B:CYS1185 3.7 1.0 1.0
N B:CYS1166 3.9 82.5 1.0
CA B:CYS1166 4.4 82.6 1.0
CB B:ILE1165 4.4 0.2 1.0
CA B:CYS1163 4.7 71.4 1.0
CB B:CYS1182 4.8 0.0 1.0
N B:GLY1167 4.9 0.2 1.0
N B:CYS1185 4.9 0.1 1.0
C B:ILE1165 4.9 97.7 1.0
CA B:CYS1185 5.0 0.8 1.0

Zinc binding site 4 out of 8 in 6bm4

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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 Umpnpp


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

b:41.6
occ:1.00
 SG C:CYS88 2.3 32.4 1.0
SG C:CYS86 2.4 37.2 1.0
SG C:CYS92 2.4 41.4 1.0
SG C:CYS95 2.4 57.2 1.0
N C:CYS92 3.2 38.5 1.0
CB C:CYS95 3.2 54.9 1.0
CB C:CYS86 3.2 35.9 1.0
CB C:CYS92 3.3 41.9 1.0
CB C:CYS88 3.4 34.4 1.0
CA C:CYS92 3.8 39.7 1.0
C C:HIS91 3.8 39.1 1.0
N C:CYS95 4.0 57.7 1.0
CA C:HIS91 4.1 37.8 1.0
CA C:CYS95 4.2 54.1 1.0
C C:CYS92 4.4 40.2 1.0
CA C:CYS88 4.6 35.0 1.0
N C:CYS88 4.6 35.0 1.0
CA C:CYS86 4.6 36.7 1.0
O C:HIS91 4.7 39.8 1.0
C C:LYS94 4.7 47.0 1.0
N C:LYS94 4.8 48.3 1.0
O C:CYS92 4.8 40.7 1.0
CB C:LYS94 4.9 49.7 1.0
N C:ASP93 4.9 54.6 1.0
C C:CYS86 5.0 37.4 1.0

Zinc binding site 5 out of 8 in 6bm4

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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 Umpnpp


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

b:49.0
occ:1.00
 SG I:CYS29 2.4 81.0 1.0
SG I:CYS7 2.4 74.0 1.0
SG I:CYS32 2.5 81.1 1.0
SG I:CYS10 2.6 66.3 1.0
CB I:CYS10 3.0 64.7 1.0
CB I:CYS7 3.0 74.0 1.0
CB I:CYS29 3.2 80.5 1.0
CB I:CYS32 3.7 84.4 1.0
N I:CYS10 3.8 64.0 1.0
CA I:CYS10 4.0 64.0 1.0
CB I:TYR34 4.0 70.7 1.0
N I:CYS32 4.1 85.3 1.0
CB I:THR31 4.5 64.1 1.0
CA I:CYS32 4.5 86.5 1.0
CA I:CYS7 4.5 73.2 1.0
CA I:CYS29 4.7 79.7 1.0
N I:TYR34 4.7 76.1 1.0
C I:THR31 4.8 66.5 1.0
CB I:ASP9 4.8 70.4 1.0
C I:ASP9 4.8 68.8 1.0
N I:SER33 4.9 92.9 1.0
CG I:TYR34 5.0 69.8 1.0
N I:THR31 5.0 65.7 1.0
C I:CYS10 5.0 62.9 1.0

Zinc binding site 6 out of 8 in 6bm4

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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 Umpnpp


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

b:34.8
occ:1.00
 SG I:CYS78 2.3 43.8 1.0
SG I:CYS106 2.4 37.4 1.0
SG I:CYS103 2.4 36.5 1.0
SG I:CYS75 2.5 37.8 1.0
CB I:CYS75 3.1 36.9 1.0
CB I:CYS103 3.3 35.4 1.0
CB I:CYS78 3.4 47.2 1.0
N I:CYS78 3.5 46.7 1.0
CB I:CYS106 3.8 38.9 1.0
CA I:CYS78 3.9 46.4 1.0
N I:CYS106 4.0 36.6 1.0
C I:CYS78 4.3 46.8 1.0
CB I:SER80 4.3 39.8 1.0
N I:SER80 4.4 41.2 1.0
N I:HIS79 4.4 36.9 1.0
CB I:SER105 4.5 40.3 1.0
CB I:LYS77 4.5 46.6 1.0
CA I:CYS106 4.5 38.0 1.0
CB I:HIS108 4.5 32.1 1.0
CA I:CYS75 4.6 37.1 1.0
C I:LYS77 4.7 47.8 1.0
CA I:CYS103 4.7 34.0 1.0
C I:SER105 4.9 41.1 1.0
CA I:SER80 4.9 40.3 1.0
CA I:LYS77 5.0 47.3 1.0

Zinc binding site 7 out of 8 in 6bm4

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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 Umpnpp


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

b:34.1
occ:1.00
 SG J:CYS45 2.3 37.2 1.0
SG J:CYS7 2.4 34.3 1.0
SG J:CYS10 2.4 40.5 1.0
SG J:CYS46 2.4 25.2 1.0
CB J:CYS10 3.3 40.2 1.0
N J:CYS46 3.3 23.3 1.0
CB J:CYS45 3.4 34.2 1.0
CB J:CYS7 3.5 31.6 1.0
N J:CYS10 3.6 38.1 1.0
CB J:CYS46 3.7 24.6 1.0
C J:CYS45 3.8 35.4 1.0
CA J:CYS46 3.9 23.4 1.0
CA J:CYS10 4.1 41.4 1.0
CA J:CYS45 4.2 33.8 1.0
NE J:ARG43 4.3 44.9 1.0
CB J:SER9 4.3 30.1 1.0
O J:CYS45 4.5 37.0 1.0
N J:GLY11 4.6 31.1 1.0
C J:SER9 4.7 30.4 1.0
N J:CYS45 4.8 34.7 1.0
NH2 J:ARG43 4.8 49.5 1.0
CA J:CYS7 4.8 31.3 1.0
C J:CYS10 4.8 39.4 1.0
CB J:ARG43 4.9 41.7 1.0
CA J:SER9 4.9 30.0 1.0
N J:SER9 4.9 29.4 1.0
CB J:LYS12 5.0 28.2 1.0

Zinc binding site 8 out of 8 in 6bm4

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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 Umpnpp


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

b:70.5
occ:1.00
 SG L:CYS34 2.4 59.1 1.0
CB L:CYS51 2.4 94.2 1.0
SG L:CYS48 2.5 86.7 1.0
SG L:CYS51 2.5 96.1 1.0
SG L:CYS31 2.7 77.5 1.0
CB L:CYS48 3.3 86.9 1.0
CB L:CYS31 3.4 72.1 1.0
CB L:CYS34 3.7 63.3 1.0
CA L:CYS51 4.0 96.7 1.0
OG L:SER36 4.3 0.1 1.0
N L:CYS51 4.6 97.6 1.0
O L:LYS49 4.7 0.1 1.0
O L:ASP50 4.7 0.5 1.0
CA L:CYS48 4.7 87.5 1.0
CA L:CYS34 4.8 65.7 1.0
N L:CYS34 4.8 61.4 1.0
C L:CYS51 4.8 98.5 1.0
N L:GLY52 4.9 0.1 1.0
CA L:CYS31 4.9 70.0 1.0
C L:ASP50 4.9 0.3 1.0
CB L:SER36 4.9 0.8 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 18:02:48 2024

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