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Zinc in PDB 6bm2: 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: 6bm2 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) 82.92 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.110, 222.270, 193.710, 90.00, 101.28, 90.00
R / Rfree (%) 21.9 / 24.4

Other elements in 6bm2:

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 6bm2). 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: 6bm2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6bm2

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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:0.7
occ:1.00
 SG A:CYS110 2.5 0.4 1.0
O A:CYS167 2.6 0.1 1.0
SG A:CYS167 2.9 0.0 1.0
CB A:CYS110 2.9 0.1 1.0
CB A:CYS167 3.2 0.8 1.0
O A:MET108 3.4 0.3 1.0
SG A:CYS148 3.5 0.6 1.0
C A:CYS167 3.6 1.0 1.0
SG A:CYS107 3.6 0.7 1.0
N A:CYS110 3.9 0.6 1.0
CA A:CYS110 4.0 0.3 1.0
CB A:CYS107 4.0 0.1 1.0
CA A:CYS167 4.0 0.1 1.0
N A:ASN169 4.2 0.7 1.0
CB A:ASN169 4.2 0.3 1.0
O A:GLY166 4.3 1.0 1.0
C A:MET108 4.6 0.6 1.0
CB A:CYS148 4.7 0.0 1.0
N A:GLY168 4.8 0.5 1.0
CA A:ASN169 4.8 0.8 1.0
C A:CYS107 5.0 0.2 1.0
N A:MET108 5.0 0.4 1.0

Zinc binding site 2 out of 8 in 6bm2

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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:82.7
occ:1.00
 NE2 A:HIS80 2.1 86.3 1.0
SG A:CYS77 2.5 78.9 1.0
SG A:CYS70 2.7 0.2 1.0
CE1 A:HIS80 3.1 86.2 1.0
CD2 A:HIS80 3.1 86.8 1.0
O A:CYS67 3.3 0.6 1.0
SG A:CYS67 3.4 0.4 1.0
CB A:CYS77 3.5 77.5 1.0
CB A:CYS67 4.2 1.0 1.0
ND1 A:HIS80 4.2 86.6 1.0
CG A:HIS80 4.2 86.9 1.0
C A:CYS67 4.3 0.2 1.0
O A:GLN71 4.3 0.5 1.0
OE1 A:GLN68 4.3 0.1 1.0
CA A:CYS77 4.5 74.9 1.0
CB A:CYS70 4.5 1.0 1.0
CB A:GLN68 4.7 0.3 1.0
CA A:CYS67 4.9 0.6 1.0
O A:GLN68 5.0 0.8 1.0

Zinc binding site 3 out of 8 in 6bm2

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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:79.6
occ:1.00
 SG B:CYS1166 2.4 88.8 1.0
SG B:CYS1163 2.5 80.1 1.0
SG B:CYS1182 3.1 93.2 1.0
CB B:CYS1163 3.2 76.7 1.0
SG B:CYS1185 3.2 0.6 1.0
CB B:CYS1166 3.5 88.1 1.0
CB B:CYS1185 3.7 0.1 1.0
N B:CYS1166 3.7 88.5 1.0
CA B:CYS1166 4.3 88.0 1.0
CB B:ILE1165 4.3 94.2 1.0
CA B:CYS1163 4.7 75.0 1.0
CB B:CYS1182 4.7 94.7 1.0
C B:ILE1165 4.8 88.9 1.0
N B:GLY1167 4.8 0.1 1.0
N B:CYS1185 4.9 0.0 1.0
CA B:ILE1165 4.9 90.4 1.0
CA B:CYS1185 4.9 0.1 1.0
CG1 B:ILE1165 4.9 95.0 1.0
N B:ILE1165 4.9 88.5 1.0

Zinc binding site 4 out of 8 in 6bm2

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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:36.3
occ:1.00
 SG C:CYS88 2.3 36.2 1.0
SG C:CYS92 2.4 38.4 1.0
SG C:CYS95 2.4 48.5 1.0
SG C:CYS86 2.5 52.4 1.0
CB C:CYS86 3.2 48.3 1.0
N C:CYS92 3.2 34.5 1.0
CB C:CYS95 3.3 47.2 1.0
CB C:CYS92 3.3 38.3 1.0
CB C:CYS88 3.5 39.0 1.0
CA C:CYS92 3.8 36.4 1.0
C C:HIS91 3.9 43.1 1.0
N C:CYS95 4.0 50.1 1.0
CA C:HIS91 4.2 41.1 1.0
CA C:CYS95 4.2 47.0 1.0
C C:CYS92 4.3 36.1 1.0
CA C:CYS86 4.6 50.8 1.0
CA C:CYS88 4.6 39.8 1.0
N C:CYS88 4.7 39.7 1.0
C C:LYS94 4.7 62.8 1.0
N C:LYS94 4.7 63.4 1.0
O C:CYS92 4.7 34.5 1.0
O C:HIS91 4.7 44.4 1.0
CB C:LYS94 4.8 65.8 1.0
CA C:LYS94 4.9 64.1 1.0
N C:ASP93 4.9 60.0 1.0
C C:CYS86 5.0 51.5 1.0

Zinc binding site 5 out of 8 in 6bm2

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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:43.1
occ:1.00
 SG I:CYS32 2.5 79.9 1.0
SG I:CYS29 2.5 89.6 1.0
SG I:CYS10 2.5 69.4 1.0
SG I:CYS7 2.7 59.6 1.0
CB I:CYS10 2.9 65.5 1.0
CB I:CYS7 3.5 58.2 1.0
CB I:CYS29 3.5 89.4 1.0
CB I:CYS32 3.6 82.7 1.0
N I:CYS10 3.7 66.4 1.0
N I:CYS32 3.8 83.0 1.0
CA I:CYS10 3.9 65.6 1.0
CB I:THR31 4.0 57.7 1.0
CA I:CYS32 4.3 84.1 1.0
CB I:TYR34 4.3 64.8 1.0
C I:THR31 4.5 60.8 1.0
CA I:THR31 4.7 59.6 1.0
OG1 I:THR31 4.7 56.8 1.0
CG2 I:THR31 4.8 58.1 1.0
N I:THR31 4.8 59.5 1.0
C I:ASP9 4.8 69.4 1.0
C I:CYS10 4.8 64.1 1.0
N I:SER33 4.9 83.9 1.0
N I:TYR34 4.9 68.7 1.0
CB I:ASP9 4.9 71.4 1.0
CA I:CYS29 4.9 90.0 1.0
CA I:CYS7 4.9 57.3 1.0

Zinc binding site 6 out of 8 in 6bm2

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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:28.9
occ:1.00
 SG I:CYS78 2.3 50.6 1.0
SG I:CYS103 2.4 37.8 1.0
SG I:CYS75 2.4 30.4 1.0
SG I:CYS106 2.4 36.2 1.0
CB I:CYS103 3.2 36.1 1.0
CB I:CYS75 3.2 30.0 1.0
CB I:CYS78 3.4 54.0 1.0
N I:CYS78 3.5 52.3 1.0
CB I:CYS106 3.9 38.4 1.0
CA I:CYS78 4.0 53.5 1.0
N I:CYS106 4.0 36.1 1.0
CB I:HIS108 4.2 38.1 1.0
CB I:LYS77 4.2 41.3 1.0
C I:CYS78 4.5 54.0 1.0
CB I:SER105 4.5 60.6 1.0
CA I:CYS106 4.5 37.5 1.0
N I:HIS79 4.5 42.8 1.0
C I:LYS77 4.6 43.4 1.0
CA I:CYS103 4.7 35.0 1.0
N I:SER80 4.7 37.6 1.0
CA I:CYS75 4.7 30.2 1.0
CB I:SER80 4.7 36.9 1.0
CA I:LYS77 4.8 42.3 1.0
N I:LYS77 4.9 40.6 1.0
N I:HIS108 4.9 37.6 1.0
C I:SER105 4.9 60.8 1.0

Zinc binding site 7 out of 8 in 6bm2

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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:27.6
occ:1.00
 SG J:CYS10 2.4 49.5 1.0
SG J:CYS45 2.4 26.7 1.0
SG J:CYS46 2.4 20.1 1.0
SG J:CYS7 2.4 28.7 1.0
CB J:CYS10 3.3 51.1 1.0
CB J:CYS7 3.4 28.1 1.0
N J:CYS46 3.4 19.1 1.0
N J:CYS10 3.5 48.7 1.0
CB J:CYS45 3.5 26.0 1.0
CB J:CYS46 3.7 19.5 1.0
CA J:CYS46 3.9 18.9 1.0
C J:CYS45 3.9 25.4 1.0
CA J:CYS10 4.0 51.8 1.0
CB J:SER9 4.2 34.4 1.0
NE J:ARG43 4.3 46.0 1.0
CA J:CYS45 4.3 25.7 1.0
N J:GLY11 4.4 31.6 1.0
C J:SER9 4.6 35.9 1.0
O J:CYS45 4.6 24.9 1.0
NH2 J:ARG43 4.6 48.5 1.0
CA J:SER9 4.8 34.3 1.0
C J:CYS10 4.8 50.8 1.0
CA J:CYS7 4.8 27.2 1.0
N J:SER9 4.8 32.5 1.0
N J:CYS45 4.9 26.3 1.0
CB J:ARG43 4.9 44.5 1.0
N J:LYS12 4.9 30.8 1.0
CZ J:ARG43 5.0 46.7 1.0
OG J:SER9 5.0 33.4 1.0
CB J:LYS12 5.0 31.6 1.0

Zinc binding site 8 out of 8 in 6bm2

Go back to Zinc Binding Sites List in 6bm2
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:83.3
occ:1.00
 SG L:CYS34 2.4 83.2 1.0
CB L:CYS51 2.4 87.7 1.0
SG L:CYS48 2.5 73.6 1.0
SG L:CYS51 2.5 90.3 1.0
SG L:CYS31 3.0 96.7 1.0
CB L:CYS48 3.4 73.0 1.0
CB L:CYS34 3.6 90.2 1.0
CB L:CYS31 3.6 92.9 1.0
CA L:CYS51 3.9 93.1 1.0
OG L:SER36 4.3 0.8 1.0
O L:LYS49 4.5 0.4 1.0
O L:ASP50 4.6 0.6 1.0
N L:CYS51 4.6 93.8 1.0
CA L:CYS48 4.8 71.8 1.0
CA L:CYS34 4.8 91.2 1.0
C L:ASP50 4.8 0.4 1.0
CB L:SER36 4.9 0.2 1.0
C L:CYS51 4.9 93.6 1.0
N L:GLY52 4.9 95.5 1.0
N L:CYS34 4.9 84.8 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 18:01:07 2024

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