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Zinc in PDB 2ja6: Cpd Lesion Containing Rna Polymerase II Elongation Complex B

Enzymatic activity of Cpd Lesion Containing Rna Polymerase II Elongation Complex B

All present enzymatic activity of Cpd Lesion Containing Rna Polymerase II Elongation Complex B:
2.7.7.6;

Protein crystallography data

The structure of Cpd Lesion Containing Rna Polymerase II Elongation Complex B, PDB code: 2ja6 was solved by F.Brueckner, U.Hennecke, T.Carell, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 223.580, 393.491, 283.505, 90.00, 90.00, 90.00
R / Rfree (%) 29.2 / 30.1

Other elements in 2ja6:

The structure of Cpd Lesion Containing Rna Polymerase II Elongation Complex B also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B (pdb code 2ja6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B, PDB code: 2ja6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2ja6

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Zinc binding site 1 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2458

b:72.5
occ:1.00
 N J:CYS46 2.2 88.3 1.0
SG J:CYS46 2.3 84.3 1.0
CB J:CYS46 2.4 85.8 1.0
CB J:CYS10 2.4 78.7 1.0
SG J:CYS45 2.5 0.2 1.0
SG J:CYS10 2.5 82.2 1.0
CA J:CYS46 2.6 87.7 1.0
SG J:CYS7 2.6 71.0 1.0
C J:CYS45 3.1 89.5 1.0
CB J:CYS45 3.1 93.8 1.0
N J:CYS10 3.3 76.9 1.0
CA J:CYS10 3.4 77.9 1.0
CB J:CYS7 3.5 69.1 1.0
CA J:CYS45 3.7 91.0 1.0
O J:CYS45 3.9 89.2 1.0
C J:CYS46 4.0 88.3 1.0
N J:GLY11 4.2 78.8 1.0
C J:CYS10 4.3 78.0 1.0
C J:SER9 4.5 74.8 1.0
CB J:SER9 4.6 72.1 1.0
OG J:SER9 4.6 70.5 1.0
N J:CYS45 4.6 90.1 1.0
N J:ARG47 4.7 89.7 1.0
O J:CYS46 4.9 88.5 1.0
NE J:ARG43 4.9 97.2 1.0
CA J:CYS7 4.9 68.9 1.0
O J:ARG43 4.9 94.4 1.0
CA J:SER9 5.0 72.2 1.0
CE J:MET49 5.0 96.5 1.0

Zinc binding site 2 out of 8 in 2ja6

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Zinc binding site 2 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2459

b:0.3
occ:1.00
 SG L:CYS34 2.4 0.0 1.0
SG L:CYS48 2.5 0.6 1.0
SG L:CYS51 2.6 0.6 1.0
SG L:CYS31 2.6 0.3 1.0
CB L:CYS48 2.6 0.8 1.0
O L:CYS51 3.0 0.3 1.0
CB L:CYS51 3.2 0.1 1.0
CB L:CYS31 3.3 0.8 1.0
C L:CYS51 3.8 0.3 1.0
CA L:CYS51 4.0 0.7 1.0
CA L:CYS48 4.1 0.5 1.0
CB L:CYS34 4.2 1.0 1.0
CA L:CYS31 4.2 0.3 1.0
N L:CYS51 4.4 0.9 1.0
O L:GLY52 4.5 1.0 1.0
C L:CYS48 4.6 0.8 1.0
O L:CYS34 4.7 0.2 1.0
N L:CYS48 4.7 0.8 1.0
N L:LYS49 4.8 0.8 1.0
N L:GLY52 4.9 0.8 1.0
O L:HIS53 5.0 0.1 1.0
C L:GLY52 5.0 0.5 1.0

Zinc binding site 3 out of 8 in 2ja6

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Zinc binding site 3 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2460

b:90.2
occ:1.00
 SG I:CYS10 2.2 0.6 1.0
SG I:CYS7 2.3 0.1 1.0
SG I:CYS32 2.4 0.8 1.0
SG I:CYS29 3.0 0.6 1.0
CB I:CYS32 3.4 0.4 1.0
CB I:CYS29 3.4 0.9 1.0
CB I:CYS10 3.6 0.5 1.0
O I:CYS10 3.7 0.7 1.0
CB I:CYS7 3.8 0.8 1.0
N I:CYS10 3.8 0.8 1.0
C I:CYS10 3.9 0.7 1.0
O I:ARG8 3.9 0.8 1.0
CA I:CYS10 3.9 0.2 1.0
OD2 I:ASP9 4.1 0.6 1.0
N I:CYS32 4.2 0.1 1.0
CA I:CYS32 4.5 0.5 1.0
CB I:TYR34 4.5 84.0 1.0
N I:ASN11 4.6 0.8 1.0
CA I:CYS29 4.9 0.1 1.0
CG I:ASP9 5.0 0.9 1.0
CB I:THR31 5.0 0.5 1.0
C I:ARG8 5.0 0.3 1.0

Zinc binding site 4 out of 8 in 2ja6

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Zinc binding site 4 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2461

b:0.5
occ:1.00
 SG I:CYS106 2.9 0.0 1.0
CB I:CYS75 3.0 0.2 1.0
CB I:CYS78 3.0 0.1 1.0
CB I:HIS108 3.1 0.3 1.0
SG I:CYS78 3.4 0.4 1.0
N I:CYS78 3.4 0.8 1.0
SG I:CYS75 3.7 0.2 1.0
CB I:CYS103 3.7 0.3 1.0
CG I:HIS108 3.8 0.7 1.0
CA I:CYS78 3.9 0.1 1.0
CD2 I:HIS108 4.0 0.8 1.0
SG I:CYS103 4.2 0.2 1.0
N I:LYS77 4.2 0.9 1.0
CA I:CYS75 4.3 0.7 1.0
CA I:HIS108 4.3 0.7 1.0
CD I:PRO76 4.3 0.9 1.0
CB I:CYS106 4.4 0.2 1.0
N I:HIS108 4.4 0.5 1.0
C I:LYS77 4.5 0.1 1.0
N I:PRO76 4.6 0.1 1.0
CB I:LYS77 4.6 0.6 1.0
C I:CYS75 4.6 0.8 1.0
CA I:LYS77 4.7 0.2 1.0
C I:CYS78 4.9 0.7 1.0
C I:HIS108 5.0 0.6 1.0

Zinc binding site 5 out of 8 in 2ja6

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Zinc binding site 5 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2462

b:42.9
occ:1.00
 SG C:CYS86 2.3 62.6 1.0
SG C:CYS95 2.4 76.2 1.0
SG C:CYS88 2.4 67.7 1.0
SG C:CYS92 2.5 84.8 1.0
N C:CYS92 2.9 87.4 1.0
CB C:CYS86 2.9 66.6 1.0
CB C:CYS95 3.3 79.1 1.0
CB C:CYS92 3.5 87.3 1.0
CB C:CYS88 3.6 70.1 1.0
CA C:CYS92 3.6 87.9 1.0
C C:HIS91 3.7 88.4 1.0
O C:CYS92 3.8 88.5 1.0
CA C:HIS91 3.9 90.6 1.0
C C:CYS92 4.1 88.4 1.0
N C:CYS95 4.1 80.9 1.0
O C:CYS86 4.3 72.1 1.0
CA C:CYS86 4.3 69.6 1.0
CA C:CYS95 4.3 79.1 1.0
C C:LYS94 4.4 82.3 1.0
N C:CYS88 4.5 69.8 1.0
C C:CYS86 4.5 70.3 1.0
CA C:CYS88 4.6 71.9 1.0
CB C:LYS94 4.6 84.5 1.0
N C:HIS91 4.7 92.8 1.0
O C:LYS94 4.8 82.0 1.0
O C:HIS91 4.8 87.6 1.0
N C:LYS94 4.8 84.6 1.0
CA C:LYS94 4.9 83.4 1.0
O C:CYS88 4.9 74.1 1.0
CB C:HIS91 4.9 92.4 1.0

Zinc binding site 6 out of 8 in 2ja6

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Zinc binding site 6 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2463

b:62.5
occ:1.00
 SG B:CYS1166 2.2 83.7 1.0
SG B:CYS1182 2.3 99.8 1.0
SG B:CYS1185 2.3 92.5 1.0
SG B:CYS1163 2.5 84.2 1.0
CB B:CYS1185 2.5 92.1 1.0
CB B:CYS1163 2.7 80.4 1.0
CB B:CYS1182 3.7 0.9 1.0
CA B:CYS1185 3.9 94.7 1.0
CB B:CYS1166 3.9 84.7 1.0
O B:CYS1182 4.0 0.0 1.0
O B:CYS1166 4.1 85.5 1.0
CA B:CYS1163 4.1 78.2 1.0
N B:CYS1185 4.2 96.3 1.0
N B:CYS1166 4.3 85.7 1.0
OG1 B:THR1170 4.3 76.8 1.0
C B:CYS1185 4.5 94.4 1.0
CA B:CYS1166 4.6 84.8 1.0
CB B:THR1170 4.6 76.8 1.0
C B:CYS1166 4.8 85.2 1.0
C B:CYS1182 4.9 0.4 1.0
CA B:CYS1182 4.9 0.2 1.0
N B:ASP1186 4.9 94.0 1.0
N B:CYS1163 5.0 75.4 1.0

Zinc binding site 7 out of 8 in 2ja6

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Zinc binding site 7 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2464

b:94.0
occ:1.00
 SG A:CYS110 2.5 0.1 1.0
SG A:CYS167 2.7 0.7 1.0
SG A:CYS148 2.9 0.4 1.0
O A:MET108 3.5 0.1 1.0
CB A:CYS110 3.6 0.1 1.0
O A:CYS167 3.6 0.8 1.0
CB A:CYS148 3.7 0.3 1.0
CB A:CYS107 3.9 0.8 1.0
N A:CYS110 4.2 0.1 1.0
O A:CYS107 4.2 0.0 1.0
CA A:CYS110 4.4 0.4 1.0
N A:GLY111 4.4 0.0 1.0
CB A:CYS167 4.4 0.1 1.0
C A:CYS107 4.5 0.4 1.0
SG A:CYS107 4.5 0.4 1.0
C A:CYS167 4.7 0.3 1.0
O A:GLY166 4.7 0.1 1.0
C A:MET108 4.7 0.8 1.0
CA A:CYS107 4.7 0.6 1.0
C A:CYS110 4.8 1.0 1.0

Zinc binding site 8 out of 8 in 2ja6

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Zinc binding site 8 out of 8 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cpd Lesion Containing Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2465

b:62.6
occ:1.00
 SG A:CYS77 2.2 0.0 1.0
NE2 A:HIS80 2.2 80.0 1.0
CB A:CYS67 2.5 0.5 1.0
SG A:CYS70 2.5 0.6 1.0
SG A:CYS67 2.7 0.0 1.0
O A:CYS67 2.8 0.8 1.0
CE1 A:HIS80 3.1 80.7 1.0
CD2 A:HIS80 3.1 79.8 1.0
CB A:CYS70 3.1 0.2 1.0
CA A:CYS67 3.5 0.2 1.0
C A:CYS67 3.6 0.5 1.0
CB A:CYS77 3.6 98.7 1.0
ND1 A:HIS80 4.1 79.8 1.0
CG A:HIS80 4.1 80.0 1.0
OE1 A:GLN68 4.3 0.9 1.0
CA A:CYS70 4.5 0.2 1.0
NE2 A:GLN68 4.5 0.5 1.0
CD A:GLN68 4.5 0.9 1.0
CA A:CYS77 4.6 94.1 1.0
O A:PRO78 4.7 83.0 1.0
N A:CYS67 4.7 0.6 1.0
O A:GLN71 4.8 0.2 1.0
C A:CYS70 4.8 0.6 1.0
N A:GLN68 4.9 0.2 1.0

Reference:

F.Brueckner, U.Hennecke, T.Carell, P.Cramer. Cpd Damage Recognition By Transcribing Rna Polymerase II. Science V. 315 859 2007.
ISSN: ESSN 1095-9203
PubMed: 17290000
DOI: 10.1126/SCIENCE.1135400
Page generated: Thu Oct 17 01:08:45 2024

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