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Zinc in PDB 2ja8: Cpd Lesion Containing Rna Polymerase II Elongation Complex D

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

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

Protein crystallography data

The structure of Cpd Lesion Containing Rna Polymerase II Elongation Complex D, PDB code: 2ja8 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 / 3.8
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.642, 392.845, 282.894, 90.00, 90.00, 90.00
R / Rfree (%) 26.86 / 28.76

Other elements in 2ja8:

The structure of Cpd Lesion Containing Rna Polymerase II Elongation Complex D 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 D (pdb code 2ja8). 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 D, PDB code: 2ja8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2458

b:57.2
occ:1.00
 N J:CYS46 2.2 66.7 1.0
SG J:CYS46 2.2 67.0 1.0
CB J:CYS10 2.4 59.2 1.0
CB J:CYS46 2.4 66.0 1.0
SG J:CYS45 2.5 78.0 1.0
SG J:CYS7 2.5 46.4 1.0
SG J:CYS10 2.5 63.9 1.0
CA J:CYS46 2.6 66.8 1.0
C J:CYS45 2.9 67.5 1.0
CB J:CYS45 3.0 72.0 1.0
N J:CYS10 3.4 55.5 1.0
CA J:CYS10 3.5 57.8 1.0
CA J:CYS45 3.5 69.0 1.0
CB J:CYS7 3.6 47.5 1.0
O J:CYS45 3.7 66.2 1.0
C J:CYS46 4.1 67.3 1.0
OG J:SER9 4.4 46.8 1.0
N J:GLY11 4.4 58.4 1.0
N J:CYS45 4.4 68.6 1.0
C J:CYS10 4.5 57.5 1.0
C J:SER9 4.6 51.9 1.0
N J:ARG47 4.6 69.2 1.0
CB J:SER9 4.7 48.0 1.0
O J:ARG43 4.8 74.2 1.0
CG J:ARG43 4.8 73.4 1.0
NE J:ARG43 4.8 72.6 1.0
CE J:MET49 4.9 75.0 1.0
O J:CYS46 4.9 67.1 1.0
CA J:CYS7 5.0 47.8 1.0

Zinc binding site 2 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2459

b:0.9
occ:1.00
 SG L:CYS34 2.5 0.8 1.0
CB L:CYS48 2.5 0.0 1.0
SG L:CYS48 2.5 0.3 1.0
SG L:CYS31 2.6 0.4 1.0
SG L:CYS51 2.7 0.0 1.0
O L:CYS51 2.9 0.7 1.0
CB L:CYS51 3.2 0.8 1.0
CB L:CYS31 3.4 0.7 1.0
C L:CYS51 3.8 0.8 1.0
CA L:CYS48 3.9 0.5 1.0
CA L:CYS51 3.9 0.7 1.0
CB L:CYS34 4.3 0.5 1.0
CA L:CYS31 4.3 0.0 1.0
N L:CYS51 4.3 0.6 1.0
C L:CYS48 4.4 0.4 1.0
N L:CYS48 4.5 0.1 1.0
O L:GLY52 4.7 0.1 1.0
N L:LYS49 4.7 0.4 1.0
O L:HIS53 4.7 0.2 1.0
O L:CYS34 4.9 0.0 1.0
N L:GLY52 5.0 0.9 1.0
O L:CYS48 5.0 0.3 1.0

Zinc binding site 3 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2460

b:88.1
occ:1.00
 SG I:CYS10 2.3 0.6 1.0
SG I:CYS32 2.3 96.6 1.0
SG I:CYS29 2.6 94.3 1.0
SG I:CYS7 2.6 0.6 1.0
CB I:CYS29 3.2 97.8 1.0
CB I:CYS32 3.3 94.8 1.0
N I:CYS32 3.8 97.8 1.0
CB I:CYS10 3.8 0.9 1.0
O I:CYS10 3.9 0.1 1.0
CB I:CYS7 4.0 0.0 1.0
C I:CYS10 4.1 0.5 1.0
CA I:CYS32 4.2 94.5 1.0
CA I:CYS10 4.3 0.9 1.0
O I:ARG8 4.3 0.6 1.0
N I:CYS10 4.4 0.2 1.0
CB I:THR31 4.5 0.3 1.0
OD2 I:ASP9 4.5 0.8 1.0
CB I:TYR34 4.7 72.8 1.0
CA I:CYS29 4.7 98.2 1.0
C I:THR31 4.8 0.1 1.0
N I:ASN11 4.9 0.4 1.0
C I:CYS32 4.9 92.1 1.0

Zinc binding site 4 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2461

b:0.0
occ:1.00
 SG I:CYS106 2.7 0.4 1.0
CB I:CYS78 3.0 0.9 1.0
CB I:CYS75 3.1 0.1 1.0
CB I:HIS108 3.2 0.5 1.0
N I:CYS78 3.3 0.5 1.0
SG I:CYS78 3.4 0.1 1.0
CA I:CYS78 3.8 0.7 1.0
SG I:CYS75 3.8 0.2 1.0
CB I:CYS103 3.8 0.6 1.0
CG I:HIS108 3.9 1.0 1.0
N I:LYS77 4.1 0.4 1.0
CD2 I:HIS108 4.2 0.3 1.0
CB I:CYS106 4.2 0.2 1.0
SG I:CYS103 4.2 0.5 1.0
CD I:PRO76 4.4 0.6 1.0
C I:LYS77 4.4 0.6 1.0
CB I:LYS77 4.4 0.8 1.0
CA I:CYS75 4.4 0.3 1.0
CA I:HIS108 4.4 0.2 1.0
N I:HIS108 4.5 0.5 1.0
CA I:LYS77 4.6 0.7 1.0
N I:PRO76 4.6 0.0 1.0
C I:CYS75 4.7 0.6 1.0
C I:CYS78 4.9 0.2 1.0

Zinc binding site 5 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2462

b:39.6
occ:1.00
 SG C:CYS88 2.2 49.0 1.0
SG C:CYS86 2.3 48.2 1.0
SG C:CYS95 2.4 66.4 1.0
SG C:CYS92 2.6 71.1 1.0
N C:CYS92 3.0 67.8 1.0
CB C:CYS86 3.1 52.1 1.0
CB C:CYS95 3.3 66.5 1.0
C C:HIS91 3.5 67.2 1.0
CA C:HIS91 3.6 67.7 1.0
CB C:CYS92 3.6 70.3 1.0
CB C:CYS88 3.7 51.8 1.0
CA C:CYS92 3.8 69.7 1.0
O C:CYS92 3.9 70.3 1.0
N C:CYS95 4.1 66.3 1.0
C C:CYS92 4.2 70.4 1.0
CA C:CYS95 4.3 65.4 1.0
O C:CYS86 4.3 55.2 1.0
CA C:CYS86 4.4 54.1 1.0
CB C:HIS91 4.5 66.8 1.0
C C:LYS94 4.5 66.9 1.0
O C:HIS91 4.5 67.2 1.0
N C:HIS91 4.5 69.5 1.0
C C:CYS86 4.6 53.6 1.0
N C:CYS88 4.6 51.1 1.0
CB C:LYS94 4.7 70.4 1.0
CA C:CYS88 4.7 53.1 1.0
O C:CYS88 4.8 56.9 1.0
N C:LYS94 4.9 68.9 1.0
CA C:LYS94 4.9 68.4 1.0

Zinc binding site 6 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2463

b:47.3
occ:1.00
 SG B:CYS1166 2.2 66.2 1.0
SG B:CYS1185 2.3 75.5 1.0
SG B:CYS1182 2.3 72.6 1.0
SG B:CYS1163 2.6 64.3 1.0
CB B:CYS1185 2.6 75.3 1.0
CB B:CYS1163 2.9 61.5 1.0
CB B:CYS1182 3.8 76.4 1.0
CA B:CYS1185 3.9 78.4 1.0
O B:CYS1182 3.9 80.0 1.0
CB B:CYS1166 4.0 67.0 1.0
N B:CYS1185 4.1 80.1 1.0
O B:CYS1166 4.2 66.1 1.0
CA B:CYS1163 4.3 60.2 1.0
N B:CYS1166 4.4 66.8 1.0
C B:CYS1185 4.4 78.2 1.0
OG1 B:THR1170 4.4 58.3 1.0
CB B:THR1170 4.6 56.4 1.0
CG2 B:ILE1165 4.7 73.0 1.0
CA B:CYS1166 4.7 65.8 1.0
N B:ASP1186 4.8 77.6 1.0
C B:CYS1182 4.8 80.1 1.0
C B:CYS1166 4.9 66.1 1.0
CA B:CYS1182 4.9 78.2 1.0
O B:CYS1185 5.0 79.5 1.0
CB B:ILE1165 5.0 71.8 1.0

Zinc binding site 7 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2464

b:87.8
occ:1.00
 SG A:CYS110 2.4 0.2 1.0
SG A:CYS167 2.5 0.2 1.0
SG A:CYS148 2.9 0.0 1.0
CB A:CYS110 3.5 0.2 1.0
O A:CYS167 3.6 0.7 1.0
O A:MET108 3.7 0.4 1.0
CB A:CYS148 3.7 0.0 1.0
CB A:CYS107 4.0 0.8 1.0
O A:CYS107 4.1 0.5 1.0
N A:CYS110 4.2 0.5 1.0
CB A:CYS167 4.2 0.7 1.0
CA A:CYS110 4.4 0.8 1.0
N A:GLY111 4.5 0.8 1.0
C A:CYS107 4.6 0.1 1.0
C A:CYS167 4.6 0.7 1.0
SG A:CYS107 4.6 0.9 1.0
O A:GLY166 4.6 0.2 1.0
C A:CYS110 4.9 0.3 1.0
C A:MET108 4.9 0.3 1.0
CA A:CYS107 4.9 0.9 1.0
CA A:CYS167 4.9 0.4 1.0

Zinc binding site 8 out of 8 in 2ja8

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


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 D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2465

b:39.7
occ:1.00
 NE2 A:HIS80 2.0 57.1 1.0
SG A:CYS77 2.1 85.2 1.0
SG A:CYS70 2.7 0.5 1.0
CB A:CYS67 2.7 0.0 1.0
SG A:CYS67 2.7 97.5 1.0
CD2 A:HIS80 2.9 56.4 1.0
O A:CYS67 3.0 0.4 1.0
CE1 A:HIS80 3.0 57.5 1.0
CB A:CYS70 3.2 0.4 1.0
CB A:CYS77 3.4 76.6 1.0
CA A:CYS67 3.7 0.2 1.0
C A:CYS67 3.8 0.1 1.0
CG A:HIS80 4.0 57.2 1.0
ND1 A:HIS80 4.1 56.1 1.0
CA A:CYS77 4.3 70.4 1.0
O A:PRO78 4.4 61.3 1.0
CA A:CYS70 4.5 0.7 1.0
NE2 A:GLN68 4.7 0.6 1.0
CD A:GLN68 4.7 0.2 1.0
OE1 A:GLN68 4.8 0.1 1.0
C A:CYS77 4.8 65.5 1.0
C A:CYS70 4.8 0.1 1.0
O A:GLN71 4.9 0.5 1.0
N A:CYS67 4.9 0.1 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: ISSN 0036-8075
PubMed: 17290000
DOI: 10.1126/SCIENCE.1135400
Page generated: Thu Oct 17 01:11:43 2024

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