Atomistry » Zinc » PDB 2ja8-2jt6 » 2ja8
Atomistry »
  Zinc »
    PDB 2ja8-2jt6 »
      2ja8 »

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

Go back to Zinc Binding Sites List in 2ja8
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

Go back to Zinc Binding Sites List in 2ja8
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

Go back to Zinc Binding Sites List in 2ja8
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

Go back to Zinc Binding Sites List in 2ja8
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

Go back to Zinc Binding Sites List in 2ja8
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

Go back to Zinc Binding Sites List in 2ja8
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

Go back to Zinc Binding Sites List in 2ja8
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

Go back to Zinc Binding Sites List in 2ja8
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy