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Zinc in PDB 2ja7: Cpd Lesion Containing Rna Polymerase II Elongation Complex C

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

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

Protein crystallography data

The structure of Cpd Lesion Containing Rna Polymerase II Elongation Complex C, PDB code: 2ja7 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 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 394.358, 221.862, 283.105, 90.00, 90.56, 90.00
R / Rfree (%) 25.74 / 27.47

Other elements in 2ja7:

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

Bromine (Br) 2 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C (pdb code 2ja7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C, PDB code: 2ja7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 2ja7

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Zinc binding site 1 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2471

b:90.9
occ:1.00
 SG A:CYS110 2.5 0.6 1.0
SG A:CYS167 2.6 0.1 1.0
SG A:CYS148 2.8 0.8 1.0
O A:CYS167 3.5 0.8 1.0
CB A:CYS148 3.6 0.0 1.0
O A:MET108 3.6 0.1 1.0
CB A:CYS110 3.8 0.2 1.0
CB A:CYS107 3.9 0.3 1.0
O A:CYS107 4.0 0.2 1.0
CB A:CYS167 4.3 0.7 1.0
N A:CYS110 4.3 0.8 1.0
C A:CYS107 4.4 0.5 1.0
SG A:CYS107 4.5 0.4 1.0
C A:CYS167 4.5 0.7 1.0
CA A:CYS110 4.6 0.0 1.0
N A:GLY111 4.6 0.5 1.0
CA A:CYS107 4.8 0.3 1.0
C A:MET108 4.8 0.5 1.0
O A:GLY166 4.8 0.9 1.0
CA A:CYS167 4.9 0.7 1.0

Zinc binding site 2 out of 16 in 2ja7

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Zinc binding site 2 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2472

b:52.3
occ:1.00
 NE2 A:HIS80 2.0 65.5 1.0
SG A:CYS77 2.1 96.0 1.0
SG A:CYS70 2.6 0.5 1.0
CB A:CYS67 2.7 0.5 1.0
SG A:CYS67 2.8 0.2 1.0
CD2 A:HIS80 2.9 65.5 1.0
CE1 A:HIS80 3.0 66.3 1.0
O A:CYS67 3.0 0.6 1.0
CB A:CYS70 3.1 0.7 1.0
CB A:CYS77 3.5 87.1 1.0
CA A:CYS67 3.7 0.4 1.0
C A:CYS67 3.7 0.6 1.0
CG A:HIS80 3.9 66.3 1.0
ND1 A:HIS80 4.0 65.2 1.0
CA A:CYS77 4.4 80.4 1.0
O A:PRO78 4.5 70.0 1.0
CA A:CYS70 4.5 0.4 1.0
NE2 A:GLN68 4.7 0.8 1.0
CD A:GLN68 4.8 0.4 1.0
OE1 A:GLN68 4.8 0.4 1.0
C A:CYS77 4.8 74.9 1.0
C A:CYS70 4.9 0.8 1.0
O A:GLN71 4.9 0.3 1.0
N A:CYS67 4.9 0.1 1.0

Zinc binding site 3 out of 16 in 2ja7

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Zinc binding site 3 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2457

b:53.7
occ:1.00
 SG B:CYS1185 2.2 83.7 1.0
SG B:CYS1166 2.3 72.1 1.0
SG B:CYS1182 2.3 86.9 1.0
SG B:CYS1163 2.5 67.1 1.0
CB B:CYS1185 2.5 83.5 1.0
CB B:CYS1163 2.9 64.5 1.0
CB B:CYS1182 3.8 89.6 1.0
CA B:CYS1185 3.8 86.5 1.0
O B:CYS1182 3.9 92.1 1.0
CB B:CYS1166 4.0 73.2 1.0
N B:CYS1185 4.0 88.4 1.0
O B:CYS1166 4.3 72.8 1.0
N B:CYS1166 4.4 73.0 1.0
OG1 B:THR1170 4.4 68.1 1.0
CA B:CYS1163 4.4 62.4 1.0
C B:CYS1185 4.4 86.5 1.0
CB B:THR1170 4.6 65.9 1.0
N B:ASP1186 4.7 86.2 1.0
CA B:CYS1166 4.7 72.4 1.0
C B:CYS1182 4.8 92.2 1.0
CG2 B:ILE1165 4.8 79.5 1.0
CA B:CYS1182 4.9 90.8 1.0
C B:CYS1166 5.0 73.2 1.0
O B:CYS1185 5.0 88.0 1.0
CB B:ILE1165 5.0 78.0 1.0

Zinc binding site 4 out of 16 in 2ja7

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Zinc binding site 4 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2457

b:48.7
occ:1.00
 SG C:CYS88 2.3 60.6 1.0
SG C:CYS86 2.3 54.0 1.0
SG C:CYS95 2.4 74.9 1.0
SG C:CYS92 2.5 76.5 1.0
CB C:CYS86 2.8 60.1 1.0
N C:CYS92 3.1 79.8 1.0
CB C:CYS95 3.2 73.8 1.0
C C:HIS91 3.6 80.7 1.0
CB C:CYS92 3.6 78.8 1.0
CA C:HIS91 3.7 81.6 1.0
CB C:CYS88 3.8 64.0 1.0
CA C:CYS92 3.8 79.3 1.0
O C:CYS92 3.9 79.2 1.0
N C:CYS95 4.1 73.2 1.0
CA C:CYS86 4.2 62.0 1.0
C C:CYS92 4.3 79.5 1.0
O C:CYS86 4.3 63.7 1.0
CA C:CYS95 4.3 72.5 1.0
C C:CYS86 4.4 62.9 1.0
C C:LYS94 4.5 73.8 1.0
N C:CYS88 4.5 63.5 1.0
O C:HIS91 4.6 81.0 1.0
CB C:HIS91 4.6 82.4 1.0
N C:HIS91 4.6 82.8 1.0
O C:CYS88 4.7 68.7 1.0
CB C:LYS94 4.7 77.0 1.0
CA C:CYS88 4.7 65.1 1.0
N C:LYS94 4.9 75.7 1.0
CA C:LYS94 4.9 75.1 1.0
O C:LYS94 4.9 72.8 1.0

Zinc binding site 5 out of 16 in 2ja7

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Zinc binding site 5 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2457

b:0.3
occ:1.00
 SG I:CYS106 2.4 0.6 1.0
CB I:CYS78 2.8 1.0 1.0
CB I:CYS75 3.0 0.1 1.0
CB I:HIS108 3.2 0.4 1.0
SG I:CYS78 3.2 0.3 1.0
N I:CYS78 3.3 0.7 1.0
SG I:CYS75 3.6 0.9 1.0
CA I:CYS78 3.7 0.9 1.0
CB I:CYS103 3.8 0.9 1.0
CB I:CYS106 3.9 0.9 1.0
CG I:HIS108 3.9 0.6 1.0
SG I:CYS103 4.1 0.1 1.0
N I:LYS77 4.2 0.7 1.0
CD2 I:HIS108 4.2 0.1 1.0
CA I:CYS75 4.4 0.4 1.0
C I:LYS77 4.4 0.1 1.0
CA I:HIS108 4.4 0.8 1.0
CD I:PRO76 4.4 0.9 1.0
CB I:LYS77 4.5 0.4 1.0
N I:HIS108 4.5 0.6 1.0
CA I:LYS77 4.6 0.1 1.0
N I:PRO76 4.6 0.3 1.0
C I:CYS75 4.7 0.2 1.0
C I:CYS78 4.8 0.4 1.0

Zinc binding site 6 out of 16 in 2ja7

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Zinc binding site 6 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2458

b:94.5
occ:1.00
 SG I:CYS32 2.3 0.8 1.0
SG I:CYS10 2.3 0.8 1.0
SG I:CYS7 2.3 0.2 1.0
SG I:CYS29 2.7 0.9 1.0
CB I:CYS29 3.1 0.6 1.0
CB I:CYS32 3.4 0.3 1.0
CB I:CYS7 3.5 0.3 1.0
CB I:CYS10 3.9 0.7 1.0
O I:ARG8 4.0 0.0 1.0
O I:CYS10 4.2 0.4 1.0
N I:CYS32 4.3 0.2 1.0
C I:CYS10 4.3 0.5 1.0
CB I:TYR34 4.3 81.7 1.0
OD2 I:ASP9 4.4 0.0 1.0
N I:CYS10 4.4 0.6 1.0
CA I:CYS10 4.4 0.4 1.0
CA I:CYS32 4.5 0.7 1.0
CA I:CYS29 4.6 0.5 1.0
CA I:CYS7 4.9 0.1 1.0
N I:ASN11 4.9 0.4 1.0

Zinc binding site 7 out of 16 in 2ja7

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Zinc binding site 7 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2457

b:70.6
occ:1.00
 N J:CYS46 2.2 76.6 1.0
SG J:CYS46 2.2 76.9 1.0
CB J:CYS10 2.3 67.9 1.0
CB J:CYS46 2.4 76.0 1.0
SG J:CYS10 2.5 71.8 1.0
SG J:CYS45 2.5 84.2 1.0
SG J:CYS7 2.5 55.6 1.0
CA J:CYS46 2.6 76.9 1.0
C J:CYS45 2.9 77.0 1.0
CB J:CYS45 3.0 80.5 1.0
N J:CYS10 3.3 65.2 1.0
CA J:CYS10 3.4 67.3 1.0
CB J:CYS7 3.6 55.4 1.0
CA J:CYS45 3.6 78.0 1.0
O J:CYS45 3.7 76.0 1.0
C J:CYS46 4.1 77.8 1.0
N J:GLY11 4.2 68.8 1.0
C J:CYS10 4.3 67.6 1.0
OG J:SER9 4.4 57.1 1.0
N J:CYS45 4.5 77.6 1.0
C J:SER9 4.6 62.5 1.0
NE J:ARG43 4.7 84.1 1.0
N J:ARG47 4.7 79.5 1.0
CB J:SER9 4.8 58.5 1.0
CG J:ARG43 4.8 84.4 1.0
O J:CYS46 4.9 78.4 1.0
O J:ARG43 4.9 82.3 1.0
CE J:MET49 5.0 90.3 1.0
CA J:CYS7 5.0 56.7 1.0

Zinc binding site 8 out of 16 in 2ja7

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Zinc binding site 8 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


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 C within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn2457

b:0.4
occ:1.00
 SG L:CYS34 2.4 0.8 1.0
CB L:CYS48 2.5 0.9 1.0
SG L:CYS48 2.5 0.8 1.0
SG L:CYS51 2.6 0.5 1.0
SG L:CYS31 2.6 0.9 1.0
O L:CYS51 2.9 0.3 1.0
CB L:CYS51 3.2 0.1 1.0
CB L:CYS31 3.4 0.8 1.0
C L:CYS51 3.8 0.3 1.0
CA L:CYS48 3.9 0.1 1.0
CA L:CYS51 3.9 0.1 1.0
CB L:CYS34 4.2 0.2 1.0
CA L:CYS31 4.2 0.2 1.0
N L:CYS51 4.3 0.5 1.0
C L:CYS48 4.4 0.9 1.0
N L:CYS48 4.6 0.5 1.0
N L:LYS49 4.6 0.8 1.0
O L:GLY52 4.8 0.3 1.0
O L:CYS34 4.9 0.2 1.0
O L:HIS53 4.9 0.5 1.0
N L:GLY52 5.0 0.6 1.0

Zinc binding site 9 out of 16 in 2ja7

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Zinc binding site 9 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cpd Lesion Containing Rna Polymerase II Elongation Complex C within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn2457

b:87.9
occ:1.00
 SG M:CYS110 2.3 0.2 1.0
SG M:CYS167 2.5 0.4 1.0
SG M:CYS148 2.8 0.5 1.0
O M:CYS167 3.5 0.4 1.0
O M:MET108 3.6 0.5 1.0
CB M:CYS110 3.6 0.8 1.0
CB M:CYS148 3.6 0.7 1.0
CB M:CYS107 3.9 0.8 1.0
O M:CYS107 4.0 0.5 1.0
N M:CYS110 4.2 0.0 1.0
CB M:CYS167 4.2 0.4 1.0
C M:CYS107 4.4 0.7 1.0
CA M:CYS110 4.4 0.1 1.0
SG M:CYS107 4.5 0.1 1.0
N M:GLY111 4.6 0.7 1.0
C M:CYS167 4.6 0.5 1.0
CA M:CYS107 4.7 0.2 1.0
C M:MET108 4.8 0.6 1.0
O M:GLY166 4.8 0.4 1.0
C M:CYS110 4.9 0.6 1.0
CA M:CYS167 4.9 0.9 1.0

Zinc binding site 10 out of 16 in 2ja7

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Zinc binding site 10 out of 16 in the Cpd Lesion Containing Rna Polymerase II Elongation Complex C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cpd Lesion Containing Rna Polymerase II Elongation Complex C within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn2458

b:51.7
occ:1.00
 SG M:CYS77 2.1 95.8 1.0
NE2 M:HIS80 2.2 71.5 1.0
CB M:CYS67 2.6 0.4 1.0
SG M:CYS70 2.6 0.1 1.0
SG M:CYS67 2.7 0.8 1.0
O M:CYS67 3.0 0.9 1.0
CD2 M:HIS80 3.0 71.3 1.0
CB M:CYS70 3.1 0.9 1.0
CE1 M:HIS80 3.2 71.8 1.0
CB M:CYS77 3.4 88.2 1.0
CA M:CYS67 3.7 0.0 1.0
C M:CYS67 3.7 0.8 1.0
CG M:HIS80 4.1 72.1 1.0
ND1 M:HIS80 4.2 70.7 1.0
CA M:CYS77 4.3 82.7 1.0
O M:PRO78 4.5 75.3 1.0
CA M:CYS70 4.5 0.8 1.0
NE2 M:GLN68 4.7 0.7 1.0
C M:CYS70 4.8 0.4 1.0
O M:GLN71 4.8 0.3 1.0
C M:CYS77 4.8 78.5 1.0
CD M:GLN68 4.8 0.8 1.0
N M:CYS67 4.9 0.8 1.0
OE1 M:GLN68 4.9 0.3 1.0
O M:CYS70 5.0 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 01:09:13 2024

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