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:
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
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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
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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
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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
|