Zinc in PDB 1twg: Rna Polymerase II Complexed with Ctp
Enzymatic activity of Rna Polymerase II Complexed with Ctp
All present enzymatic activity of Rna Polymerase II Complexed with Ctp:
2.7.7.6;
Protein crystallography data
The structure of Rna Polymerase II Complexed with Ctp, PDB code: 1twg
was solved by
K.D.Westover,
D.A.Bushnell,
R.D.Kornberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
3.30
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
123.000,
223.000,
374.000,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.3 /
28.1
|
Other elements in 1twg:
The structure of Rna Polymerase II Complexed with Ctp also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Rna Polymerase II Complexed with Ctp
(pdb code 1twg). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Rna Polymerase II Complexed with Ctp, PDB code: 1twg:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 1 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3006
b:48.2
occ:1.00
|
SG
|
A:CYS110
|
1.2
|
0.2
|
1.0
|
SG
|
A:CYS107
|
1.5
|
0.7
|
1.0
|
SG
|
A:CYS148
|
1.6
|
47.6
|
1.0
|
SG
|
A:CYS167
|
2.2
|
0.5
|
1.0
|
CB
|
A:CYS148
|
2.6
|
55.2
|
1.0
|
CB
|
A:CYS107
|
2.7
|
0.6
|
1.0
|
CB
|
A:CYS167
|
3.1
|
0.2
|
1.0
|
CB
|
A:CYS110
|
3.2
|
0.1
|
1.0
|
O
|
A:GLY166
|
3.9
|
39.4
|
1.0
|
CA
|
A:CYS148
|
4.1
|
31.0
|
1.0
|
N
|
A:CYS110
|
4.2
|
46.5
|
1.0
|
CA
|
A:CYS107
|
4.3
|
42.4
|
1.0
|
CA
|
A:CYS110
|
4.4
|
45.6
|
1.0
|
CA
|
A:CYS167
|
4.4
|
78.3
|
1.0
|
O
|
A:CYS148
|
4.7
|
31.3
|
1.0
|
OE1
|
A:GLN171
|
4.7
|
41.5
|
1.0
|
N
|
A:GLY168
|
4.7
|
54.6
|
1.0
|
C
|
A:CYS107
|
4.8
|
40.8
|
1.0
|
C
|
A:CYS148
|
4.9
|
31.4
|
1.0
|
C
|
A:GLY166
|
4.9
|
40.8
|
1.0
|
C
|
A:CYS167
|
5.0
|
74.3
|
1.0
|
N
|
A:GLY111
|
5.0
|
51.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 2 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3008
b:87.6
occ:1.00
|
SG
|
A:CYS70
|
1.2
|
0.8
|
1.0
|
NE2
|
A:HIS80
|
1.7
|
0.9
|
1.0
|
SG
|
A:CYS77
|
2.1
|
52.0
|
1.0
|
CD2
|
A:HIS80
|
2.5
|
0.7
|
1.0
|
CE1
|
A:HIS80
|
3.0
|
0.3
|
1.0
|
CB
|
A:CYS70
|
3.0
|
0.4
|
1.0
|
SG
|
A:CYS67
|
3.1
|
0.7
|
1.0
|
CB
|
A:CYS67
|
3.5
|
0.1
|
1.0
|
CB
|
A:CYS77
|
3.6
|
69.0
|
1.0
|
CG
|
A:HIS80
|
3.8
|
0.7
|
1.0
|
ND1
|
A:HIS80
|
4.0
|
0.4
|
1.0
|
CA
|
A:CYS77
|
4.3
|
77.6
|
1.0
|
CA
|
A:CYS70
|
4.4
|
0.2
|
1.0
|
C
|
A:CYS70
|
4.5
|
0.3
|
1.0
|
O
|
A:CYS70
|
4.8
|
0.6
|
1.0
|
CD
|
A:PRO78
|
4.9
|
68.7
|
1.0
|
N
|
A:GLN71
|
5.0
|
85.4
|
1.0
|
|
Zinc binding site 3 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 3 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3007
b:37.9
occ:1.00
|
SG
|
B:CYS1185
|
0.9
|
0.0
|
1.0
|
CB
|
B:CYS1185
|
1.9
|
0.0
|
1.0
|
SG
|
B:CYS1182
|
2.1
|
51.0
|
1.0
|
SG
|
B:CYS1163
|
2.2
|
50.7
|
1.0
|
SG
|
B:CYS1166
|
2.2
|
33.3
|
1.0
|
CB
|
B:CYS1163
|
2.8
|
44.0
|
1.0
|
CB
|
B:CYS1166
|
2.9
|
37.2
|
1.0
|
CB
|
B:CYS1182
|
3.2
|
73.4
|
1.0
|
CA
|
B:CYS1185
|
3.6
|
47.7
|
1.0
|
N
|
B:CYS1166
|
4.3
|
29.9
|
1.0
|
N
|
B:CYS1185
|
4.3
|
49.5
|
1.0
|
CA
|
B:CYS1166
|
4.4
|
31.1
|
1.0
|
OG1
|
B:THR1170
|
4.5
|
19.8
|
1.0
|
CG1
|
B:ILE1165
|
4.6
|
73.6
|
1.0
|
CA
|
B:CYS1163
|
4.6
|
36.0
|
1.0
|
CB
|
B:ILE1165
|
4.7
|
70.8
|
1.0
|
CA
|
B:CYS1182
|
4.8
|
94.8
|
1.0
|
C
|
B:CYS1185
|
4.9
|
49.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 4 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn3002
b:35.2
occ:1.00
|
SG
|
C:CYS86
|
1.3
|
9.5
|
1.0
|
SG
|
C:CYS95
|
1.9
|
28.4
|
1.0
|
SG
|
C:CYS92
|
2.2
|
16.4
|
1.0
|
SG
|
C:CYS88
|
2.2
|
23.4
|
1.0
|
CB
|
C:CYS88
|
2.7
|
26.1
|
1.0
|
CB
|
C:CYS95
|
2.9
|
26.2
|
1.0
|
CB
|
C:CYS86
|
3.3
|
20.9
|
1.0
|
CB
|
C:CYS92
|
3.4
|
25.8
|
1.0
|
N
|
C:CYS88
|
3.8
|
6.6
|
1.0
|
N
|
C:CYS92
|
3.8
|
46.4
|
1.0
|
CA
|
C:CYS88
|
3.9
|
11.4
|
1.0
|
N
|
C:CYS95
|
4.0
|
36.4
|
1.0
|
CA
|
C:CYS95
|
4.2
|
35.8
|
1.0
|
C
|
C:HIS91
|
4.2
|
64.7
|
1.0
|
CA
|
C:CYS92
|
4.2
|
47.2
|
1.0
|
O
|
C:CYS92
|
4.5
|
47.0
|
1.0
|
CA
|
C:HIS91
|
4.5
|
63.0
|
1.0
|
CA
|
C:CYS86
|
4.6
|
29.4
|
1.0
|
N
|
C:LYS94
|
4.6
|
28.3
|
1.0
|
C
|
C:CYS92
|
4.6
|
48.2
|
1.0
|
C
|
C:LYS94
|
4.7
|
29.7
|
1.0
|
C
|
C:CYS86
|
4.8
|
28.3
|
1.0
|
O
|
C:HIS91
|
4.9
|
68.7
|
1.0
|
CB
|
C:LYS94
|
5.0
|
79.3
|
1.0
|
C
|
C:CYS88
|
5.0
|
9.5
|
1.0
|
CA
|
C:LYS94
|
5.0
|
32.2
|
1.0
|
|
Zinc binding site 5 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 5 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn3003
b:46.0
occ:1.00
|
SG
|
I:CYS32
|
1.1
|
0.3
|
1.0
|
SG
|
I:CYS7
|
1.5
|
9.6
|
1.0
|
SG
|
I:CYS10
|
1.7
|
50.4
|
1.0
|
SG
|
I:CYS29
|
2.1
|
42.3
|
1.0
|
CB
|
I:CYS32
|
2.5
|
0.5
|
1.0
|
CB
|
I:CYS7
|
2.8
|
24.0
|
1.0
|
CB
|
I:CYS29
|
3.3
|
41.1
|
1.0
|
N
|
I:CYS32
|
3.5
|
58.9
|
1.0
|
CA
|
I:CYS32
|
3.6
|
56.6
|
1.0
|
CB
|
I:CYS10
|
3.6
|
52.6
|
1.0
|
CG2
|
I:THR31
|
4.0
|
35.1
|
1.0
|
N
|
I:CYS10
|
4.1
|
56.8
|
1.0
|
CB
|
I:TYR34
|
4.3
|
2.0
|
1.0
|
CB
|
I:THR31
|
4.4
|
28.6
|
1.0
|
CA
|
I:CYS7
|
4.4
|
18.9
|
1.0
|
CA
|
I:CYS10
|
4.5
|
53.7
|
1.0
|
C
|
I:THR31
|
4.5
|
34.5
|
1.0
|
C
|
I:CYS32
|
4.5
|
59.1
|
1.0
|
CA
|
I:CYS29
|
4.7
|
21.8
|
1.0
|
N
|
I:TYR34
|
4.9
|
1.9
|
1.0
|
CA
|
I:THR31
|
4.9
|
32.6
|
1.0
|
N
|
I:THR31
|
5.0
|
31.3
|
1.0
|
|
Zinc binding site 6 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 6 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn3004
b:49.1
occ:1.00
|
SG
|
I:CYS106
|
1.3
|
48.5
|
1.0
|
SG
|
I:CYS78
|
1.6
|
50.6
|
1.0
|
SG
|
I:CYS75
|
1.8
|
42.2
|
1.0
|
SG
|
I:CYS103
|
2.6
|
58.1
|
1.0
|
CB
|
I:CYS78
|
3.1
|
71.8
|
1.0
|
CB
|
I:CYS106
|
3.1
|
65.5
|
1.0
|
CB
|
I:CYS103
|
3.2
|
48.2
|
1.0
|
CB
|
I:CYS75
|
3.2
|
59.5
|
1.0
|
N
|
I:CYS78
|
3.2
|
91.1
|
1.0
|
CB
|
I:LYS77
|
3.7
|
62.4
|
1.0
|
CA
|
I:CYS78
|
3.8
|
86.3
|
1.0
|
CB
|
I:HIS108
|
3.8
|
55.0
|
1.0
|
N
|
I:LYS77
|
4.2
|
41.7
|
1.0
|
CA
|
I:LYS77
|
4.2
|
42.4
|
1.0
|
C
|
I:LYS77
|
4.2
|
41.6
|
1.0
|
CA
|
I:CYS106
|
4.5
|
56.3
|
1.0
|
CA
|
I:CYS75
|
4.6
|
39.9
|
1.0
|
CG
|
I:HIS108
|
4.6
|
56.8
|
1.0
|
N
|
I:HIS108
|
4.7
|
38.6
|
1.0
|
CA
|
I:CYS103
|
4.7
|
17.8
|
1.0
|
N
|
I:CYS106
|
4.8
|
61.3
|
1.0
|
C
|
I:CYS106
|
4.8
|
55.9
|
1.0
|
CD2
|
I:HIS108
|
4.8
|
61.6
|
1.0
|
CA
|
I:HIS108
|
4.9
|
37.1
|
1.0
|
C
|
I:CYS78
|
4.9
|
87.0
|
1.0
|
O
|
I:CYS106
|
5.0
|
56.6
|
1.0
|
N
|
I:SER107
|
5.0
|
22.7
|
1.0
|
|
Zinc binding site 7 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 7 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn3001
b:31.7
occ:1.00
|
SG
|
J:CYS45
|
1.5
|
61.2
|
1.0
|
SG
|
J:CYS7
|
1.6
|
31.8
|
1.0
|
SG
|
J:CYS10
|
1.9
|
24.3
|
1.0
|
SG
|
J:CYS46
|
2.3
|
1.0
|
1.0
|
N
|
J:CYS46
|
2.8
|
14.8
|
1.0
|
CB
|
J:CYS7
|
2.9
|
28.2
|
1.0
|
CB
|
J:CYS45
|
3.0
|
62.3
|
1.0
|
CB
|
J:CYS10
|
3.0
|
26.5
|
1.0
|
C
|
J:CYS45
|
3.6
|
8.6
|
1.0
|
CA
|
J:CYS46
|
3.7
|
13.8
|
1.0
|
CB
|
J:CYS46
|
3.8
|
1.0
|
1.0
|
N
|
J:CYS10
|
3.8
|
35.3
|
1.0
|
CA
|
J:CYS45
|
3.9
|
6.5
|
1.0
|
CA
|
J:CYS10
|
4.0
|
33.8
|
1.0
|
NE
|
J:ARG43
|
4.2
|
43.5
|
1.0
|
O
|
J:CYS45
|
4.3
|
3.7
|
1.0
|
CA
|
J:CYS7
|
4.6
|
14.7
|
1.0
|
N
|
J:CYS45
|
4.6
|
6.9
|
1.0
|
CG
|
J:ARG43
|
4.6
|
43.0
|
1.0
|
CB
|
J:SER9
|
4.8
|
30.5
|
1.0
|
C
|
J:SER9
|
4.8
|
7.8
|
1.0
|
N
|
J:SER9
|
5.0
|
1.4
|
1.0
|
CZ
|
J:ARG43
|
5.0
|
40.2
|
1.0
|
|
Zinc binding site 8 out
of 8 in 1twg
Go back to
Zinc Binding Sites List in 1twg
Zinc binding site 8 out
of 8 in the Rna Polymerase II Complexed with Ctp
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Rna Polymerase II Complexed with Ctp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn3005
b:84.7
occ:1.00
|
SG
|
L:CYS31
|
1.7
|
0.6
|
1.0
|
SG
|
L:CYS34
|
1.8
|
25.0
|
1.0
|
SG
|
L:CYS48
|
1.9
|
71.5
|
1.0
|
SG
|
L:CYS51
|
2.1
|
89.4
|
1.0
|
CB
|
L:CYS51
|
2.7
|
0.5
|
1.0
|
CB
|
L:CYS34
|
2.9
|
52.0
|
1.0
|
CB
|
L:CYS31
|
3.1
|
0.4
|
1.0
|
CB
|
L:CYS48
|
3.5
|
90.9
|
1.0
|
OG
|
L:SER36
|
3.6
|
51.5
|
1.0
|
O
|
L:CYS51
|
3.6
|
1.0
|
1.0
|
CA
|
L:CYS51
|
3.7
|
0.5
|
1.0
|
N
|
L:CYS51
|
3.8
|
0.8
|
1.0
|
C
|
L:CYS51
|
4.0
|
0.7
|
1.0
|
CA
|
L:CYS34
|
4.0
|
67.0
|
1.0
|
N
|
L:CYS34
|
4.1
|
74.1
|
1.0
|
C
|
L:CYS34
|
4.4
|
66.4
|
1.0
|
O
|
L:CYS34
|
4.6
|
66.7
|
1.0
|
CA
|
L:CYS31
|
4.6
|
0.2
|
1.0
|
N
|
L:HIS53
|
4.6
|
0.8
|
1.0
|
N
|
L:LYS49
|
4.7
|
98.7
|
1.0
|
CA
|
L:CYS48
|
4.8
|
0.2
|
1.0
|
CB
|
L:HIS53
|
4.9
|
0.3
|
1.0
|
N
|
L:SER35
|
4.9
|
47.5
|
1.0
|
N
|
L:ASP50
|
5.0
|
0.8
|
1.0
|
|
Reference:
K.D.Westover,
D.A.Bushnell,
R.D.Kornberg.
Structural Basis of Transcription: Nucleotide Selection By Rotation in the Rna Polymerase II Active Center. Cell(Cambridge,Mass.) V. 119 481 2004.
ISSN: ISSN 0092-8674
PubMed: 15537538
DOI: 10.1016/J.CELL.2004.10.016
Page generated: Wed Oct 16 19:19:04 2024
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