Zinc in PDB 3gtq: Backtracked Rna Polymerase II Complex Induced By Damage
Enzymatic activity of Backtracked Rna Polymerase II Complex Induced By Damage
All present enzymatic activity of Backtracked Rna Polymerase II Complex Induced By Damage:
2.7.7.6;
Protein crystallography data
The structure of Backtracked Rna Polymerase II Complex Induced By Damage, PDB code: 3gtq
was solved by
D.Wang,
D.A.Bushnell,
X.Huang,
K.D.Westover,
M.Levitt,
R.D.Kornberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
3.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
168.186,
221.581,
192.800,
90.00,
101.81,
90.00
|
R / Rfree (%)
|
27.1 /
33.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Backtracked Rna Polymerase II Complex Induced By Damage
(pdb code 3gtq). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Backtracked Rna Polymerase II Complex Induced By Damage, PDB code: 3gtq:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 1 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1734
b:0.4
occ:1.00
|
SG
|
A:CYS167
|
2.3
|
0.8
|
1.0
|
CB
|
A:CYS110
|
3.0
|
0.8
|
1.0
|
SG
|
A:CYS110
|
3.4
|
0.5
|
1.0
|
SG
|
A:CYS148
|
3.5
|
0.6
|
1.0
|
CB
|
A:CYS167
|
3.8
|
0.1
|
1.0
|
O
|
A:MET108
|
3.8
|
0.5
|
1.0
|
SG
|
A:CYS107
|
4.2
|
0.1
|
1.0
|
CA
|
A:CYS110
|
4.2
|
0.8
|
1.0
|
CB
|
A:CYS107
|
4.2
|
0.3
|
1.0
|
N
|
A:GLY111
|
4.3
|
0.5
|
1.0
|
N
|
A:CYS110
|
4.3
|
0.4
|
1.0
|
O
|
A:CYS167
|
4.6
|
0.7
|
1.0
|
N
|
A:CYS167
|
4.6
|
0.5
|
1.0
|
CA
|
A:CYS167
|
4.7
|
0.1
|
1.0
|
C
|
A:CYS110
|
4.8
|
0.1
|
1.0
|
CB
|
A:CYS148
|
4.9
|
0.9
|
1.0
|
C
|
A:CYS167
|
5.0
|
0.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 2 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1735
b:0.1
occ:1.00
|
SG
|
A:CYS77
|
1.8
|
1.0
|
1.0
|
CE1
|
A:HIS80
|
2.2
|
0.4
|
1.0
|
SG
|
A:CYS70
|
2.4
|
0.5
|
1.0
|
CB
|
A:CYS67
|
2.6
|
0.4
|
1.0
|
SG
|
A:CYS67
|
2.8
|
0.1
|
1.0
|
ND1
|
A:HIS80
|
2.9
|
0.6
|
1.0
|
CB
|
A:CYS77
|
3.0
|
0.7
|
1.0
|
NE2
|
A:HIS80
|
3.3
|
0.5
|
1.0
|
CA
|
A:CYS77
|
3.6
|
0.3
|
1.0
|
CB
|
A:CYS70
|
3.8
|
0.5
|
1.0
|
NE2
|
A:GLN68
|
4.1
|
0.4
|
1.0
|
CA
|
A:CYS67
|
4.1
|
0.9
|
1.0
|
CG
|
A:HIS80
|
4.2
|
0.9
|
1.0
|
CD2
|
A:HIS80
|
4.4
|
0.9
|
1.0
|
CD
|
A:PRO78
|
4.4
|
0.8
|
1.0
|
C
|
A:CYS77
|
4.5
|
0.1
|
1.0
|
O
|
A:CYS67
|
4.5
|
0.5
|
1.0
|
O
|
A:GLN71
|
4.5
|
0.1
|
1.0
|
C
|
A:CYS67
|
4.6
|
0.4
|
1.0
|
N
|
A:CYS77
|
4.7
|
0.3
|
1.0
|
N
|
A:PRO78
|
4.8
|
0.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 3 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1307
b:0.7
occ:1.00
|
SG
|
B:CYS1166
|
1.9
|
0.6
|
1.0
|
SG
|
B:CYS1163
|
2.5
|
97.9
|
1.0
|
SG
|
B:CYS1182
|
2.5
|
0.1
|
1.0
|
CB
|
B:CYS1166
|
3.0
|
0.6
|
1.0
|
SG
|
B:CYS1185
|
3.0
|
0.2
|
1.0
|
CB
|
B:CYS1163
|
3.1
|
99.1
|
1.0
|
CB
|
B:CYS1185
|
3.3
|
0.2
|
1.0
|
N
|
B:CYS1166
|
3.7
|
0.4
|
1.0
|
CA
|
B:CYS1166
|
3.9
|
0.1
|
1.0
|
OG1
|
B:THR1170
|
4.3
|
0.1
|
1.0
|
CB
|
B:CYS1182
|
4.3
|
0.9
|
1.0
|
N
|
B:GLY1167
|
4.5
|
0.0
|
1.0
|
CA
|
B:CYS1163
|
4.5
|
99.2
|
1.0
|
CB
|
B:THR1170
|
4.7
|
0.8
|
1.0
|
C
|
B:CYS1166
|
4.7
|
0.4
|
1.0
|
CA
|
B:CYS1185
|
4.8
|
0.8
|
1.0
|
O
|
B:CYS1182
|
4.9
|
0.5
|
1.0
|
C
|
B:ILE1165
|
4.9
|
0.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 4 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn319
b:84.0
occ:1.00
|
SG
|
C:CYS95
|
2.0
|
80.3
|
1.0
|
SG
|
C:CYS88
|
2.1
|
91.7
|
1.0
|
SG
|
C:CYS86
|
2.7
|
93.6
|
1.0
|
SG
|
C:CYS92
|
2.8
|
92.0
|
1.0
|
CB
|
C:CYS95
|
3.1
|
81.2
|
1.0
|
CB
|
C:CYS92
|
3.4
|
91.6
|
1.0
|
CB
|
C:CYS86
|
3.4
|
93.3
|
1.0
|
N
|
C:CYS92
|
3.5
|
92.3
|
1.0
|
CB
|
C:CYS88
|
3.7
|
93.0
|
1.0
|
CA
|
C:CYS92
|
3.9
|
91.5
|
1.0
|
C
|
C:HIS91
|
3.9
|
93.4
|
1.0
|
N
|
C:CYS95
|
4.0
|
82.9
|
1.0
|
O
|
C:CYS92
|
4.1
|
90.9
|
1.0
|
CA
|
C:CYS95
|
4.2
|
81.1
|
1.0
|
O
|
C:HIS91
|
4.3
|
93.4
|
1.0
|
O
|
C:ASP90
|
4.3
|
95.0
|
1.0
|
C
|
C:CYS92
|
4.3
|
90.8
|
1.0
|
N
|
C:CYS88
|
4.4
|
92.9
|
1.0
|
CA
|
C:CYS88
|
4.6
|
93.2
|
1.0
|
CA
|
C:HIS91
|
4.7
|
94.2
|
1.0
|
CA
|
C:CYS86
|
4.7
|
93.4
|
1.0
|
O
|
C:CYS88
|
4.8
|
94.4
|
1.0
|
C
|
C:CYS86
|
4.8
|
93.5
|
1.0
|
O
|
C:SER83
|
4.9
|
92.8
|
1.0
|
C
|
C:LYS94
|
4.9
|
84.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 5 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn203
b:1.0
occ:1.00
|
SG
|
I:CYS10
|
2.0
|
0.6
|
1.0
|
CB
|
I:CYS7
|
2.5
|
0.8
|
1.0
|
SG
|
I:CYS7
|
2.7
|
0.1
|
1.0
|
CB
|
I:CYS10
|
3.3
|
0.5
|
1.0
|
N
|
I:ASN11
|
3.5
|
1.0
|
1.0
|
N
|
I:CYS10
|
3.5
|
0.4
|
1.0
|
N
|
I:ASN12
|
3.5
|
1.0
|
1.0
|
CA
|
I:CYS10
|
3.5
|
0.1
|
1.0
|
CB
|
I:CYS29
|
3.6
|
0.8
|
1.0
|
C
|
I:CYS10
|
3.6
|
0.2
|
1.0
|
SG
|
I:CYS29
|
3.7
|
0.6
|
1.0
|
SG
|
I:CYS32
|
3.7
|
0.1
|
1.0
|
CD2
|
I:LEU14
|
3.8
|
0.8
|
1.0
|
CA
|
I:CYS7
|
3.8
|
0.7
|
1.0
|
CA
|
I:ASN11
|
4.0
|
0.6
|
1.0
|
O
|
I:ASN12
|
4.0
|
0.5
|
1.0
|
N
|
I:CYS7
|
4.2
|
0.2
|
1.0
|
C
|
I:ASN11
|
4.2
|
0.1
|
1.0
|
CA
|
I:ASN12
|
4.3
|
0.9
|
1.0
|
CB
|
I:ASN12
|
4.4
|
0.6
|
1.0
|
C
|
I:CYS7
|
4.5
|
0.2
|
1.0
|
O
|
I:CYS10
|
4.5
|
1.0
|
1.0
|
C
|
I:ASN12
|
4.5
|
0.4
|
1.0
|
OG1
|
I:THR31
|
4.5
|
99.4
|
1.0
|
C
|
I:ASP9
|
4.7
|
0.7
|
1.0
|
CB
|
I:TYR34
|
4.8
|
98.1
|
1.0
|
N
|
I:ASP9
|
4.9
|
0.1
|
1.0
|
N
|
I:ARG8
|
5.0
|
0.4
|
1.0
|
O
|
I:CYS7
|
5.0
|
0.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 6 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn204
b:0.5
occ:1.00
|
SG
|
I:CYS75
|
1.9
|
96.8
|
1.0
|
SG
|
I:CYS106
|
2.0
|
90.5
|
1.0
|
CB
|
I:CYS78
|
2.5
|
92.5
|
1.0
|
SG
|
I:CYS78
|
2.7
|
92.6
|
1.0
|
SG
|
I:CYS103
|
3.0
|
79.3
|
1.0
|
CB
|
I:CYS75
|
3.1
|
96.1
|
1.0
|
N
|
I:CYS78
|
3.2
|
93.5
|
1.0
|
CB
|
I:CYS103
|
3.2
|
80.6
|
1.0
|
CA
|
I:CYS78
|
3.4
|
93.0
|
1.0
|
CD2
|
I:HIS108
|
3.6
|
86.9
|
1.0
|
CB
|
I:HIS108
|
3.7
|
88.4
|
1.0
|
CB
|
I:CYS106
|
3.8
|
88.7
|
1.0
|
O
|
I:CYS75
|
3.9
|
95.7
|
1.0
|
CG
|
I:HIS108
|
4.0
|
87.6
|
1.0
|
CG
|
I:LYS77
|
4.3
|
95.3
|
1.0
|
CA
|
I:CYS75
|
4.3
|
95.9
|
1.0
|
C
|
I:CYS75
|
4.3
|
95.6
|
1.0
|
C
|
I:LYS77
|
4.4
|
94.1
|
1.0
|
C
|
I:CYS78
|
4.5
|
92.3
|
1.0
|
N
|
I:HIS79
|
4.5
|
91.7
|
1.0
|
N
|
I:CYS106
|
4.5
|
87.8
|
1.0
|
CA
|
I:CYS106
|
4.7
|
88.5
|
1.0
|
CA
|
I:CYS103
|
4.7
|
80.7
|
1.0
|
N
|
I:LYS77
|
4.7
|
94.8
|
1.0
|
N
|
I:HIS108
|
4.7
|
88.6
|
1.0
|
CA
|
I:HIS108
|
4.8
|
88.7
|
1.0
|
CA
|
I:LYS77
|
4.9
|
94.4
|
1.0
|
O
|
I:HIS108
|
4.9
|
89.2
|
1.0
|
NE2
|
I:HIS108
|
4.9
|
87.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 7 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:0.9
occ:1.00
|
SG
|
J:CYS46
|
1.9
|
64.1
|
1.0
|
SG
|
J:CYS45
|
1.9
|
64.1
|
1.0
|
SG
|
J:CYS7
|
1.9
|
73.1
|
1.0
|
CB
|
J:CYS10
|
2.6
|
69.7
|
1.0
|
SG
|
J:CYS10
|
2.6
|
68.3
|
1.0
|
N
|
J:CYS46
|
2.9
|
67.1
|
1.0
|
CB
|
J:CYS46
|
2.9
|
66.2
|
1.0
|
CA
|
J:CYS46
|
3.1
|
66.9
|
1.0
|
CB
|
J:CYS45
|
3.1
|
66.5
|
1.0
|
C
|
J:CYS45
|
3.3
|
66.9
|
1.0
|
N
|
J:CYS10
|
3.4
|
69.4
|
1.0
|
CA
|
J:CYS10
|
3.5
|
70.0
|
1.0
|
CB
|
J:CYS7
|
3.5
|
69.8
|
1.0
|
OG
|
J:SER9
|
3.9
|
68.8
|
1.0
|
CA
|
J:CYS45
|
3.9
|
66.5
|
1.0
|
O
|
J:CYS45
|
3.9
|
66.4
|
1.0
|
O
|
J:CYS7
|
4.2
|
68.5
|
1.0
|
N
|
J:GLY11
|
4.2
|
71.5
|
1.0
|
C
|
J:SER9
|
4.3
|
69.3
|
1.0
|
C
|
J:CYS10
|
4.3
|
70.7
|
1.0
|
CD
|
J:ARG43
|
4.4
|
73.6
|
1.0
|
C
|
J:CYS7
|
4.5
|
68.9
|
1.0
|
N
|
J:SER9
|
4.6
|
69.1
|
1.0
|
CA
|
J:CYS7
|
4.6
|
69.5
|
1.0
|
C
|
J:CYS46
|
4.7
|
67.4
|
1.0
|
CG
|
J:ARG43
|
4.7
|
70.7
|
1.0
|
CA
|
J:SER9
|
4.8
|
69.2
|
1.0
|
CB
|
J:SER9
|
4.9
|
69.1
|
1.0
|
N
|
J:CYS45
|
4.9
|
66.8
|
1.0
|
|
Zinc binding site 8 out
of 8 in 3gtq
Go back to
Zinc Binding Sites List in 3gtq
Zinc binding site 8 out
of 8 in the Backtracked Rna Polymerase II Complex Induced By Damage
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Backtracked Rna Polymerase II Complex Induced By Damage within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn105
b:0.6
occ:1.00
|
SG
|
L:CYS51
|
2.0
|
1.0
|
1.0
|
SG
|
L:CYS34
|
2.1
|
0.0
|
1.0
|
SG
|
L:CYS48
|
2.1
|
0.4
|
1.0
|
CB
|
L:CYS51
|
2.8
|
0.8
|
1.0
|
CB
|
L:CYS31
|
3.4
|
0.9
|
1.0
|
CB
|
L:CYS48
|
3.6
|
0.7
|
1.0
|
CB
|
L:CYS34
|
3.7
|
0.2
|
1.0
|
SG
|
L:CYS31
|
3.8
|
0.6
|
1.0
|
CA
|
L:CYS51
|
4.1
|
0.5
|
1.0
|
CB
|
L:SER36
|
4.1
|
0.3
|
1.0
|
N
|
L:CYS51
|
4.3
|
0.6
|
1.0
|
CD1
|
L:LEU38
|
4.6
|
0.9
|
1.0
|
CA
|
L:CYS34
|
4.7
|
0.2
|
1.0
|
CA
|
L:CYS31
|
4.7
|
0.9
|
1.0
|
N
|
L:GLY52
|
4.8
|
0.8
|
1.0
|
N
|
L:CYS34
|
4.8
|
0.0
|
1.0
|
O
|
L:LYS49
|
4.8
|
0.6
|
1.0
|
C
|
L:CYS51
|
4.8
|
0.4
|
1.0
|
OG
|
L:SER36
|
4.8
|
0.4
|
1.0
|
N
|
L:LYS49
|
4.9
|
0.3
|
1.0
|
CA
|
L:CYS48
|
4.9
|
0.9
|
1.0
|
N
|
L:SER36
|
5.0
|
0.0
|
1.0
|
|
Reference:
D.Wang,
D.A.Bushnell,
X.Huang,
K.D.Westover,
M.Levitt,
R.D.Kornberg.
Structural Basis of Transcription: Backtracked Rna Polymerase II at 3.4 Angstrom Resolution. Science V. 324 1203 2009.
ISSN: ISSN 0036-8075
PubMed: 19478184
DOI: 10.1126/SCIENCE.1168729
Page generated: Thu Oct 24 14:00:12 2024
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