Zinc in PDB 6tps: Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Enzymatic activity of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
All present enzymatic activity of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic:
2.7.7.6;
Other elements in 6tps:
The structure of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
(pdb code 6tps). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the
Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic, PDB code: 6tps:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
Zinc binding site 1 out
of 7 in 6tps
Go back to
Zinc Binding Sites List in 6tps
Zinc binding site 1 out
of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1701
b:0.9
occ:1.00
|
SG
|
A:CYS65
|
2.4
|
62.7
|
1.0
|
SG
|
A:CYS72
|
2.4
|
61.6
|
1.0
|
SG
|
A:CYS62
|
2.4
|
63.2
|
1.0
|
CB
|
A:CYS62
|
2.6
|
63.2
|
1.0
|
NE2
|
A:HIS75
|
2.8
|
61.6
|
1.0
|
CD2
|
A:HIS75
|
3.2
|
61.6
|
1.0
|
OG1
|
A:THR64
|
3.4
|
62.4
|
1.0
|
CB
|
A:CYS65
|
3.9
|
62.7
|
1.0
|
N
|
A:CYS65
|
3.9
|
62.7
|
1.0
|
CE1
|
A:HIS75
|
4.0
|
61.6
|
1.0
|
CA
|
A:CYS62
|
4.1
|
63.2
|
1.0
|
CB
|
A:CYS72
|
4.1
|
61.6
|
1.0
|
C
|
A:CYS62
|
4.4
|
63.2
|
1.0
|
CA
|
A:CYS65
|
4.5
|
62.7
|
1.0
|
O
|
A:CYS62
|
4.5
|
63.2
|
1.0
|
CG
|
A:HIS75
|
4.5
|
61.6
|
1.0
|
N
|
A:GLY66
|
4.7
|
61.6
|
1.0
|
CB
|
A:THR64
|
4.7
|
62.4
|
1.0
|
N
|
A:THR64
|
4.8
|
62.4
|
1.0
|
CA
|
A:CYS72
|
4.9
|
61.6
|
1.0
|
ND1
|
A:HIS75
|
4.9
|
61.6
|
1.0
|
N
|
A:CYS62
|
4.9
|
63.2
|
1.0
|
N
|
A:GLY74
|
4.9
|
61.6
|
1.0
|
C
|
A:THR64
|
5.0
|
62.4
|
1.0
|
C
|
A:CYS65
|
5.0
|
62.7
|
1.0
|
|
Zinc binding site 2 out
of 7 in 6tps
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Zinc Binding Sites List in 6tps
Zinc binding site 2 out
of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1702
b:0.0
occ:1.00
|
SG
|
A:CYS105
|
3.6
|
88.2
|
1.0
|
O
|
A:CYS105
|
3.6
|
88.2
|
1.0
|
CD2
|
A:HIS107
|
4.3
|
76.0
|
1.0
|
NE2
|
A:HIS107
|
4.3
|
76.0
|
1.0
|
C
|
A:CYS105
|
4.6
|
88.2
|
1.0
|
SG
|
A:CYS236
|
4.6
|
95.4
|
1.0
|
CA
|
A:CYS105
|
4.7
|
88.2
|
1.0
|
CB
|
A:CYS105
|
4.8
|
88.2
|
1.0
|
|
Zinc binding site 3 out
of 7 in 6tps
Go back to
Zinc Binding Sites List in 6tps
Zinc binding site 3 out
of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1301
b:0.3
occ:1.00
|
SG
|
B:CYS1107
|
2.4
|
60.2
|
1.0
|
SG
|
B:CYS1104
|
2.5
|
60.5
|
1.0
|
SG
|
B:CYS1131
|
2.5
|
72.4
|
1.0
|
SG
|
B:CYS1128
|
2.5
|
64.5
|
1.0
|
CB
|
B:CYS1104
|
2.8
|
60.5
|
1.0
|
CB
|
B:CYS1107
|
3.4
|
60.2
|
1.0
|
CB
|
B:CYS1128
|
3.5
|
64.5
|
1.0
|
CB
|
B:CYS1131
|
3.7
|
72.4
|
1.0
|
N
|
B:CYS1107
|
3.8
|
60.2
|
1.0
|
N
|
B:CYS1131
|
4.0
|
72.4
|
1.0
|
CA
|
B:CYS1107
|
4.2
|
60.2
|
1.0
|
CA
|
B:CYS1104
|
4.3
|
60.5
|
1.0
|
CA
|
B:CYS1131
|
4.4
|
72.4
|
1.0
|
CB
|
B:ARG1130
|
4.6
|
65.4
|
1.0
|
OG1
|
B:THR1112
|
4.8
|
51.3
|
1.0
|
N
|
B:GLY1108
|
4.9
|
54.4
|
1.0
|
C
|
B:ARG1130
|
4.9
|
65.4
|
1.0
|
C
|
B:CYS1107
|
4.9
|
60.2
|
1.0
|
CA
|
B:CYS1128
|
4.9
|
64.5
|
1.0
|
C
|
B:GLU1106
|
5.0
|
60.7
|
1.0
|
N
|
B:ARG1130
|
5.0
|
65.4
|
1.0
|
CB
|
B:GLU1106
|
5.0
|
60.7
|
1.0
|
|
Zinc binding site 4 out
of 7 in 6tps
Go back to
Zinc Binding Sites List in 6tps
Zinc binding site 4 out
of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:0.9
occ:1.00
|
SG
|
I:CYS30
|
2.5
|
98.3
|
1.0
|
SG
|
I:CYS10
|
2.5
|
99.1
|
1.0
|
SG
|
I:CYS33
|
2.6
|
0.5
|
1.0
|
SG
|
I:CYS13
|
2.6
|
0.4
|
1.0
|
CB
|
I:CYS10
|
2.7
|
99.1
|
1.0
|
CB
|
I:CYS30
|
2.7
|
98.3
|
1.0
|
CB
|
I:CYS33
|
3.8
|
0.5
|
1.0
|
CB
|
I:CYS13
|
4.1
|
0.4
|
1.0
|
CA
|
I:CYS10
|
4.2
|
99.1
|
1.0
|
CA
|
I:CYS30
|
4.2
|
98.3
|
1.0
|
N
|
I:CYS33
|
4.2
|
0.5
|
1.0
|
N
|
I:CYS13
|
4.2
|
0.4
|
1.0
|
CA
|
I:CYS33
|
4.5
|
0.5
|
1.0
|
O
|
I:ASP15
|
4.6
|
90.1
|
1.0
|
CA
|
I:CYS13
|
4.7
|
0.4
|
1.0
|
CD2
|
I:LEU17
|
4.8
|
96.6
|
1.0
|
CB
|
I:ASP15
|
4.9
|
90.1
|
1.0
|
N
|
I:ASP15
|
4.9
|
90.1
|
1.0
|
C
|
I:CYS13
|
4.9
|
0.4
|
1.0
|
N
|
I:CYS10
|
4.9
|
99.1
|
1.0
|
N
|
I:LYS34
|
4.9
|
96.2
|
1.0
|
C
|
I:CYS33
|
5.0
|
0.5
|
1.0
|
N
|
I:CYS30
|
5.0
|
98.3
|
1.0
|
C
|
I:CYS10
|
5.0
|
99.1
|
1.0
|
|
Zinc binding site 5 out
of 7 in 6tps
Go back to
Zinc Binding Sites List in 6tps
Zinc binding site 5 out
of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:57.4
occ:1.00
|
N
|
J:CYS46
|
2.3
|
36.2
|
1.0
|
SG
|
J:CYS7
|
2.4
|
30.0
|
1.0
|
SG
|
J:CYS10
|
2.4
|
27.8
|
1.0
|
SG
|
J:CYS45
|
2.5
|
31.9
|
1.0
|
CB
|
J:CYS46
|
2.5
|
36.2
|
1.0
|
CA
|
J:CYS46
|
2.6
|
36.2
|
1.0
|
C
|
J:CYS45
|
2.9
|
31.9
|
1.0
|
CB
|
J:CYS7
|
3.3
|
30.0
|
1.0
|
SG
|
J:CYS46
|
3.3
|
36.2
|
1.0
|
CB
|
J:CYS45
|
3.4
|
31.9
|
1.0
|
O
|
J:CYS45
|
3.4
|
31.9
|
1.0
|
CB
|
J:CYS10
|
3.7
|
27.8
|
1.0
|
CA
|
J:CYS45
|
3.7
|
31.9
|
1.0
|
N
|
J:CYS10
|
4.0
|
27.8
|
1.0
|
C
|
J:CYS46
|
4.1
|
36.2
|
1.0
|
NH1
|
J:ARG43
|
4.2
|
39.1
|
1.0
|
N
|
J:CYS45
|
4.4
|
31.9
|
1.0
|
CA
|
J:CYS10
|
4.5
|
27.8
|
1.0
|
CA
|
J:CYS7
|
4.7
|
30.0
|
1.0
|
N
|
J:ARG47
|
4.8
|
37.2
|
1.0
|
N
|
J:GLY11
|
4.9
|
28.3
|
1.0
|
O
|
J:CYS46
|
4.9
|
36.2
|
1.0
|
N
|
J:SER9
|
5.0
|
28.1
|
1.0
|
|
Zinc binding site 6 out
of 7 in 6tps
Go back to
Zinc Binding Sites List in 6tps
Zinc binding site 6 out
of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:79.5
occ:1.00
|
SG
|
L:CYS34
|
2.4
|
50.3
|
1.0
|
SG
|
L:CYS31
|
2.4
|
49.9
|
1.0
|
SG
|
L:CYS48
|
2.5
|
59.6
|
1.0
|
CB
|
L:CYS48
|
2.6
|
59.6
|
1.0
|
CB
|
L:CYS51
|
3.2
|
58.5
|
1.0
|
CB
|
L:CYS31
|
3.4
|
49.9
|
1.0
|
N
|
L:CYS51
|
3.7
|
58.5
|
1.0
|
CA
|
L:CYS51
|
3.9
|
58.5
|
1.0
|
CB
|
L:CYS34
|
4.0
|
50.3
|
1.0
|
CA
|
L:CYS48
|
4.1
|
59.6
|
1.0
|
N
|
L:HIS53
|
4.2
|
53.6
|
1.0
|
N
|
L:GLY52
|
4.3
|
57.6
|
1.0
|
N
|
L:CYS34
|
4.3
|
50.3
|
1.0
|
CB
|
L:HIS53
|
4.3
|
53.6
|
1.0
|
C
|
L:CYS51
|
4.4
|
58.5
|
1.0
|
C
|
L:ASP50
|
4.6
|
59.3
|
1.0
|
SG
|
L:CYS51
|
4.6
|
58.5
|
1.0
|
N
|
L:ASP50
|
4.7
|
59.3
|
1.0
|
C
|
L:CYS48
|
4.7
|
59.6
|
1.0
|
CA
|
L:CYS34
|
4.7
|
50.3
|
1.0
|
N
|
L:CYS48
|
4.8
|
59.6
|
1.0
|
CA
|
L:CYS31
|
4.8
|
49.9
|
1.0
|
CA
|
L:HIS53
|
4.8
|
53.6
|
1.0
|
N
|
L:LYS49
|
4.9
|
54.2
|
1.0
|
CB
|
L:GLU33
|
4.9
|
50.5
|
1.0
|
CB
|
L:ASP50
|
5.0
|
59.3
|
1.0
|
CA
|
L:ASP50
|
5.0
|
59.3
|
1.0
|
|
Zinc binding site 7 out
of 7 in 6tps
Go back to
Zinc Binding Sites List in 6tps
Zinc binding site 7 out
of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Zn601
b:92.6
occ:1.00
|
SG
|
Q:CYS15
|
2.4
|
69.0
|
1.0
|
SG
|
Q:CYS29
|
2.5
|
65.6
|
1.0
|
SG
|
Q:CYS10
|
2.5
|
86.6
|
1.0
|
CB
|
Q:CYS29
|
2.6
|
65.6
|
1.0
|
ND1
|
Q:HIS33
|
3.1
|
53.3
|
1.0
|
CB
|
Q:HIS33
|
3.3
|
53.3
|
1.0
|
CB
|
Q:CYS15
|
3.5
|
69.0
|
1.0
|
CG
|
Q:HIS33
|
3.6
|
53.3
|
1.0
|
CB
|
Q:CYS10
|
3.9
|
86.6
|
1.0
|
O
|
Q:HIS33
|
4.0
|
53.3
|
1.0
|
CA
|
Q:CYS29
|
4.0
|
65.6
|
1.0
|
N
|
Q:HIS33
|
4.2
|
53.3
|
1.0
|
CA
|
Q:HIS33
|
4.2
|
53.3
|
1.0
|
CE1
|
Q:HIS33
|
4.2
|
53.3
|
1.0
|
N
|
Q:CYS29
|
4.5
|
65.6
|
1.0
|
C
|
Q:HIS33
|
4.6
|
53.3
|
1.0
|
C
|
Q:CYS29
|
4.8
|
65.6
|
1.0
|
CA
|
Q:CYS15
|
4.8
|
69.0
|
1.0
|
CD2
|
Q:HIS33
|
4.9
|
53.3
|
1.0
|
O
|
Q:ILE9
|
5.0
|
76.8
|
1.0
|
CG2
|
Q:THR12
|
5.0
|
87.6
|
1.0
|
|
Reference:
M.Pilsl,
C.Engel.
Structural Basis of Rna Polymerase I Pre-Initiation Complex Formation and Promoter Melting. Nat Commun V. 11 1206 2020.
ISSN: ESSN 2041-1723
PubMed: 32139698
DOI: 10.1038/S41467-020-15052-Y
Page generated: Tue Oct 29 08:09:28 2024
|