Zinc in PDB 5n61: Rna Polymerase I Initially Transcribing Complex
Enzymatic activity of Rna Polymerase I Initially Transcribing Complex
All present enzymatic activity of Rna Polymerase I Initially Transcribing Complex:
2.7.7.6;
Other elements in 5n61:
The structure of Rna Polymerase I Initially Transcribing Complex also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Rna Polymerase I Initially Transcribing Complex
(pdb code 5n61). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the
Rna Polymerase I Initially Transcribing Complex, PDB code: 5n61:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
Zinc binding site 1 out
of 7 in 5n61
Go back to
Zinc Binding Sites List in 5n61
Zinc binding site 1 out
of 7 in the Rna Polymerase I Initially Transcribing Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3001
b:0.0
occ:1.00
|
CD2
|
A:HIS75
|
1.6
|
0.0
|
1.0
|
NE2
|
A:HIS75
|
2.1
|
0.0
|
1.0
|
SG
|
A:CYS72
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS62
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS65
|
2.3
|
0.0
|
1.0
|
CA
|
A:GLY55
|
2.7
|
0.0
|
1.0
|
CG
|
A:HIS75
|
2.9
|
0.0
|
1.0
|
N
|
A:GLY55
|
3.3
|
0.0
|
1.0
|
CE1
|
A:HIS75
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS65
|
3.5
|
0.0
|
1.0
|
ND1
|
A:HIS75
|
3.7
|
0.0
|
1.0
|
CB
|
A:CYS62
|
3.7
|
0.0
|
1.0
|
C
|
A:GLY55
|
3.7
|
0.0
|
1.0
|
N
|
A:CYS65
|
3.7
|
0.0
|
1.0
|
C
|
A:LEU54
|
3.8
|
0.0
|
1.0
|
O
|
A:LEU54
|
3.8
|
0.0
|
1.0
|
CB
|
A:HIS75
|
3.9
|
0.0
|
1.0
|
CA
|
A:GLY74
|
3.9
|
0.0
|
1.0
|
C
|
A:GLY74
|
3.9
|
0.0
|
1.0
|
N
|
A:HIS75
|
3.9
|
0.0
|
1.0
|
N
|
A:GLY74
|
3.9
|
0.0
|
1.0
|
N
|
A:ALA56
|
4.0
|
0.0
|
1.0
|
CB
|
A:CYS72
|
4.1
|
0.0
|
1.0
|
CB
|
A:THR64
|
4.2
|
0.0
|
1.0
|
CA
|
A:CYS65
|
4.3
|
0.0
|
1.0
|
O
|
A:GLY74
|
4.5
|
0.0
|
1.0
|
CA
|
A:HIS75
|
4.6
|
0.0
|
1.0
|
O
|
A:ALA53
|
4.6
|
0.0
|
1.0
|
O
|
A:GLY55
|
4.6
|
0.0
|
1.0
|
C
|
A:THR64
|
4.8
|
0.0
|
1.0
|
CA
|
A:CYS62
|
4.8
|
0.0
|
1.0
|
CG2
|
A:THR64
|
4.8
|
0.0
|
1.0
|
O
|
A:LEU52
|
4.9
|
0.0
|
1.0
|
CA
|
A:THR64
|
4.9
|
0.0
|
1.0
|
N
|
A:THR64
|
4.9
|
0.0
|
1.0
|
CA
|
A:LEU54
|
5.0
|
0.0
|
1.0
|
CA
|
A:CYS72
|
5.0
|
0.0
|
1.0
|
C
|
A:CYS72
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 2 out
of 7 in 5n61
Go back to
Zinc Binding Sites List in 5n61
Zinc binding site 2 out
of 7 in the Rna Polymerase I Initially Transcribing Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3002
b:0.0
occ:1.00
|
CB
|
A:CYS233
|
1.3
|
0.0
|
1.0
|
SG
|
A:CYS233
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS102
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS236
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS105
|
2.4
|
0.0
|
1.0
|
CA
|
A:CYS233
|
2.8
|
0.0
|
1.0
|
CB
|
A:CYS102
|
3.2
|
0.0
|
1.0
|
N
|
A:CYS233
|
3.3
|
0.0
|
1.0
|
C
|
A:CYS233
|
3.7
|
0.0
|
1.0
|
O
|
A:CYS233
|
3.9
|
0.0
|
1.0
|
N
|
A:MET238
|
3.9
|
0.0
|
1.0
|
O
|
A:MET238
|
4.0
|
0.0
|
1.0
|
CA
|
A:CYS102
|
4.0
|
0.0
|
1.0
|
CB
|
A:CYS105
|
4.1
|
0.0
|
1.0
|
CB
|
A:CYS236
|
4.1
|
0.0
|
1.0
|
CB
|
A:MET238
|
4.1
|
0.0
|
1.0
|
C
|
A:MET238
|
4.1
|
0.0
|
1.0
|
N
|
A:CYS105
|
4.2
|
0.0
|
1.0
|
CA
|
A:MET238
|
4.3
|
0.0
|
1.0
|
CG
|
A:ARG109
|
4.5
|
0.0
|
1.0
|
N
|
A:GLY237
|
4.5
|
0.0
|
1.0
|
N
|
A:CYS236
|
4.6
|
0.0
|
1.0
|
C
|
A:LYS232
|
4.7
|
0.0
|
1.0
|
N
|
A:ASP234
|
4.7
|
0.0
|
1.0
|
N
|
A:PHE239
|
4.8
|
0.0
|
1.0
|
CA
|
A:CYS105
|
4.8
|
0.0
|
1.0
|
CA
|
A:CYS236
|
4.8
|
0.0
|
1.0
|
C
|
A:GLY237
|
4.8
|
0.0
|
1.0
|
CB
|
A:PHE104
|
4.8
|
0.0
|
1.0
|
C
|
A:CYS102
|
4.9
|
0.0
|
1.0
|
N
|
A:PHE104
|
4.9
|
0.0
|
1.0
|
CD2
|
A:PHE104
|
5.0
|
0.0
|
1.0
|
N
|
A:LEU103
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 3 out
of 7 in 5n61
Go back to
Zinc Binding Sites List in 5n61
Zinc binding site 3 out
of 7 in the Rna Polymerase I Initially Transcribing Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1302
b:0.0
occ:1.00
|
SG
|
B:CYS1128
|
2.3
|
0.0
|
1.0
|
SG
|
B:CYS1131
|
2.3
|
0.0
|
1.0
|
SG
|
B:CYS1107
|
2.3
|
0.0
|
1.0
|
SG
|
B:CYS1104
|
2.3
|
0.0
|
1.0
|
CB
|
B:CYS1131
|
2.5
|
0.0
|
1.0
|
CB
|
B:CYS1107
|
2.8
|
0.0
|
1.0
|
CB
|
B:CYS1128
|
2.8
|
0.0
|
1.0
|
N
|
B:CYS1131
|
3.1
|
0.0
|
1.0
|
CB
|
B:CYS1104
|
3.3
|
0.0
|
1.0
|
CA
|
B:CYS1131
|
3.4
|
0.0
|
1.0
|
N
|
B:CYS1107
|
3.5
|
0.0
|
1.0
|
CA
|
B:CYS1107
|
3.8
|
0.0
|
1.0
|
CA
|
B:CYS1128
|
4.1
|
0.0
|
1.0
|
O
|
B:CYS1128
|
4.2
|
0.0
|
1.0
|
C
|
B:ARG1130
|
4.2
|
0.0
|
1.0
|
C
|
B:CYS1128
|
4.2
|
0.0
|
1.0
|
CA
|
B:GLY1170
|
4.4
|
0.0
|
1.0
|
CB
|
B:ARG1130
|
4.4
|
0.0
|
1.0
|
C
|
B:CYS1131
|
4.4
|
0.0
|
1.0
|
N
|
B:ARG1130
|
4.5
|
0.0
|
1.0
|
CA
|
B:ARG1130
|
4.6
|
0.0
|
1.0
|
CB
|
B:GLU1106
|
4.7
|
0.0
|
1.0
|
CA
|
B:CYS1104
|
4.7
|
0.0
|
1.0
|
OG1
|
B:THR1112
|
4.7
|
0.0
|
1.0
|
C
|
B:GLU1106
|
4.7
|
0.0
|
1.0
|
OE1
|
B:GLU1106
|
4.8
|
0.0
|
1.0
|
C
|
B:CYS1107
|
4.9
|
0.0
|
1.0
|
|
Zinc binding site 4 out
of 7 in 5n61
Go back to
Zinc Binding Sites List in 5n61
Zinc binding site 4 out
of 7 in the Rna Polymerase I Initially Transcribing Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn3001
b:0.0
occ:1.00
|
CB
|
I:CYS30
|
1.4
|
0.0
|
1.0
|
SG
|
I:CYS33
|
2.3
|
0.0
|
1.0
|
SG
|
I:CYS10
|
2.3
|
0.0
|
1.0
|
SG
|
I:CYS30
|
2.3
|
0.0
|
1.0
|
SG
|
I:CYS13
|
2.3
|
0.0
|
1.0
|
CB
|
I:CYS10
|
2.6
|
0.0
|
1.0
|
CA
|
I:CYS30
|
2.7
|
0.0
|
1.0
|
N
|
I:CYS30
|
3.3
|
0.0
|
1.0
|
CB
|
I:ALA35
|
3.3
|
0.0
|
1.0
|
N
|
I:ALA35
|
3.4
|
0.0
|
1.0
|
O
|
I:ALA35
|
3.4
|
0.0
|
1.0
|
CA
|
I:ALA35
|
3.7
|
0.0
|
1.0
|
C
|
I:CYS30
|
3.9
|
0.0
|
1.0
|
CA
|
I:CYS10
|
3.9
|
0.0
|
1.0
|
C
|
I:ALA35
|
4.0
|
0.0
|
1.0
|
CB
|
I:CYS33
|
4.1
|
0.0
|
1.0
|
CB
|
I:CYS13
|
4.1
|
0.0
|
1.0
|
N
|
I:LYS34
|
4.2
|
0.0
|
1.0
|
C
|
I:LYS34
|
4.4
|
0.0
|
1.0
|
N
|
I:CYS13
|
4.5
|
0.0
|
1.0
|
N
|
I:CYS33
|
4.5
|
0.0
|
1.0
|
N
|
I:SER31
|
4.5
|
0.0
|
1.0
|
CE2
|
I:TYR37
|
4.5
|
0.0
|
1.0
|
C
|
I:GLU29
|
4.6
|
0.0
|
1.0
|
C
|
I:CYS33
|
4.6
|
0.0
|
1.0
|
O
|
I:CYS30
|
4.6
|
0.0
|
1.0
|
CA
|
I:CYS33
|
4.6
|
0.0
|
1.0
|
N
|
I:CYS10
|
4.7
|
0.0
|
1.0
|
CA
|
I:LYS34
|
4.8
|
0.0
|
1.0
|
CA
|
I:CYS13
|
4.8
|
0.0
|
1.0
|
C
|
I:CYS10
|
4.9
|
0.0
|
1.0
|
|
Zinc binding site 5 out
of 7 in 5n61
Go back to
Zinc Binding Sites List in 5n61
Zinc binding site 5 out
of 7 in the Rna Polymerase I Initially Transcribing Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn3001
b:0.0
occ:1.00
|
CB
|
J:CYS10
|
1.3
|
0.0
|
1.0
|
CA
|
J:CYS10
|
2.0
|
0.0
|
1.0
|
N
|
J:CYS10
|
2.1
|
0.0
|
1.0
|
SG
|
J:CYS10
|
2.3
|
0.0
|
1.0
|
SG
|
J:CYS7
|
2.3
|
0.0
|
1.0
|
SG
|
J:CYS46
|
2.3
|
0.0
|
1.0
|
SG
|
J:CYS45
|
2.4
|
0.0
|
1.0
|
CB
|
J:CYS7
|
2.5
|
0.0
|
1.0
|
C
|
J:CYS10
|
2.8
|
0.0
|
1.0
|
N
|
J:GLY11
|
2.9
|
0.0
|
1.0
|
C
|
J:SER9
|
3.4
|
0.0
|
1.0
|
O
|
J:CYS7
|
3.6
|
0.0
|
1.0
|
N
|
J:LYS12
|
3.6
|
0.0
|
1.0
|
CA
|
J:CYS7
|
3.7
|
0.0
|
1.0
|
C
|
J:CYS7
|
3.8
|
0.0
|
1.0
|
O
|
J:CYS10
|
3.9
|
0.0
|
1.0
|
CB
|
J:CYS45
|
4.0
|
0.0
|
1.0
|
CB
|
J:CYS46
|
4.0
|
0.0
|
1.0
|
CA
|
J:GLY11
|
4.1
|
0.0
|
1.0
|
O
|
J:SER9
|
4.2
|
0.0
|
1.0
|
CB
|
J:LYS12
|
4.2
|
0.0
|
1.0
|
N
|
J:CYS46
|
4.2
|
0.0
|
1.0
|
CA
|
J:SER9
|
4.3
|
0.0
|
1.0
|
C
|
J:GLY11
|
4.3
|
0.0
|
1.0
|
N
|
J:SER9
|
4.3
|
0.0
|
1.0
|
CA
|
J:CYS46
|
4.4
|
0.0
|
1.0
|
N
|
J:CYS7
|
4.4
|
0.0
|
1.0
|
CA
|
J:LYS12
|
4.5
|
0.0
|
1.0
|
CB
|
J:SER9
|
4.6
|
0.0
|
1.0
|
N
|
J:PHE8
|
4.6
|
0.0
|
1.0
|
C
|
J:CYS45
|
4.7
|
0.0
|
1.0
|
C
|
J:PHE8
|
4.7
|
0.0
|
1.0
|
O
|
J:LYS12
|
4.8
|
0.0
|
1.0
|
O
|
C:SER223
|
4.8
|
0.0
|
1.0
|
|
Zinc binding site 6 out
of 7 in 5n61
Go back to
Zinc Binding Sites List in 5n61
Zinc binding site 6 out
of 7 in the Rna Polymerase I Initially Transcribing Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn3001
b:0.0
occ:1.00
|
SG
|
L:CYS48
|
2.3
|
0.0
|
1.0
|
SG
|
L:CYS31
|
2.3
|
0.0
|
1.0
|
SG
|
L:CYS34
|
2.4
|
0.0
|
1.0
|
CB
|
L:CYS51
|
2.5
|
0.0
|
1.0
|
CB
|
L:CYS48
|
2.6
|
0.0
|
1.0
|
SG
|
L:CYS51
|
2.8
|
0.0
|
1.0
|
N
|
L:CYS51
|
3.2
|
0.0
|
1.0
|
CB
|
L:CYS31
|
3.3
|
0.0
|
1.0
|
CA
|
L:CYS51
|
3.4
|
0.0
|
1.0
|
CB
|
L:CYS34
|
3.4
|
0.0
|
1.0
|
N
|
L:CYS34
|
3.7
|
0.0
|
1.0
|
OG
|
L:SER36
|
4.1
|
0.0
|
1.0
|
N
|
L:GLY52
|
4.1
|
0.0
|
1.0
|
CA
|
L:CYS48
|
4.1
|
0.0
|
1.0
|
CA
|
L:CYS34
|
4.2
|
0.0
|
1.0
|
C
|
L:CYS51
|
4.2
|
0.0
|
1.0
|
CD2
|
L:HIS53
|
4.2
|
0.0
|
1.0
|
C
|
L:ASP50
|
4.4
|
0.0
|
1.0
|
CB
|
L:ASP50
|
4.6
|
0.0
|
1.0
|
CB
|
L:GLU33
|
4.6
|
0.0
|
1.0
|
CA
|
L:CYS31
|
4.7
|
0.0
|
1.0
|
N
|
L:HIS53
|
4.7
|
0.0
|
1.0
|
C
|
L:CYS48
|
4.8
|
0.0
|
1.0
|
C
|
L:GLU33
|
4.9
|
0.0
|
1.0
|
CA
|
L:ASP50
|
4.9
|
0.0
|
1.0
|
CB
|
L:HIS53
|
4.9
|
0.0
|
1.0
|
CG
|
L:HIS53
|
4.9
|
0.0
|
1.0
|
O
|
L:CYS48
|
5.0
|
0.0
|
1.0
|
N
|
L:CYS48
|
5.0
|
0.0
|
1.0
|
C
|
L:CYS34
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 7 out
of 7 in 5n61
Go back to
Zinc Binding Sites List in 5n61
Zinc binding site 7 out
of 7 in the Rna Polymerase I Initially Transcribing Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Zn1001
b:0.0
occ:1.00
|
SG
|
Q:CYS10
|
2.2
|
0.0
|
1.0
|
SG
|
Q:CYS15
|
2.7
|
0.0
|
1.0
|
SG
|
Q:CYS29
|
2.8
|
0.0
|
1.0
|
ND1
|
Q:HIS33
|
2.8
|
0.0
|
1.0
|
CB
|
Q:THR12
|
3.3
|
0.0
|
1.0
|
CE1
|
Q:HIS33
|
3.5
|
0.0
|
1.0
|
CB
|
Q:CYS15
|
3.6
|
0.0
|
1.0
|
CG
|
Q:HIS33
|
3.6
|
0.0
|
1.0
|
CG2
|
Q:THR12
|
3.7
|
0.0
|
1.0
|
CB
|
Q:CYS10
|
3.8
|
0.0
|
1.0
|
CB
|
Q:CYS29
|
3.9
|
0.0
|
1.0
|
CB
|
Q:HIS33
|
4.0
|
0.0
|
1.0
|
O
|
Q:THR12
|
4.1
|
0.0
|
1.0
|
OG1
|
Q:THR12
|
4.1
|
0.0
|
1.0
|
O
|
Q:SER17
|
4.3
|
0.0
|
1.0
|
CA
|
Q:THR12
|
4.3
|
0.0
|
1.0
|
NE2
|
Q:HIS33
|
4.4
|
0.0
|
1.0
|
N
|
Q:THR12
|
4.4
|
0.0
|
1.0
|
OD1
|
Q:ASN14
|
4.5
|
0.0
|
1.0
|
CD2
|
Q:HIS33
|
4.5
|
0.0
|
1.0
|
C
|
Q:THR12
|
4.6
|
0.0
|
1.0
|
N
|
Q:CYS15
|
4.7
|
0.0
|
1.0
|
N
|
Q:SER17
|
4.7
|
0.0
|
1.0
|
CA
|
Q:CYS15
|
4.8
|
0.0
|
1.0
|
CB
|
Q:SER17
|
4.8
|
0.0
|
1.0
|
CD2
|
Q:TYR31
|
4.9
|
0.0
|
1.0
|
CA
|
Q:CYS10
|
5.0
|
0.0
|
1.0
|
|
Reference:
C.Engel,
T.Gubbey,
S.Neyer,
S.Sainsbury,
C.Oberthuer,
C.Baejen,
C.Bernecky,
P.Cramer.
Structural Basis of Rna Polymerase I Transcription Initiation. Cell V. 169 120 2017.
ISSN: ISSN 1097-4172
PubMed: 28340337
DOI: 10.1016/J.CELL.2017.03.003
Page generated: Sun Oct 27 22:37:27 2024
|