Zinc in PDB 5w64: Rna Polymerase I Initial Transcribing Complex State 1
Enzymatic activity of Rna Polymerase I Initial Transcribing Complex State 1
All present enzymatic activity of Rna Polymerase I Initial Transcribing Complex State 1:
2.7.7.6;
Zinc Binding Sites:
The binding sites of Zinc atom in the Rna Polymerase I Initial Transcribing Complex State 1
(pdb code 5w64). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Rna Polymerase I Initial Transcribing Complex State 1, PDB code: 5w64:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5w64
Go back to
Zinc Binding Sites List in 5w64
Zinc binding site 1 out
of 6 in the Rna Polymerase I Initial Transcribing Complex State 1
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 Initial Transcribing Complex State 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1701
b:0.0
occ:1.00
|
CB
|
A:CYS102
|
1.9
|
0.0
|
1.0
|
SG
|
A:CYS105
|
1.9
|
0.0
|
1.0
|
SG
|
A:CYS233
|
2.1
|
0.0
|
1.0
|
SG
|
A:CYS102
|
2.2
|
0.0
|
1.0
|
SG
|
A:CYS236
|
2.2
|
0.0
|
1.0
|
O
|
A:HIS107
|
3.0
|
0.0
|
1.0
|
CB
|
A:CYS236
|
3.3
|
0.0
|
1.0
|
CA
|
A:CYS102
|
3.4
|
0.0
|
1.0
|
C
|
A:HIS107
|
3.6
|
0.0
|
1.0
|
CB
|
A:CYS233
|
3.6
|
0.0
|
1.0
|
CB
|
A:CYS105
|
3.7
|
0.0
|
1.0
|
N
|
A:HIS107
|
3.7
|
0.0
|
1.0
|
CB
|
A:HIS107
|
3.8
|
0.0
|
1.0
|
CA
|
A:HIS107
|
3.9
|
0.0
|
1.0
|
N
|
A:CYS236
|
4.0
|
0.0
|
1.0
|
N
|
A:CYS102
|
4.1
|
0.0
|
1.0
|
CA
|
A:CYS236
|
4.2
|
0.0
|
1.0
|
C
|
A:CYS102
|
4.3
|
0.0
|
1.0
|
N
|
A:HIS106
|
4.4
|
0.0
|
1.0
|
N
|
A:PHE108
|
4.5
|
0.0
|
1.0
|
C
|
A:PHE108
|
4.5
|
0.0
|
1.0
|
CA
|
A:CYS105
|
4.6
|
0.0
|
1.0
|
N
|
A:ARG109
|
4.6
|
0.0
|
1.0
|
N
|
A:CYS105
|
4.7
|
0.0
|
1.0
|
O
|
A:CYS102
|
4.7
|
0.0
|
1.0
|
O
|
A:PHE108
|
4.8
|
0.0
|
1.0
|
CA
|
A:CYS233
|
4.8
|
0.0
|
1.0
|
C
|
A:CYS105
|
4.8
|
0.0
|
1.0
|
CA
|
A:PHE108
|
4.8
|
0.0
|
1.0
|
C
|
A:HIS106
|
4.9
|
0.0
|
1.0
|
CG
|
A:HIS107
|
4.9
|
0.0
|
1.0
|
ND2
|
A:ASN235
|
4.9
|
0.0
|
1.0
|
C
|
A:CYS236
|
4.9
|
0.0
|
1.0
|
CB
|
A:ASN235
|
4.9
|
0.0
|
1.0
|
C
|
A:ASN235
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5w64
Go back to
Zinc Binding Sites List in 5w64
Zinc binding site 2 out
of 6 in the Rna Polymerase I Initial Transcribing Complex State 1
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 Initial Transcribing Complex State 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1702
b:0.0
occ:1.00
|
CD2
|
A:HIS75
|
1.9
|
0.0
|
1.0
|
NE2
|
A:HIS75
|
2.0
|
0.0
|
1.0
|
SG
|
A:CYS72
|
2.2
|
0.0
|
1.0
|
SG
|
A:CYS62
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS65
|
2.3
|
0.0
|
1.0
|
CB
|
A:CYS62
|
2.7
|
0.0
|
1.0
|
CG
|
A:HIS75
|
2.9
|
0.0
|
1.0
|
CA
|
A:GLY74
|
2.9
|
0.0
|
1.0
|
CE1
|
A:HIS75
|
2.9
|
0.0
|
1.0
|
N
|
A:GLY74
|
3.1
|
0.0
|
1.0
|
C
|
A:GLY74
|
3.2
|
0.0
|
1.0
|
ND1
|
A:HIS75
|
3.4
|
0.0
|
1.0
|
N
|
A:HIS75
|
3.4
|
0.0
|
1.0
|
CB
|
A:CYS65
|
3.5
|
0.0
|
1.0
|
O
|
A:GLY74
|
3.8
|
0.0
|
1.0
|
CA
|
A:GLY55
|
4.0
|
0.0
|
1.0
|
CB
|
A:CYS72
|
4.0
|
0.0
|
1.0
|
CB
|
A:HIS75
|
4.0
|
0.0
|
1.0
|
N
|
A:CYS65
|
4.2
|
0.0
|
1.0
|
CA
|
A:CYS62
|
4.2
|
0.0
|
1.0
|
CA
|
A:HIS75
|
4.3
|
0.0
|
1.0
|
CA
|
A:CYS65
|
4.4
|
0.0
|
1.0
|
C
|
A:PRO73
|
4.4
|
0.0
|
1.0
|
N
|
A:GLY55
|
4.6
|
0.0
|
1.0
|
N
|
A:PRO73
|
4.6
|
0.0
|
1.0
|
C
|
A:CYS72
|
4.6
|
0.0
|
1.0
|
CD
|
A:PRO73
|
4.7
|
0.0
|
1.0
|
CA
|
A:CYS72
|
4.7
|
0.0
|
1.0
|
C
|
A:GLY55
|
4.8
|
0.0
|
1.0
|
C
|
A:CYS62
|
4.8
|
0.0
|
1.0
|
O
|
A:CYS62
|
4.9
|
0.0
|
1.0
|
CB
|
A:THR64
|
4.9
|
0.0
|
1.0
|
CG
|
A:PRO73
|
4.9
|
0.0
|
1.0
|
C
|
A:THR64
|
5.0
|
0.0
|
1.0
|
O
|
A:ALA53
|
5.0
|
0.0
|
1.0
|
N
|
A:ALA56
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 3 out
of 6 in 5w64
Go back to
Zinc Binding Sites List in 5w64
Zinc binding site 3 out
of 6 in the Rna Polymerase I Initial Transcribing Complex State 1
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 Initial Transcribing Complex State 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1301
b:0.0
occ:1.00
|
CB
|
B:CYS1107
|
2.0
|
0.0
|
1.0
|
SG
|
B:CYS1104
|
2.1
|
0.0
|
1.0
|
SG
|
B:CYS1128
|
2.3
|
0.0
|
1.0
|
SG
|
B:CYS1131
|
2.3
|
0.0
|
1.0
|
SG
|
B:CYS1107
|
2.8
|
0.0
|
1.0
|
N
|
B:CYS1107
|
2.9
|
0.0
|
1.0
|
CA
|
B:CYS1107
|
2.9
|
0.0
|
1.0
|
CB
|
B:CYS1104
|
3.2
|
0.0
|
1.0
|
C
|
B:GLU1106
|
3.5
|
0.0
|
1.0
|
CB
|
B:ARG1130
|
3.6
|
0.0
|
1.0
|
CB
|
B:CYS1128
|
3.7
|
0.0
|
1.0
|
N
|
B:CYS1131
|
3.8
|
0.0
|
1.0
|
CB
|
B:CYS1131
|
3.9
|
0.0
|
1.0
|
NE
|
B:ARG1130
|
3.9
|
0.0
|
1.0
|
O
|
B:GLU1106
|
3.9
|
0.0
|
1.0
|
CB
|
B:GLU1106
|
4.1
|
0.0
|
1.0
|
CA
|
B:GLU1106
|
4.2
|
0.0
|
1.0
|
C
|
B:CYS1107
|
4.3
|
0.0
|
1.0
|
C
|
B:ARG1130
|
4.3
|
0.0
|
1.0
|
CA
|
B:ARG1130
|
4.3
|
0.0
|
1.0
|
CA
|
B:CYS1131
|
4.4
|
0.0
|
1.0
|
OG1
|
B:THR1112
|
4.4
|
0.0
|
1.0
|
CG
|
B:ARG1130
|
4.4
|
0.0
|
1.0
|
N
|
B:GLU1106
|
4.4
|
0.0
|
1.0
|
CA
|
B:CYS1104
|
4.5
|
0.0
|
1.0
|
N
|
B:ARG1130
|
4.5
|
0.0
|
1.0
|
NH2
|
B:ARG1130
|
4.6
|
0.0
|
1.0
|
O
|
B:CYS1104
|
4.6
|
0.0
|
1.0
|
C
|
B:CYS1104
|
4.7
|
0.0
|
1.0
|
N
|
B:GLY1108
|
4.7
|
0.0
|
1.0
|
CZ
|
B:ARG1130
|
4.7
|
0.0
|
1.0
|
CD
|
B:ARG1130
|
4.7
|
0.0
|
1.0
|
CA
|
B:CYS1128
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5w64
Go back to
Zinc Binding Sites List in 5w64
Zinc binding site 4 out
of 6 in the Rna Polymerase I Initial Transcribing Complex State 1
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 Initial Transcribing Complex State 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:0.0
occ:1.00
|
CB
|
I:CYS10
|
1.8
|
0.0
|
1.0
|
SG
|
I:CYS10
|
1.8
|
0.0
|
1.0
|
SG
|
I:CYS33
|
1.9
|
0.0
|
1.0
|
SG
|
I:CYS30
|
2.1
|
0.0
|
1.0
|
SG
|
I:CYS13
|
2.2
|
0.0
|
1.0
|
CB
|
I:CYS30
|
2.6
|
0.0
|
1.0
|
CB
|
I:CYS33
|
3.3
|
0.0
|
1.0
|
CA
|
I:CYS10
|
3.3
|
0.0
|
1.0
|
CB
|
I:ASP15
|
3.4
|
0.0
|
1.0
|
CB
|
I:CYS13
|
3.6
|
0.0
|
1.0
|
N
|
I:ASP15
|
3.9
|
0.0
|
1.0
|
N
|
I:CYS13
|
3.9
|
0.0
|
1.0
|
N
|
I:CYS33
|
3.9
|
0.0
|
1.0
|
CA
|
I:CYS30
|
4.0
|
0.0
|
1.0
|
O
|
I:ASP15
|
4.1
|
0.0
|
1.0
|
C
|
I:CYS10
|
4.1
|
0.0
|
1.0
|
N
|
I:CYS10
|
4.1
|
0.0
|
1.0
|
CA
|
I:ASP15
|
4.1
|
0.0
|
1.0
|
CA
|
I:CYS33
|
4.2
|
0.0
|
1.0
|
CA
|
I:CYS13
|
4.2
|
0.0
|
1.0
|
N
|
I:GLY14
|
4.3
|
0.0
|
1.0
|
O
|
I:CYS10
|
4.5
|
0.0
|
1.0
|
C
|
I:CYS13
|
4.5
|
0.0
|
1.0
|
C
|
I:ASP15
|
4.5
|
0.0
|
1.0
|
CG
|
I:ASP15
|
4.5
|
0.0
|
1.0
|
C
|
I:CYS33
|
4.7
|
0.0
|
1.0
|
OD2
|
I:ASP15
|
4.8
|
0.0
|
1.0
|
N
|
I:CYS30
|
4.8
|
0.0
|
1.0
|
O
|
I:CYS33
|
4.9
|
0.0
|
1.0
|
N
|
I:LEU11
|
4.9
|
0.0
|
1.0
|
C
|
I:CYS30
|
4.9
|
0.0
|
1.0
|
C
|
I:GLN32
|
4.9
|
0.0
|
1.0
|
CB
|
I:GLN32
|
4.9
|
0.0
|
1.0
|
C
|
I:GLY14
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5w64
Go back to
Zinc Binding Sites List in 5w64
Zinc binding site 5 out
of 6 in the Rna Polymerase I Initial Transcribing Complex State 1
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 Initial Transcribing Complex State 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:0.0
occ:1.00
|
N
|
J:CYS46
|
2.1
|
0.0
|
1.0
|
SG
|
J:CYS45
|
2.1
|
0.0
|
1.0
|
SG
|
J:CYS7
|
2.2
|
0.0
|
1.0
|
SG
|
J:CYS46
|
2.2
|
0.0
|
1.0
|
SG
|
J:CYS10
|
2.3
|
0.0
|
1.0
|
C
|
J:CYS45
|
2.4
|
0.0
|
1.0
|
CA
|
J:CYS46
|
2.5
|
0.0
|
1.0
|
CB
|
J:CYS7
|
2.7
|
0.0
|
1.0
|
CB
|
J:CYS46
|
2.8
|
0.0
|
1.0
|
O
|
J:CYS45
|
2.9
|
0.0
|
1.0
|
CB
|
J:CYS45
|
2.9
|
0.0
|
1.0
|
CA
|
J:CYS45
|
3.2
|
0.0
|
1.0
|
CB
|
J:CYS10
|
3.3
|
0.0
|
1.0
|
C
|
J:CYS46
|
3.9
|
0.0
|
1.0
|
N
|
J:CYS45
|
4.0
|
0.0
|
1.0
|
NH2
|
J:ARG43
|
4.1
|
0.0
|
1.0
|
NE
|
J:ARG43
|
4.1
|
0.0
|
1.0
|
N
|
J:CYS10
|
4.2
|
0.0
|
1.0
|
CA
|
J:CYS7
|
4.2
|
0.0
|
1.0
|
CA
|
J:CYS10
|
4.3
|
0.0
|
1.0
|
CZ
|
J:ARG43
|
4.6
|
0.0
|
1.0
|
O
|
J:ARG43
|
4.6
|
0.0
|
1.0
|
N
|
J:ARG47
|
4.6
|
0.0
|
1.0
|
O
|
J:CYS46
|
4.7
|
0.0
|
1.0
|
C
|
J:CYS7
|
4.8
|
0.0
|
1.0
|
CB
|
J:ARG43
|
4.8
|
0.0
|
1.0
|
O
|
J:CYS7
|
4.9
|
0.0
|
1.0
|
N
|
J:GLY11
|
4.9
|
0.0
|
1.0
|
CE
|
J:MET49
|
5.0
|
0.0
|
1.0
|
CB
|
J:LYS12
|
5.0
|
0.0
|
1.0
|
C
|
J:TYR44
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 6 out
of 6 in 5w64
Go back to
Zinc Binding Sites List in 5w64
Zinc binding site 6 out
of 6 in the Rna Polymerase I Initial Transcribing Complex State 1
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 Initial Transcribing Complex State 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:0.0
occ:1.00
|
CB
|
L:CYS34
|
1.1
|
0.0
|
1.0
|
CA
|
L:CYS34
|
2.1
|
0.0
|
1.0
|
SG
|
L:CYS34
|
2.1
|
0.0
|
1.0
|
SG
|
L:CYS51
|
2.1
|
0.0
|
1.0
|
CB
|
L:CYS51
|
2.2
|
0.0
|
1.0
|
N
|
L:CYS34
|
2.3
|
0.0
|
1.0
|
SG
|
L:CYS31
|
2.3
|
0.0
|
1.0
|
SG
|
L:CYS48
|
2.6
|
0.0
|
1.0
|
C
|
L:GLU33
|
3.2
|
0.0
|
1.0
|
C
|
L:CYS34
|
3.3
|
0.0
|
1.0
|
CB
|
L:CYS31
|
3.3
|
0.0
|
1.0
|
CA
|
L:CYS51
|
3.5
|
0.0
|
1.0
|
CB
|
L:CYS48
|
3.6
|
0.0
|
1.0
|
N
|
L:CYS51
|
3.7
|
0.0
|
1.0
|
O
|
L:GLU33
|
3.7
|
0.0
|
1.0
|
N
|
L:SER35
|
4.0
|
0.0
|
1.0
|
O
|
L:CYS34
|
4.0
|
0.0
|
1.0
|
CA
|
L:GLU33
|
4.2
|
0.0
|
1.0
|
N
|
L:GLU33
|
4.3
|
0.0
|
1.0
|
OG
|
L:SER36
|
4.4
|
0.0
|
1.0
|
CB
|
L:GLU33
|
4.5
|
0.0
|
1.0
|
C
|
L:ASP50
|
4.5
|
0.0
|
1.0
|
C
|
L:CYS51
|
4.5
|
0.0
|
1.0
|
N
|
L:GLY52
|
4.7
|
0.0
|
1.0
|
CA
|
L:CYS31
|
4.7
|
0.0
|
1.0
|
N
|
L:SER36
|
4.8
|
0.0
|
1.0
|
CB
|
L:HIS53
|
4.8
|
0.0
|
1.0
|
O
|
L:CYS31
|
4.8
|
0.0
|
1.0
|
C
|
L:CYS31
|
4.9
|
0.0
|
1.0
|
|
Reference:
Y.Han,
C.Yan,
T.H.D.Nguyen,
A.J.Jackobel,
I.Ivanov,
B.A.Knutson,
Y.He.
Structural Mechanism of Atp-Independent Transcription Initiation By Rna Polymerase I. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28623663
DOI: 10.7554/ELIFE.27414
Page generated: Mon Oct 28 13:48:21 2024
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