Zinc in PDB 5oa1: Rna Polymerase I Pre-Initiation Complex
Enzymatic activity of Rna Polymerase I Pre-Initiation Complex
All present enzymatic activity of Rna Polymerase I Pre-Initiation Complex:
2.7.7.6;
Zinc Binding Sites:
The binding sites of Zinc atom in the Rna Polymerase I Pre-Initiation Complex
(pdb code 5oa1). 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 Pre-Initiation Complex, PDB code: 5oa1:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
Zinc binding site 1 out
of 7 in 5oa1
Go back to
Zinc Binding Sites List in 5oa1
Zinc binding site 1 out
of 7 in the Rna Polymerase I Pre-Initiation 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 Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1701
b:0.1
occ:1.00
|
SG
|
A:CYS105
|
2.2
|
0.3
|
1.0
|
SG
|
A:CYS233
|
2.4
|
0.2
|
1.0
|
SG
|
A:CYS102
|
2.4
|
0.9
|
1.0
|
SG
|
A:CYS236
|
2.4
|
0.8
|
1.0
|
CB
|
A:CYS102
|
3.1
|
0.1
|
1.0
|
CB
|
A:CYS233
|
3.3
|
0.3
|
1.0
|
CB
|
A:CYS105
|
3.3
|
0.3
|
1.0
|
O
|
A:CYS236
|
3.6
|
0.3
|
1.0
|
N
|
A:CYS236
|
3.7
|
0.9
|
1.0
|
CB
|
A:CYS236
|
3.7
|
0.9
|
1.0
|
N
|
A:CYS105
|
3.8
|
1.0
|
1.0
|
CA
|
A:CYS236
|
4.1
|
0.4
|
1.0
|
CA
|
A:CYS105
|
4.1
|
0.9
|
1.0
|
C
|
A:CYS236
|
4.3
|
0.8
|
1.0
|
CB
|
A:ASN235
|
4.5
|
0.9
|
1.0
|
CA
|
A:CYS102
|
4.6
|
0.4
|
1.0
|
CA
|
A:CYS233
|
4.8
|
0.2
|
1.0
|
C
|
A:ASN235
|
4.8
|
0.3
|
1.0
|
C
|
A:CYS105
|
4.9
|
0.3
|
1.0
|
N
|
A:HIS106
|
4.9
|
0.6
|
1.0
|
CB
|
A:PHE104
|
5.0
|
0.1
|
1.0
|
|
Zinc binding site 2 out
of 7 in 5oa1
Go back to
Zinc Binding Sites List in 5oa1
Zinc binding site 2 out
of 7 in the Rna Polymerase I Pre-Initiation 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 Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1702
b:95.4
occ:1.00
|
NE2
|
A:HIS75
|
2.0
|
92.3
|
1.0
|
SG
|
A:CYS65
|
2.2
|
92.3
|
1.0
|
SG
|
A:CYS62
|
2.3
|
94.9
|
1.0
|
SG
|
A:CYS72
|
2.3
|
92.9
|
1.0
|
CD2
|
A:HIS75
|
2.7
|
92.3
|
1.0
|
CB
|
A:CYS62
|
3.0
|
90.8
|
1.0
|
CE1
|
A:HIS75
|
3.1
|
92.0
|
1.0
|
CB
|
A:CYS65
|
3.3
|
89.3
|
1.0
|
CB
|
A:CYS72
|
3.7
|
89.0
|
1.0
|
N
|
A:CYS65
|
3.7
|
90.1
|
1.0
|
CG
|
A:HIS75
|
4.0
|
90.5
|
1.0
|
CA
|
A:CYS65
|
4.0
|
89.9
|
1.0
|
ND1
|
A:HIS75
|
4.1
|
92.2
|
1.0
|
CA
|
A:GLY55
|
4.3
|
81.8
|
1.0
|
CD
|
A:PRO73
|
4.4
|
90.2
|
1.0
|
CA
|
A:CYS72
|
4.4
|
88.5
|
1.0
|
CA
|
A:CYS62
|
4.5
|
91.1
|
1.0
|
N
|
A:GLY66
|
4.6
|
89.8
|
1.0
|
C
|
A:CYS65
|
4.6
|
93.2
|
1.0
|
N
|
A:GLY74
|
4.6
|
85.8
|
1.0
|
CB
|
A:THR64
|
4.7
|
93.7
|
1.0
|
C
|
A:THR64
|
4.8
|
94.5
|
1.0
|
N
|
A:PRO73
|
4.9
|
87.8
|
1.0
|
N
|
A:ALA56
|
4.9
|
83.7
|
1.0
|
C
|
A:CYS72
|
4.9
|
91.5
|
1.0
|
CA
|
A:GLY74
|
4.9
|
85.5
|
1.0
|
N
|
A:LEU67
|
5.0
|
89.2
|
1.0
|
|
Zinc binding site 3 out
of 7 in 5oa1
Go back to
Zinc Binding Sites List in 5oa1
Zinc binding site 3 out
of 7 in the Rna Polymerase I Pre-Initiation 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 Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1301
b:79.3
occ:1.00
|
SG
|
B:CYS1131
|
2.2
|
88.5
|
1.0
|
SG
|
B:CYS1104
|
2.2
|
81.6
|
1.0
|
SG
|
B:CYS1128
|
2.3
|
84.6
|
1.0
|
SG
|
B:CYS1107
|
2.4
|
88.7
|
1.0
|
CB
|
B:CYS1104
|
3.2
|
76.8
|
1.0
|
CB
|
B:CYS1107
|
3.3
|
85.5
|
1.0
|
CB
|
B:CYS1131
|
3.3
|
86.2
|
1.0
|
CB
|
B:CYS1128
|
3.4
|
81.5
|
1.0
|
N
|
B:CYS1107
|
3.7
|
85.1
|
1.0
|
N
|
B:CYS1131
|
3.8
|
86.3
|
1.0
|
CA
|
B:CYS1107
|
4.1
|
84.9
|
1.0
|
CA
|
B:CYS1131
|
4.2
|
87.1
|
1.0
|
CB
|
B:ARG1130
|
4.3
|
83.0
|
1.0
|
OG1
|
B:THR1112
|
4.3
|
0.9
|
1.0
|
CB
|
B:GLU1106
|
4.4
|
86.4
|
1.0
|
CG
|
B:ARG1130
|
4.6
|
89.1
|
1.0
|
C
|
B:GLU1106
|
4.6
|
88.1
|
1.0
|
CA
|
B:CYS1104
|
4.6
|
76.2
|
1.0
|
C
|
B:ARG1130
|
4.8
|
89.9
|
1.0
|
OG
|
B:SER1109
|
4.8
|
0.5
|
1.0
|
CA
|
B:CYS1128
|
4.8
|
82.0
|
1.0
|
CA
|
B:GLU1106
|
4.9
|
83.9
|
1.0
|
CA
|
B:ARG1130
|
4.9
|
84.5
|
1.0
|
C
|
B:CYS1107
|
4.9
|
89.3
|
1.0
|
|
Zinc binding site 4 out
of 7 in 5oa1
Go back to
Zinc Binding Sites List in 5oa1
Zinc binding site 4 out
of 7 in the Rna Polymerase I Pre-Initiation 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 Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:0.0
occ:1.00
|
SG
|
I:CYS30
|
2.2
|
0.7
|
1.0
|
SG
|
I:CYS13
|
2.5
|
0.4
|
1.0
|
CB
|
I:CYS30
|
2.8
|
0.9
|
1.0
|
SG
|
I:CYS10
|
3.0
|
0.9
|
1.0
|
SG
|
I:CYS33
|
3.1
|
0.3
|
1.0
|
CB
|
I:CYS10
|
3.5
|
0.8
|
1.0
|
O
|
I:CYS33
|
3.8
|
0.5
|
1.0
|
CB
|
I:CYS13
|
4.1
|
0.7
|
1.0
|
N
|
I:CYS33
|
4.2
|
0.5
|
1.0
|
CA
|
I:CYS30
|
4.3
|
0.2
|
1.0
|
CB
|
I:ALA35
|
4.5
|
0.3
|
1.0
|
CB
|
I:CYS33
|
4.6
|
0.7
|
1.0
|
CB
|
I:GLN32
|
4.6
|
0.2
|
1.0
|
CB
|
I:ASP15
|
4.6
|
0.5
|
1.0
|
N
|
I:CYS13
|
4.6
|
0.5
|
1.0
|
C
|
I:CYS33
|
4.7
|
0.2
|
1.0
|
CA
|
I:CYS33
|
4.7
|
0.4
|
1.0
|
C
|
I:CYS30
|
4.9
|
0.7
|
1.0
|
CA
|
I:CYS13
|
5.0
|
0.3
|
1.0
|
CA
|
I:CYS10
|
5.0
|
0.1
|
1.0
|
|
Zinc binding site 5 out
of 7 in 5oa1
Go back to
Zinc Binding Sites List in 5oa1
Zinc binding site 5 out
of 7 in the Rna Polymerase I Pre-Initiation 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 Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn202
b:0.2
occ:1.00
|
SG
|
I:CYS86
|
3.1
|
0.9
|
1.0
|
SG
|
I:CYS89
|
3.1
|
0.6
|
1.0
|
SG
|
I:CYS114
|
3.2
|
0.7
|
1.0
|
CB
|
I:GLN88
|
3.7
|
0.9
|
1.0
|
CB
|
I:SER116
|
4.1
|
0.7
|
1.0
|
CB
|
I:CYS86
|
4.2
|
0.6
|
1.0
|
N
|
I:CYS89
|
4.2
|
0.9
|
1.0
|
CG
|
I:GLN88
|
4.3
|
0.3
|
1.0
|
SG
|
I:CYS117
|
4.3
|
0.1
|
1.0
|
CB
|
I:ASN91
|
4.4
|
0.3
|
1.0
|
CB
|
I:CYS89
|
4.5
|
0.9
|
1.0
|
OG
|
I:SER116
|
4.6
|
0.7
|
1.0
|
CB
|
I:CYS114
|
4.6
|
1.0
|
1.0
|
CA
|
I:GLN88
|
4.8
|
0.1
|
1.0
|
N
|
I:GLY90
|
4.8
|
0.5
|
1.0
|
C
|
I:GLN88
|
4.9
|
0.9
|
1.0
|
CA
|
I:CYS89
|
4.9
|
0.7
|
1.0
|
|
Zinc binding site 6 out
of 7 in 5oa1
Go back to
Zinc Binding Sites List in 5oa1
Zinc binding site 6 out
of 7 in the Rna Polymerase I Pre-Initiation 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 Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:0.1
occ:1.00
|
SG
|
J:CYS7
|
2.2
|
1.0
|
1.0
|
SG
|
J:CYS46
|
2.3
|
0.6
|
1.0
|
SG
|
J:CYS45
|
2.3
|
0.2
|
1.0
|
SG
|
J:CYS10
|
2.6
|
97.7
|
1.0
|
CB
|
J:CYS7
|
3.1
|
99.2
|
1.0
|
N
|
J:CYS46
|
3.3
|
97.3
|
1.0
|
CB
|
J:CYS45
|
3.5
|
95.9
|
1.0
|
CB
|
J:CYS46
|
3.6
|
98.9
|
1.0
|
CA
|
J:CYS46
|
3.6
|
97.6
|
1.0
|
CB
|
J:CYS10
|
3.7
|
92.5
|
1.0
|
C
|
J:CYS45
|
3.7
|
0.5
|
1.0
|
N
|
J:CYS10
|
3.7
|
90.8
|
1.0
|
CA
|
J:CYS45
|
4.2
|
96.3
|
1.0
|
NE
|
J:ARG43
|
4.2
|
84.9
|
1.0
|
O
|
J:CYS45
|
4.2
|
99.9
|
1.0
|
CA
|
J:CYS10
|
4.3
|
91.2
|
1.0
|
CB
|
J:SER9
|
4.4
|
94.1
|
1.0
|
CA
|
J:CYS7
|
4.5
|
98.1
|
1.0
|
N
|
J:GLY11
|
4.7
|
93.0
|
1.0
|
C
|
J:SER9
|
4.8
|
93.8
|
1.0
|
C
|
J:CYS7
|
4.8
|
98.7
|
1.0
|
CB
|
J:ARG43
|
4.8
|
95.6
|
1.0
|
O
|
J:CYS7
|
4.9
|
98.0
|
1.0
|
CD
|
J:ARG43
|
4.9
|
87.4
|
1.0
|
CB
|
J:LYS12
|
4.9
|
1.0
|
1.0
|
NH2
|
J:ARG43
|
4.9
|
78.6
|
1.0
|
N
|
J:SER9
|
4.9
|
91.3
|
1.0
|
CA
|
J:SER9
|
4.9
|
90.3
|
1.0
|
N
|
J:LYS12
|
5.0
|
97.4
|
1.0
|
N
|
J:CYS45
|
5.0
|
97.5
|
1.0
|
C
|
J:CYS10
|
5.0
|
95.7
|
1.0
|
|
Zinc binding site 7 out
of 7 in 5oa1
Go back to
Zinc Binding Sites List in 5oa1
Zinc binding site 7 out
of 7 in the Rna Polymerase I Pre-Initiation 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 Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:0.5
occ:1.00
|
SG
|
L:CYS34
|
2.4
|
0.1
|
1.0
|
SG
|
L:CYS51
|
2.4
|
0.6
|
1.0
|
SG
|
L:CYS31
|
2.4
|
0.0
|
1.0
|
SG
|
L:CYS48
|
2.4
|
0.2
|
1.0
|
CB
|
L:CYS48
|
2.9
|
0.5
|
1.0
|
CB
|
L:CYS31
|
3.3
|
0.4
|
1.0
|
CB
|
L:CYS51
|
3.6
|
0.6
|
1.0
|
CB
|
L:CYS34
|
3.7
|
0.9
|
1.0
|
O
|
L:CYS51
|
3.7
|
0.9
|
1.0
|
N
|
L:CYS51
|
3.7
|
0.4
|
1.0
|
OG
|
L:SER36
|
4.0
|
0.6
|
1.0
|
CA
|
L:CYS51
|
4.0
|
0.5
|
1.0
|
N
|
L:CYS34
|
4.0
|
0.2
|
1.0
|
C
|
L:CYS51
|
4.2
|
0.9
|
1.0
|
CA
|
L:CYS48
|
4.4
|
0.2
|
1.0
|
CB
|
L:HIS53
|
4.4
|
0.0
|
1.0
|
CA
|
L:CYS34
|
4.4
|
0.7
|
1.0
|
CB
|
L:ASP50
|
4.7
|
0.4
|
1.0
|
C
|
L:ASP50
|
4.7
|
0.6
|
1.0
|
CA
|
L:CYS31
|
4.7
|
0.5
|
1.0
|
C
|
L:CYS48
|
4.9
|
0.1
|
1.0
|
N
|
L:HIS53
|
5.0
|
0.2
|
1.0
|
|
Reference:
Y.Sadian,
L.Tafur,
J.Kosinski,
A.J.Jakobi,
R.Wetzel,
K.Buczak,
W.J.Hagen,
M.Beck,
C.Sachse,
C.W.Muller.
Structural Insights Into Transcription Initiation By Yeast Rna Polymerase I. Embo J. V. 36 2698 2017.
ISSN: ESSN 1460-2075
PubMed: 28739580
DOI: 10.15252/EMBJ.201796958
Page generated: Sun Oct 27 23:21:01 2024
|