Zinc in PDB 5n5y: Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Enzymatic activity of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
All present enzymatic activity of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III):
2.7.7.6;
Other elements in 5n5y:
The structure of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
(pdb code 5n5y). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III), PDB code: 5n5y:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5n5y
Go back to
Zinc Binding Sites List in 5n5y
Zinc binding site 1 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2001
b:0.0
occ:1.00
|
SG
|
A:CYS65
|
1.8
|
0.0
|
1.0
|
NE2
|
A:HIS75
|
2.0
|
0.0
|
1.0
|
SG
|
A:CYS62
|
2.1
|
0.0
|
1.0
|
SG
|
A:CYS72
|
2.3
|
0.0
|
1.0
|
CD2
|
A:HIS75
|
2.8
|
0.0
|
1.0
|
CE1
|
A:HIS75
|
3.0
|
0.0
|
1.0
|
CB
|
A:CYS62
|
3.2
|
0.0
|
1.0
|
CB
|
A:CYS65
|
3.4
|
0.0
|
1.0
|
CB
|
A:CYS72
|
3.6
|
0.0
|
1.0
|
N
|
A:CYS65
|
3.9
|
0.0
|
1.0
|
CG
|
A:HIS75
|
3.9
|
0.0
|
1.0
|
CD
|
A:PRO73
|
3.9
|
0.0
|
1.0
|
ND1
|
A:HIS75
|
4.0
|
0.0
|
1.0
|
CA
|
A:CYS65
|
4.3
|
0.0
|
1.0
|
CA
|
A:CYS72
|
4.3
|
0.0
|
1.0
|
N
|
A:GLY74
|
4.4
|
0.0
|
1.0
|
CA
|
A:GLY55
|
4.5
|
0.0
|
1.0
|
N
|
A:PRO73
|
4.5
|
0.0
|
1.0
|
C
|
A:CYS72
|
4.6
|
0.0
|
1.0
|
CA
|
A:CYS62
|
4.7
|
0.0
|
1.0
|
CB
|
A:THR64
|
4.7
|
0.0
|
1.0
|
CG
|
A:PRO73
|
4.7
|
0.0
|
1.0
|
CA
|
A:GLY74
|
4.7
|
0.0
|
1.0
|
C
|
A:THR64
|
4.9
|
0.0
|
1.0
|
C
|
A:GLY74
|
4.9
|
0.0
|
1.0
|
N
|
A:GLY66
|
5.0
|
0.0
|
1.0
|
C
|
A:CYS65
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5n5y
Go back to
Zinc Binding Sites List in 5n5y
Zinc binding site 2 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2002
b:0.0
occ:1.00
|
SG
|
A:CYS105
|
2.1
|
0.0
|
1.0
|
SG
|
A:CYS236
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS233
|
2.4
|
0.0
|
1.0
|
SG
|
A:CYS102
|
2.4
|
0.0
|
1.0
|
CB
|
A:CYS105
|
3.1
|
0.0
|
1.0
|
CB
|
A:CYS102
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS233
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS236
|
3.4
|
0.0
|
1.0
|
N
|
A:CYS105
|
3.6
|
0.0
|
1.0
|
N
|
A:CYS236
|
3.8
|
0.0
|
1.0
|
CA
|
A:CYS105
|
3.9
|
0.0
|
1.0
|
CA
|
A:CYS236
|
4.2
|
0.0
|
1.0
|
C
|
A:CYS105
|
4.6
|
0.0
|
1.0
|
N
|
A:HIS106
|
4.7
|
0.0
|
1.0
|
CB
|
A:ASN235
|
4.7
|
0.0
|
1.0
|
C
|
A:ASN235
|
4.7
|
0.0
|
1.0
|
CA
|
A:CYS102
|
4.8
|
0.0
|
1.0
|
CA
|
A:CYS233
|
4.8
|
0.0
|
1.0
|
C
|
A:PHE104
|
4.8
|
0.0
|
1.0
|
C
|
A:CYS236
|
4.9
|
0.0
|
1.0
|
CB
|
A:PHE104
|
4.9
|
0.0
|
1.0
|
N
|
A:GLY237
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5n5y
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Zinc Binding Sites List in 5n5y
Zinc binding site 3 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2001
b:0.0
occ:1.00
|
SG
|
B:CYS1104
|
2.2
|
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
|
2.3
|
0.0
|
1.0
|
CB
|
B:CYS1104
|
3.0
|
0.0
|
1.0
|
CB
|
B:CYS1107
|
3.1
|
0.0
|
1.0
|
CB
|
B:CYS1128
|
3.3
|
0.0
|
1.0
|
CB
|
B:CYS1131
|
3.3
|
0.0
|
1.0
|
N
|
B:CYS1107
|
3.6
|
0.0
|
1.0
|
CA
|
B:CYS1107
|
4.0
|
0.0
|
1.0
|
N
|
B:CYS1131
|
4.0
|
0.0
|
1.0
|
CA
|
B:CYS1131
|
4.3
|
0.0
|
1.0
|
CB
|
B:ARG1130
|
4.3
|
0.0
|
1.0
|
CA
|
B:CYS1104
|
4.5
|
0.0
|
1.0
|
CB
|
B:GLU1106
|
4.5
|
0.0
|
1.0
|
OG1
|
B:THR1112
|
4.5
|
0.0
|
1.0
|
C
|
B:GLU1106
|
4.6
|
0.0
|
1.0
|
CA
|
B:CYS1128
|
4.7
|
0.0
|
1.0
|
CD
|
B:ARG1130
|
4.7
|
0.0
|
1.0
|
C
|
B:ARG1130
|
4.8
|
0.0
|
1.0
|
C
|
B:CYS1107
|
4.8
|
0.0
|
1.0
|
N
|
B:ARG1130
|
4.9
|
0.0
|
1.0
|
CA
|
B:ARG1130
|
4.9
|
0.0
|
1.0
|
CG
|
B:ARG1130
|
4.9
|
0.0
|
1.0
|
CA
|
B:GLU1106
|
4.9
|
0.0
|
1.0
|
C
|
B:CYS1104
|
4.9
|
0.0
|
1.0
|
O
|
B:CYS1104
|
4.9
|
0.0
|
1.0
|
N
|
B:GLU1106
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5n5y
Go back to
Zinc Binding Sites List in 5n5y
Zinc binding site 4 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn1001
b:0.0
occ:1.00
|
SG
|
I:CYS10
|
2.2
|
0.0
|
1.0
|
SG
|
I:CYS13
|
2.2
|
0.0
|
1.0
|
SG
|
I:CYS33
|
2.3
|
0.0
|
1.0
|
SG
|
I:CYS30
|
2.4
|
0.0
|
1.0
|
CB
|
I:CYS10
|
3.1
|
0.0
|
1.0
|
CB
|
I:CYS30
|
3.4
|
0.0
|
1.0
|
CB
|
I:CYS13
|
3.4
|
0.0
|
1.0
|
N
|
I:CYS13
|
3.5
|
0.0
|
1.0
|
CB
|
I:CYS33
|
3.7
|
0.0
|
1.0
|
CA
|
I:CYS13
|
3.9
|
0.0
|
1.0
|
N
|
I:CYS33
|
4.0
|
0.0
|
1.0
|
C
|
I:CYS13
|
4.3
|
0.0
|
1.0
|
CB
|
I:ASP12
|
4.4
|
0.0
|
1.0
|
CA
|
I:CYS33
|
4.4
|
0.0
|
1.0
|
CB
|
I:ALA35
|
4.4
|
0.0
|
1.0
|
O
|
I:CYS13
|
4.5
|
0.0
|
1.0
|
CB
|
I:GLN32
|
4.5
|
0.0
|
1.0
|
CA
|
I:CYS10
|
4.5
|
0.0
|
1.0
|
C
|
I:ASP12
|
4.6
|
0.0
|
1.0
|
N
|
I:ASP12
|
4.8
|
0.0
|
1.0
|
CA
|
I:ASP12
|
4.8
|
0.0
|
1.0
|
CA
|
I:CYS30
|
4.8
|
0.0
|
1.0
|
N
|
I:ASP15
|
4.9
|
0.0
|
1.0
|
C
|
I:CYS10
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5n5y
Go back to
Zinc Binding Sites List in 5n5y
Zinc binding site 5 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn1002
b:0.0
occ:0.75
|
SG
|
I:CYS114
|
2.2
|
0.0
|
1.0
|
SG
|
I:CYS117
|
2.2
|
0.0
|
1.0
|
SG
|
I:CYS89
|
2.2
|
0.0
|
1.0
|
SG
|
I:CYS86
|
2.5
|
0.0
|
1.0
|
CB
|
I:CYS117
|
3.1
|
0.0
|
1.0
|
CB
|
I:CYS86
|
3.1
|
0.0
|
1.0
|
CB
|
I:CYS89
|
3.1
|
0.0
|
1.0
|
CB
|
I:CYS114
|
3.2
|
0.0
|
1.0
|
N
|
I:CYS89
|
3.7
|
0.0
|
1.0
|
CA
|
I:CYS89
|
3.9
|
0.0
|
1.0
|
N
|
I:CYS117
|
3.9
|
0.0
|
1.0
|
CA
|
I:CYS117
|
4.0
|
0.0
|
1.0
|
CB
|
I:ASN91
|
4.1
|
0.0
|
1.0
|
OG
|
I:SER116
|
4.6
|
0.0
|
1.0
|
N
|
I:GLY90
|
4.6
|
0.0
|
1.0
|
C
|
I:CYS89
|
4.6
|
0.0
|
1.0
|
CA
|
I:CYS114
|
4.6
|
0.0
|
1.0
|
CA
|
I:CYS86
|
4.6
|
0.0
|
1.0
|
N
|
I:ASN91
|
4.6
|
0.0
|
1.0
|
C
|
I:CYS117
|
4.7
|
0.0
|
1.0
|
CB
|
I:GLN88
|
4.8
|
0.0
|
1.0
|
C
|
I:GLN88
|
4.9
|
0.0
|
1.0
|
N
|
I:GLY118
|
4.9
|
0.0
|
1.0
|
CB
|
I:TYR119
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5n5y
Go back to
Zinc Binding Sites List in 5n5y
Zinc binding site 6 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn1001
b:0.0
occ:1.00
|
CA
|
J:CYS46
|
1.7
|
0.0
|
1.0
|
N
|
J:CYS46
|
1.8
|
0.0
|
1.0
|
SG
|
J:CYS7
|
2.2
|
0.0
|
1.0
|
SG
|
J:CYS46
|
2.3
|
0.0
|
1.0
|
CB
|
J:CYS46
|
2.3
|
0.0
|
1.0
|
SG
|
J:CYS45
|
2.3
|
0.0
|
1.0
|
C
|
J:CYS45
|
2.3
|
0.0
|
1.0
|
SG
|
J:CYS10
|
2.4
|
0.0
|
1.0
|
O
|
J:CYS45
|
2.8
|
0.0
|
1.0
|
CB
|
J:CYS7
|
3.1
|
0.0
|
1.0
|
C
|
J:CYS46
|
3.2
|
0.0
|
1.0
|
CB
|
J:CYS45
|
3.4
|
0.0
|
1.0
|
CA
|
J:CYS45
|
3.4
|
0.0
|
1.0
|
O
|
J:CYS46
|
3.8
|
0.0
|
1.0
|
CG
|
J:MET49
|
4.0
|
0.0
|
1.0
|
N
|
J:ARG47
|
4.1
|
0.0
|
1.0
|
CB
|
J:CYS10
|
4.1
|
0.0
|
1.0
|
NH1
|
J:ARG48
|
4.4
|
0.0
|
1.0
|
CA
|
J:CYS7
|
4.4
|
0.0
|
1.0
|
N
|
J:CYS45
|
4.4
|
0.0
|
1.0
|
O
|
J:ARG43
|
4.5
|
0.0
|
1.0
|
CB
|
J:MET49
|
4.9
|
0.0
|
1.0
|
N
|
J:CYS10
|
4.9
|
0.0
|
1.0
|
C
|
J:TYR44
|
4.9
|
0.0
|
1.0
|
O
|
J:TYR44
|
4.9
|
0.0
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5n5y
Go back to
Zinc Binding Sites List in 5n5y
Zinc binding site 7 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn1001
b:0.0
occ:1.00
|
SG
|
L:CYS34
|
2.2
|
0.0
|
1.0
|
SG
|
L:CYS48
|
2.2
|
0.0
|
1.0
|
SG
|
L:CYS51
|
2.3
|
0.0
|
1.0
|
SG
|
L:CYS31
|
2.5
|
0.0
|
1.0
|
CB
|
L:CYS51
|
2.7
|
0.0
|
1.0
|
CB
|
L:CYS48
|
2.9
|
0.0
|
1.0
|
CB
|
L:CYS34
|
3.3
|
0.0
|
1.0
|
N
|
L:CYS51
|
3.3
|
0.0
|
1.0
|
CB
|
L:CYS31
|
3.4
|
0.0
|
1.0
|
CA
|
L:CYS51
|
3.6
|
0.0
|
1.0
|
N
|
L:CYS34
|
4.0
|
0.0
|
1.0
|
CA
|
L:CYS34
|
4.2
|
0.0
|
1.0
|
CA
|
L:CYS48
|
4.4
|
0.0
|
1.0
|
CB
|
L:ASP50
|
4.4
|
0.0
|
1.0
|
C
|
L:ASP50
|
4.5
|
0.0
|
1.0
|
OG
|
L:SER36
|
4.5
|
0.0
|
1.0
|
C
|
L:CYS51
|
4.7
|
0.0
|
1.0
|
N
|
L:GLY52
|
4.7
|
0.0
|
1.0
|
CA
|
L:ASP50
|
4.8
|
0.0
|
1.0
|
CA
|
L:CYS31
|
4.8
|
0.0
|
1.0
|
N
|
L:ASP50
|
4.8
|
0.0
|
1.0
|
C
|
L:CYS34
|
4.9
|
0.0
|
1.0
|
N
|
L:SER35
|
4.9
|
0.0
|
1.0
|
C
|
L:CYS48
|
4.9
|
0.0
|
1.0
|
CB
|
L:HIS53
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5n5y
Go back to
Zinc Binding Sites List in 5n5y
Zinc binding site 8 out
of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) 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
|
4.2
|
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 22:35:37 2024
|