Zinc in PDB 7oqy: Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
Enzymatic activity of Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
All present enzymatic activity of Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase:
2.7.7.6;
Other elements in 7oqy:
The structure of Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
(pdb code 7oqy). 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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase, PDB code: 7oqy:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7oqy
Go back to
Zinc Binding Sites List in 7oqy
Zinc binding site 1 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn902
b:94.0
occ:1.00
|
NE2
|
A:HIS71
|
2.1
|
86.6
|
1.0
|
SG
|
A:CYS68
|
2.3
|
87.5
|
1.0
|
SG
|
A:CYS61
|
2.3
|
96.7
|
1.0
|
SG
|
A:CYS58
|
2.3
|
99.6
|
1.0
|
CD2
|
A:HIS71
|
3.0
|
86.6
|
1.0
|
CB
|
A:CYS58
|
3.1
|
99.6
|
1.0
|
CE1
|
A:HIS71
|
3.1
|
86.6
|
1.0
|
CB
|
A:CYS68
|
3.6
|
87.5
|
1.0
|
O
|
A:PRO69
|
3.8
|
85.0
|
1.0
|
CB
|
A:CYS61
|
4.0
|
96.7
|
1.0
|
N
|
A:CYS61
|
4.0
|
96.7
|
1.0
|
CG
|
A:HIS71
|
4.2
|
86.6
|
1.0
|
ND1
|
A:HIS71
|
4.2
|
86.6
|
1.0
|
O
|
A:CYS61
|
4.3
|
96.7
|
1.0
|
CA
|
A:CYS68
|
4.3
|
87.5
|
1.0
|
CA
|
A:CYS61
|
4.5
|
96.7
|
1.0
|
CB
|
A:VAL60
|
4.5
|
95.5
|
1.0
|
CA
|
A:CYS58
|
4.6
|
99.6
|
1.0
|
C
|
A:CYS68
|
4.8
|
87.5
|
1.0
|
C
|
A:CYS61
|
4.8
|
96.7
|
1.0
|
C
|
A:PRO69
|
4.9
|
85.0
|
1.0
|
C
|
A:VAL60
|
4.9
|
95.5
|
1.0
|
N
|
A:PRO69
|
4.9
|
85.0
|
1.0
|
CA
|
A:GLY50
|
5.0
|
96.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7oqy
Go back to
Zinc Binding Sites List in 7oqy
Zinc binding site 2 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn903
b:143.4
occ:1.00
|
SG
|
A:CYS149
|
2.3
|
136.6
|
1.0
|
SG
|
A:CYS101
|
2.3
|
124.3
|
1.0
|
SG
|
A:CYS146
|
2.3
|
134.5
|
1.0
|
SG
|
A:CYS98
|
2.3
|
123.0
|
1.0
|
CB
|
A:CYS98
|
3.0
|
123.0
|
1.0
|
CB
|
A:CYS146
|
3.2
|
134.5
|
1.0
|
CB
|
A:CYS149
|
3.4
|
136.6
|
1.0
|
CB
|
A:CYS101
|
3.8
|
124.3
|
1.0
|
N
|
A:CYS101
|
4.0
|
124.3
|
1.0
|
N
|
A:CYS149
|
4.0
|
136.6
|
1.0
|
CA
|
A:CYS149
|
4.4
|
136.6
|
1.0
|
CB
|
A:HIS148
|
4.4
|
132.1
|
1.0
|
NH2
|
A:ARG100
|
4.4
|
125.7
|
1.0
|
CA
|
A:CYS101
|
4.5
|
124.3
|
1.0
|
CA
|
A:CYS98
|
4.5
|
123.0
|
1.0
|
C
|
A:HIS148
|
4.6
|
132.1
|
1.0
|
NE2
|
A:GLN153
|
4.6
|
130.8
|
1.0
|
CB
|
A:ARG100
|
4.6
|
125.7
|
1.0
|
CA
|
A:CYS146
|
4.6
|
134.5
|
1.0
|
NE
|
A:ARG100
|
4.7
|
125.7
|
1.0
|
ND1
|
A:HIS148
|
4.8
|
132.1
|
1.0
|
CZ
|
A:ARG100
|
4.8
|
125.7
|
1.0
|
CA
|
A:HIS148
|
4.9
|
132.1
|
1.0
|
N
|
A:ARG100
|
4.9
|
125.7
|
1.0
|
N
|
A:GLY102
|
4.9
|
120.9
|
1.0
|
C
|
A:ARG100
|
4.9
|
125.7
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7oqy
Go back to
Zinc Binding Sites List in 7oqy
Zinc binding site 3 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn904
b:87.9
occ:1.00
|
O
|
A:ARG573
|
2.0
|
70.2
|
1.0
|
SG
|
A:CYS580
|
2.3
|
67.5
|
1.0
|
SG
|
A:CYS575
|
2.3
|
79.0
|
1.0
|
ND1
|
A:HIS582
|
2.3
|
62.2
|
1.0
|
CE1
|
A:HIS582
|
3.0
|
62.2
|
1.0
|
C
|
A:ARG573
|
3.1
|
70.2
|
1.0
|
CG
|
A:HIS582
|
3.3
|
62.2
|
1.0
|
CB
|
A:CYS575
|
3.7
|
79.0
|
1.0
|
CA
|
A:ARG573
|
3.8
|
70.2
|
1.0
|
CB
|
A:CYS580
|
3.8
|
67.5
|
1.0
|
CB
|
A:HIS582
|
3.8
|
62.2
|
1.0
|
N
|
A:CYS575
|
3.9
|
79.0
|
1.0
|
CD
|
A:PRO581
|
3.9
|
65.0
|
1.0
|
C
|
A:ALA574
|
4.0
|
77.1
|
1.0
|
N
|
A:ALA574
|
4.1
|
77.1
|
1.0
|
CA
|
A:CYS580
|
4.1
|
67.5
|
1.0
|
NE2
|
A:HIS582
|
4.1
|
62.2
|
1.0
|
N
|
A:HIS582
|
4.2
|
62.2
|
1.0
|
N
|
A:PRO581
|
4.2
|
65.0
|
1.0
|
CD2
|
A:HIS582
|
4.3
|
62.2
|
1.0
|
CB
|
A:ARG573
|
4.3
|
70.2
|
1.0
|
CA
|
A:CYS575
|
4.3
|
79.0
|
1.0
|
CA
|
A:ALA574
|
4.3
|
77.1
|
1.0
|
O
|
A:ALA574
|
4.4
|
77.1
|
1.0
|
OG
|
A:SER584
|
4.5
|
47.0
|
1.0
|
C
|
A:CYS580
|
4.5
|
67.5
|
1.0
|
CA
|
A:HIS582
|
4.6
|
62.2
|
1.0
|
CB
|
A:SER584
|
4.6
|
47.0
|
1.0
|
O
|
A:PRO572
|
4.9
|
77.9
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7oqy
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Zinc Binding Sites List in 7oqy
Zinc binding site 4 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1201
b:103.7
occ:1.00
|
CD2
|
B:HIS1081
|
1.7
|
101.3
|
1.0
|
CG
|
B:HIS1081
|
1.9
|
101.3
|
1.0
|
NE2
|
B:HIS1081
|
2.1
|
101.3
|
1.0
|
SG
|
B:CYS1060
|
2.3
|
83.2
|
1.0
|
SG
|
B:CYS1063
|
2.3
|
81.5
|
1.0
|
SG
|
B:CYS1078
|
2.4
|
97.8
|
1.0
|
ND1
|
B:HIS1081
|
2.5
|
101.3
|
1.0
|
CE1
|
B:HIS1081
|
2.5
|
101.3
|
1.0
|
CB
|
B:CYS1060
|
2.9
|
83.2
|
1.0
|
CB
|
B:HIS1081
|
3.0
|
101.3
|
1.0
|
CB
|
B:CYS1078
|
3.7
|
97.8
|
1.0
|
CB
|
B:CYS1063
|
3.8
|
81.5
|
1.0
|
N
|
B:CYS1063
|
4.3
|
81.5
|
1.0
|
CA
|
B:HIS1081
|
4.3
|
101.3
|
1.0
|
CA
|
B:CYS1060
|
4.4
|
83.2
|
1.0
|
N
|
B:HIS1081
|
4.5
|
101.3
|
1.0
|
OG
|
B:SER1085
|
4.5
|
100.7
|
1.0
|
CA
|
B:CYS1063
|
4.7
|
81.5
|
1.0
|
CB
|
B:SER1085
|
4.8
|
100.7
|
1.0
|
CB
|
B:GLN1062
|
4.9
|
88.1
|
1.0
|
C
|
B:VAL1080
|
4.9
|
96.7
|
1.0
|
CB
|
B:VAL1080
|
4.9
|
96.7
|
1.0
|
N
|
B:VAL1080
|
5.0
|
96.7
|
1.0
|
CA
|
B:CYS1078
|
5.0
|
97.8
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7oqy
Go back to
Zinc Binding Sites List in 7oqy
Zinc binding site 5 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn101
b:39.1
occ:1.00
|
SG
|
N:CYS45
|
2.3
|
19.9
|
1.0
|
SG
|
N:CYS10
|
2.3
|
19.4
|
1.0
|
SG
|
N:CYS44
|
2.3
|
18.9
|
1.0
|
SG
|
N:CYS7
|
2.3
|
15.4
|
1.0
|
CB
|
N:CYS7
|
3.2
|
15.4
|
1.0
|
N
|
N:CYS45
|
3.5
|
19.9
|
1.0
|
CB
|
N:CYS45
|
3.7
|
19.9
|
1.0
|
CB
|
N:CYS44
|
3.7
|
18.9
|
1.0
|
CB
|
N:CYS10
|
3.7
|
19.4
|
1.0
|
N
|
N:CYS10
|
3.8
|
19.4
|
1.0
|
CA
|
N:CYS45
|
3.8
|
19.9
|
1.0
|
C
|
N:CYS44
|
3.9
|
18.9
|
1.0
|
CA
|
N:CYS10
|
4.2
|
19.4
|
1.0
|
O
|
N:CYS44
|
4.4
|
18.9
|
1.0
|
CA
|
N:CYS44
|
4.4
|
18.9
|
1.0
|
CB
|
N:THR9
|
4.4
|
19.3
|
1.0
|
O
|
N:CYS10
|
4.4
|
19.4
|
1.0
|
NE
|
N:ARG42
|
4.4
|
20.7
|
1.0
|
C
|
N:CYS10
|
4.6
|
19.4
|
1.0
|
CA
|
N:CYS7
|
4.7
|
15.4
|
1.0
|
NH2
|
N:ARG42
|
4.8
|
20.7
|
1.0
|
C
|
N:THR9
|
4.8
|
19.3
|
1.0
|
CB
|
N:ALA12
|
4.9
|
21.3
|
1.0
|
N
|
N:THR9
|
4.9
|
19.3
|
1.0
|
CA
|
N:THR9
|
5.0
|
19.3
|
1.0
|
CG2
|
N:THR9
|
5.0
|
19.3
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7oqy
Go back to
Zinc Binding Sites List in 7oqy
Zinc binding site 6 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Zn101
b:90.7
occ:1.00
|
OE2
|
P:GLU12
|
2.0
|
71.6
|
1.0
|
SG
|
P:CYS29
|
2.3
|
81.4
|
1.0
|
SG
|
P:CYS6
|
2.3
|
68.5
|
1.0
|
SG
|
P:CYS26
|
2.3
|
77.4
|
1.0
|
CD
|
P:GLU12
|
2.6
|
71.6
|
1.0
|
OE1
|
P:GLU12
|
3.0
|
71.6
|
1.0
|
CB
|
P:CYS6
|
3.1
|
68.5
|
1.0
|
CB
|
P:CYS26
|
3.5
|
77.4
|
1.0
|
CB
|
P:CYS29
|
3.6
|
81.4
|
1.0
|
CG
|
P:GLU12
|
3.6
|
71.6
|
1.0
|
N
|
P:CYS29
|
4.2
|
81.4
|
1.0
|
CA
|
P:CYS29
|
4.5
|
81.4
|
1.0
|
CA
|
P:CYS6
|
4.5
|
68.5
|
1.0
|
O
|
P:CYS6
|
4.7
|
68.5
|
1.0
|
CB
|
P:GLU12
|
4.7
|
71.6
|
1.0
|
CB
|
P:TYR28
|
4.7
|
82.8
|
1.0
|
C
|
P:CYS6
|
4.7
|
68.5
|
1.0
|
CG
|
P:LYS8
|
4.8
|
73.6
|
1.0
|
CD2
|
P:TYR28
|
4.9
|
82.8
|
1.0
|
CA
|
P:CYS26
|
4.9
|
77.4
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7oqy
Go back to
Zinc Binding Sites List in 7oqy
Zinc binding site 7 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Zn101
b:128.9
occ:1.00
|
SG
|
Y:CYS20
|
2.3
|
128.0
|
1.0
|
SG
|
Y:CYS4
|
2.3
|
114.1
|
1.0
|
CB
|
Y:CYS7
|
2.6
|
115.5
|
1.0
|
CB
|
Y:CYS4
|
2.9
|
114.1
|
1.0
|
CB
|
Y:CYS20
|
3.2
|
128.0
|
1.0
|
CB
|
Y:CYS23
|
3.4
|
129.1
|
1.0
|
N
|
Y:CYS7
|
3.4
|
115.5
|
1.0
|
CA
|
Y:CYS7
|
3.6
|
115.5
|
1.0
|
SG
|
Y:CYS7
|
3.9
|
115.5
|
1.0
|
SG
|
Y:CYS23
|
3.9
|
129.1
|
1.0
|
N
|
Y:CYS23
|
4.2
|
129.1
|
1.0
|
CA
|
Y:CYS4
|
4.4
|
114.1
|
1.0
|
CA
|
Y:CYS23
|
4.4
|
129.1
|
1.0
|
C
|
Y:CYS7
|
4.4
|
115.5
|
1.0
|
N
|
Y:GLY8
|
4.4
|
109.8
|
1.0
|
CB
|
Y:TYR25
|
4.7
|
127.1
|
1.0
|
CA
|
Y:CYS20
|
4.7
|
128.0
|
1.0
|
C
|
Y:LYS6
|
4.7
|
117.7
|
1.0
|
N
|
Y:SER9
|
4.9
|
108.4
|
1.0
|
C
|
Y:CYS4
|
5.0
|
114.1
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7oqy
Go back to
Zinc Binding Sites List in 7oqy
Zinc binding site 8 out
of 8 in the Cryo-Em Structure of the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase
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 the Cellular Negative Regulator TFS4 Bound to the Archaeal Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Zn102
b:72.1
occ:1.00
|
SG
|
Y:CYS66
|
2.3
|
50.8
|
1.0
|
SG
|
Y:CYS83
|
2.3
|
45.5
|
1.0
|
SG
|
Y:CYS86
|
2.3
|
48.9
|
1.0
|
SG
|
Y:CYS63
|
2.3
|
48.5
|
1.0
|
CB
|
Y:CYS83
|
3.1
|
45.5
|
1.0
|
CB
|
Y:CYS63
|
3.1
|
48.5
|
1.0
|
CB
|
Y:CYS66
|
3.5
|
50.8
|
1.0
|
CB
|
Y:CYS86
|
3.6
|
48.9
|
1.0
|
N
|
Y:CYS66
|
3.9
|
50.8
|
1.0
|
N
|
Y:CYS86
|
4.0
|
48.9
|
1.0
|
CA
|
Y:CYS66
|
4.3
|
50.8
|
1.0
|
CA
|
Y:CYS86
|
4.4
|
48.9
|
1.0
|
OG
|
Y:SER68
|
4.4
|
50.1
|
1.0
|
CB
|
Y:PHE88
|
4.5
|
45.8
|
1.0
|
CA
|
Y:CYS83
|
4.5
|
45.5
|
1.0
|
CA
|
Y:CYS63
|
4.6
|
48.5
|
1.0
|
N
|
Y:GLY67
|
4.6
|
51.1
|
1.0
|
CB
|
Y:THR85
|
4.7
|
47.5
|
1.0
|
CB
|
Y:ARG65
|
4.7
|
46.5
|
1.0
|
C
|
Y:CYS66
|
4.9
|
50.8
|
1.0
|
N
|
Y:SER68
|
4.9
|
50.1
|
1.0
|
C
|
Y:THR85
|
4.9
|
47.5
|
1.0
|
C
|
Y:CYS86
|
4.9
|
48.9
|
1.0
|
CB
|
Y:SER68
|
5.0
|
50.1
|
1.0
|
C
|
Y:ARG65
|
5.0
|
46.5
|
1.0
|
N
|
Y:PHE88
|
5.0
|
45.8
|
1.0
|
|
Reference:
S.Pilotto,
T.Fouqueau,
N.Lukoyanova,
C.Sheppard,
S.Lucas-Staat,
L.M.Diaz-Santin,
D.Matelska,
D.Prangishvili,
A.C.M.Cheung,
F.Werner.
Structural Basis of Rna Polymerase Inhibition By Viral and Host Factors Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Wed Oct 30 08:43:49 2024
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