Zinc in PDB 7oq4: Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase
Enzymatic activity of Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase
All present enzymatic activity of Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase:
2.7.7.6;
Other elements in 7oq4:
The structure of Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase
(pdb code 7oq4). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase, PDB code: 7oq4:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 7oq4
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Zinc Binding Sites List in 7oq4
Zinc binding site 1 out
of 6 in the Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S 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 Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn902
b:70.5
occ:1.00
|
NE2
|
A:HIS71
|
2.1
|
34.2
|
1.0
|
SG
|
A:CYS58
|
2.3
|
49.3
|
1.0
|
SG
|
A:CYS61
|
2.3
|
48.7
|
1.0
|
SG
|
A:CYS68
|
2.3
|
35.5
|
1.0
|
CD2
|
A:HIS71
|
3.0
|
34.2
|
1.0
|
CB
|
A:CYS58
|
3.0
|
49.3
|
1.0
|
CE1
|
A:HIS71
|
3.1
|
34.2
|
1.0
|
CB
|
A:CYS61
|
3.6
|
48.7
|
1.0
|
CB
|
A:CYS68
|
3.7
|
35.5
|
1.0
|
N
|
A:CYS61
|
4.1
|
48.7
|
1.0
|
CG
|
A:HIS71
|
4.2
|
34.2
|
1.0
|
ND1
|
A:HIS71
|
4.2
|
34.2
|
1.0
|
CA
|
A:CYS68
|
4.3
|
35.5
|
1.0
|
CA
|
A:CYS61
|
4.4
|
48.7
|
1.0
|
CA
|
A:CYS58
|
4.5
|
49.3
|
1.0
|
CB
|
A:VAL60
|
4.8
|
44.4
|
1.0
|
CD
|
A:PRO69
|
4.9
|
30.8
|
1.0
|
C
|
A:CYS58
|
4.9
|
49.3
|
1.0
|
C
|
A:CYS68
|
4.9
|
35.5
|
1.0
|
|
Zinc binding site 2 out
of 6 in 7oq4
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Zinc Binding Sites List in 7oq4
Zinc binding site 2 out
of 6 in the Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S 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 Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn903
b:102.8
occ:1.00
|
SG
|
A:CYS101
|
2.3
|
68.8
|
1.0
|
SG
|
A:CYS98
|
2.3
|
66.3
|
1.0
|
SG
|
A:CYS149
|
2.3
|
73.5
|
1.0
|
SG
|
A:CYS146
|
2.3
|
71.2
|
1.0
|
CB
|
A:CYS146
|
3.4
|
71.2
|
1.0
|
CB
|
A:CYS101
|
3.5
|
68.8
|
1.0
|
CB
|
A:CYS149
|
3.5
|
73.5
|
1.0
|
N
|
A:CYS101
|
3.7
|
68.8
|
1.0
|
CB
|
A:CYS98
|
3.9
|
66.3
|
1.0
|
N
|
A:CYS149
|
3.9
|
73.5
|
1.0
|
CA
|
A:CYS101
|
4.1
|
68.8
|
1.0
|
CB
|
A:HIS148
|
4.2
|
71.6
|
1.0
|
CB
|
A:ARG100
|
4.3
|
64.7
|
1.0
|
CA
|
A:CYS149
|
4.3
|
73.5
|
1.0
|
N
|
A:GLY102
|
4.6
|
62.1
|
1.0
|
C
|
A:HIS148
|
4.7
|
71.6
|
1.0
|
C
|
A:ARG100
|
4.7
|
64.7
|
1.0
|
C
|
A:CYS101
|
4.8
|
68.8
|
1.0
|
CA
|
A:CYS146
|
4.8
|
71.2
|
1.0
|
N
|
A:ARG103
|
4.8
|
60.2
|
1.0
|
CA
|
A:HIS148
|
4.9
|
71.6
|
1.0
|
CA
|
A:ARG100
|
4.9
|
64.7
|
1.0
|
CG
|
A:HIS148
|
4.9
|
71.6
|
1.0
|
CD2
|
A:HIS148
|
4.9
|
71.6
|
1.0
|
CB
|
A:ARG103
|
5.0
|
60.2
|
1.0
|
O
|
A:ARG103
|
5.0
|
60.2
|
1.0
|
N
|
A:HIS148
|
5.0
|
71.6
|
1.0
|
|
Zinc binding site 3 out
of 6 in 7oq4
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Zinc Binding Sites List in 7oq4
Zinc binding site 3 out
of 6 in the Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S 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 Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn904
b:91.9
occ:1.00
|
O
|
A:ARG573
|
2.3
|
78.6
|
1.0
|
SG
|
A:CYS580
|
2.3
|
61.6
|
1.0
|
ND1
|
A:HIS582
|
2.3
|
55.3
|
1.0
|
CG
|
A:HIS582
|
2.9
|
55.3
|
1.0
|
CB
|
A:HIS582
|
3.0
|
55.3
|
1.0
|
CE1
|
A:HIS582
|
3.3
|
55.3
|
1.0
|
C
|
A:ARG573
|
3.5
|
78.6
|
1.0
|
CD2
|
A:HIS582
|
4.0
|
55.3
|
1.0
|
N
|
A:HIS582
|
4.1
|
55.3
|
1.0
|
CB
|
A:CYS580
|
4.1
|
61.6
|
1.0
|
CA
|
A:HIS582
|
4.1
|
55.3
|
1.0
|
CA
|
A:ARG573
|
4.1
|
78.6
|
1.0
|
SG
|
A:CYS575
|
4.1
|
81.1
|
1.0
|
CB
|
A:ARG573
|
4.1
|
78.6
|
1.0
|
NE2
|
A:HIS582
|
4.2
|
55.3
|
1.0
|
OG
|
A:SER584
|
4.3
|
32.6
|
1.0
|
O
|
A:HIS582
|
4.4
|
55.3
|
1.0
|
N
|
A:ALA574
|
4.5
|
75.3
|
1.0
|
C
|
A:HIS582
|
4.7
|
55.3
|
1.0
|
N
|
A:CYS575
|
4.8
|
81.1
|
1.0
|
CA
|
A:ALA574
|
4.8
|
75.3
|
1.0
|
CD
|
A:PRO581
|
4.9
|
58.7
|
1.0
|
C
|
A:ALA574
|
5.0
|
75.3
|
1.0
|
|
Zinc binding site 4 out
of 6 in 7oq4
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Zinc Binding Sites List in 7oq4
Zinc binding site 4 out
of 6 in the Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S 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 Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1201
b:66.0
occ:1.00
|
ND1
|
B:HIS1081
|
2.2
|
41.9
|
1.0
|
SG
|
B:CYS1063
|
2.3
|
34.4
|
1.0
|
SG
|
B:CYS1060
|
2.3
|
38.1
|
1.0
|
SG
|
B:CYS1078
|
2.3
|
40.3
|
1.0
|
CG
|
B:HIS1081
|
2.7
|
41.9
|
1.0
|
CB
|
B:HIS1081
|
3.0
|
41.9
|
1.0
|
CB
|
B:CYS1060
|
3.0
|
38.1
|
1.0
|
CE1
|
B:HIS1081
|
3.0
|
41.9
|
1.0
|
CB
|
B:CYS1078
|
3.6
|
40.3
|
1.0
|
CD2
|
B:HIS1081
|
3.7
|
41.9
|
1.0
|
N
|
B:HIS1081
|
3.7
|
41.9
|
1.0
|
CB
|
B:CYS1063
|
3.8
|
34.4
|
1.0
|
NE2
|
B:HIS1081
|
3.8
|
41.9
|
1.0
|
OG
|
B:SER1085
|
3.9
|
46.3
|
1.0
|
CA
|
B:HIS1081
|
3.9
|
41.9
|
1.0
|
N
|
B:CYS1063
|
4.1
|
34.4
|
1.0
|
CB
|
B:SER1085
|
4.5
|
46.3
|
1.0
|
CA
|
B:CYS1060
|
4.5
|
38.1
|
1.0
|
CB
|
B:VAL1080
|
4.5
|
36.8
|
1.0
|
CA
|
B:CYS1063
|
4.6
|
34.4
|
1.0
|
C
|
B:VAL1080
|
4.7
|
36.8
|
1.0
|
N
|
B:VAL1080
|
4.9
|
36.8
|
1.0
|
CA
|
B:VAL1080
|
5.0
|
36.8
|
1.0
|
N
|
B:GLY1064
|
5.0
|
31.8
|
1.0
|
CA
|
B:CYS1078
|
5.0
|
40.3
|
1.0
|
CG1
|
B:VAL1080
|
5.0
|
36.8
|
1.0
|
|
Zinc binding site 5 out
of 6 in 7oq4
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Zinc Binding Sites List in 7oq4
Zinc binding site 5 out
of 6 in the Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S 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 Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn101
b:30.5
occ:1.00
|
SG
|
N:CYS44
|
2.3
|
12.8
|
1.0
|
SG
|
N:CYS45
|
2.3
|
15.1
|
1.0
|
SG
|
N:CYS10
|
2.3
|
16.3
|
1.0
|
SG
|
N:CYS7
|
2.3
|
10.1
|
1.0
|
CB
|
N:CYS7
|
3.1
|
10.1
|
1.0
|
N
|
N:CYS45
|
3.3
|
15.1
|
1.0
|
CB
|
N:CYS44
|
3.6
|
12.8
|
1.0
|
CB
|
N:CYS45
|
3.7
|
15.1
|
1.0
|
C
|
N:CYS44
|
3.7
|
12.8
|
1.0
|
CA
|
N:CYS45
|
3.8
|
15.1
|
1.0
|
CB
|
N:CYS10
|
3.8
|
16.3
|
1.0
|
O
|
N:CYS10
|
3.9
|
16.3
|
1.0
|
N
|
N:CYS10
|
3.9
|
16.3
|
1.0
|
O
|
N:CYS44
|
4.3
|
12.8
|
1.0
|
CA
|
N:CYS44
|
4.3
|
12.8
|
1.0
|
CA
|
N:CYS10
|
4.3
|
16.3
|
1.0
|
NE
|
N:ARG42
|
4.4
|
15.7
|
1.0
|
C
|
N:CYS10
|
4.5
|
16.3
|
1.0
|
CA
|
N:CYS7
|
4.6
|
10.1
|
1.0
|
CB
|
N:ALA12
|
4.7
|
18.9
|
1.0
|
CB
|
N:THR9
|
4.7
|
10.1
|
1.0
|
CB
|
N:ARG42
|
4.8
|
15.7
|
1.0
|
N
|
N:CYS44
|
5.0
|
12.8
|
1.0
|
|
Zinc binding site 6 out
of 6 in 7oq4
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Zinc Binding Sites List in 7oq4
Zinc binding site 6 out
of 6 in the Cryo-Em Structure of the Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S 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 Atv Rnap Inhibitory Protein (Rip) Bound to the Dna-Binding Channel of the Host'S Rna Polymerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Zn101
b:98.2
occ:1.00
|
OE1
|
P:GLU12
|
2.0
|
66.5
|
1.0
|
OE2
|
P:GLU12
|
2.0
|
66.5
|
1.0
|
CD
|
P:GLU12
|
2.2
|
66.5
|
1.0
|
SG
|
P:CYS6
|
2.3
|
61.8
|
1.0
|
SG
|
P:CYS29
|
2.3
|
66.6
|
1.0
|
SG
|
P:CYS26
|
2.3
|
64.5
|
1.0
|
CB
|
P:CYS6
|
3.1
|
61.8
|
1.0
|
CG
|
P:GLU12
|
3.6
|
66.5
|
1.0
|
CB
|
P:CYS29
|
3.7
|
66.6
|
1.0
|
N
|
P:CYS29
|
3.7
|
66.6
|
1.0
|
CB
|
P:CYS26
|
3.8
|
64.5
|
1.0
|
CB
|
P:TYR28
|
3.8
|
71.3
|
1.0
|
CD2
|
P:TYR28
|
4.0
|
71.3
|
1.0
|
CA
|
P:CYS29
|
4.2
|
66.6
|
1.0
|
C
|
P:TYR28
|
4.4
|
71.3
|
1.0
|
CG
|
P:TYR28
|
4.4
|
71.3
|
1.0
|
CB
|
P:GLU12
|
4.5
|
66.5
|
1.0
|
CA
|
P:TYR28
|
4.5
|
71.3
|
1.0
|
CA
|
P:CYS6
|
4.6
|
61.8
|
1.0
|
O
|
P:CYS29
|
4.6
|
66.6
|
1.0
|
CB
|
P:LYS8
|
4.6
|
67.9
|
1.0
|
C
|
P:CYS29
|
4.7
|
66.6
|
1.0
|
N
|
P:TYR28
|
4.8
|
71.3
|
1.0
|
O
|
P:GLU12
|
4.9
|
66.5
|
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 08:42:47 2024
|