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:

Iron (Fe) 3 atoms
Magnesium (Mg) 1 atom

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

Go back to 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 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 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 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 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 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: Fri Sep 24 17:09:20 2021

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