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:

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

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

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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

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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

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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 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

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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

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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

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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

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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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