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Zinc in PDB 7ok0: Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A

Enzymatic activity of Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A

All present enzymatic activity of Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A:
2.7.7.6;

Other elements in 7ok0:

The structure of Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A 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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A (pdb code 7ok0). 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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A, PDB code: 7ok0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7ok0

Go back to Zinc Binding Sites List in 7ok0
Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A


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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:127.6
occ:1.00
 NE2 A:HIS71 2.1 113.0 1.0
SG A:CYS61 2.3 122.8 1.0
SG A:CYS68 2.3 117.6 1.0
SG A:CYS58 2.3 125.0 1.0
CB A:CYS58 3.0 125.0 1.0
CD2 A:HIS71 3.0 113.0 1.0
CE1 A:HIS71 3.1 113.0 1.0
CB A:CYS68 3.8 117.6 1.0
O A:PRO69 4.0 113.2 1.0
CB A:CYS61 4.0 122.8 1.0
N A:CYS61 4.2 122.8 1.0
CG A:HIS71 4.2 113.0 1.0
ND1 A:HIS71 4.2 113.0 1.0
CA A:CYS68 4.4 117.6 1.0
O A:CYS61 4.4 122.8 1.0
CA A:CYS58 4.5 125.0 1.0
CA A:CYS61 4.6 122.8 1.0
CB A:VAL60 4.6 121.8 1.0
C A:CYS68 4.7 117.6 1.0
C A:CYS61 5.0 122.8 1.0
CA A:GLY50 5.0 122.4 1.0

Zinc binding site 2 out of 6 in 7ok0

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A


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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:148.8
occ:1.00
 SG A:CYS98 2.3 133.8 1.0
SG A:CYS101 2.3 135.0 1.0
SG A:CYS146 2.3 136.0 1.0
SG A:CYS149 2.3 138.6 1.0
CB A:CYS98 2.9 133.8 1.0
CB A:CYS146 3.2 136.0 1.0
CB A:CYS149 3.4 138.6 1.0
CB A:CYS101 3.6 135.0 1.0
N A:CYS149 4.0 138.6 1.0
NE2 A:GLN153 4.0 135.9 1.0
N A:CYS101 4.0 135.0 1.0
CA A:CYS149 4.3 138.6 1.0
CA A:CYS101 4.4 135.0 1.0
CA A:CYS98 4.4 133.8 1.0
CA A:CYS146 4.6 136.0 1.0
CB A:HIS148 4.8 134.5 1.0
O A:CYS146 4.9 136.0 1.0
C A:CYS149 5.0 138.6 1.0
CD A:GLN153 5.0 135.9 1.0
C A:HIS148 5.0 134.5 1.0

Zinc binding site 3 out of 6 in 7ok0

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A


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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:122.1
occ:1.00
 OG A:SER584 2.1 83.4 1.0
O A:ARG573 2.1 95.7 1.0
SG A:CYS580 2.3 95.7 1.0
SG A:CYS575 2.3 101.4 1.0
ND1 A:HIS582 2.3 92.8 1.0
CG A:HIS582 2.9 92.8 1.0
CB A:HIS582 2.9 92.8 1.0
CB A:SER584 3.1 83.4 1.0
C A:ARG573 3.1 95.7 1.0
CE1 A:HIS582 3.4 92.8 1.0
CA A:ARG573 3.6 95.7 1.0
CB A:ARG573 3.7 95.7 1.0
CB A:CYS575 3.8 101.4 1.0
CA A:HIS582 3.9 92.8 1.0
N A:HIS582 3.9 92.8 1.0
CD2 A:HIS582 4.1 92.8 1.0
CB A:CYS580 4.1 95.7 1.0
N A:CYS575 4.1 101.4 1.0
NE2 A:HIS582 4.3 92.8 1.0
CA A:SER584 4.3 83.4 1.0
N A:ALA574 4.3 99.8 1.0
N A:SER584 4.4 83.4 1.0
C A:HIS582 4.4 92.8 1.0
CG A:ARG573 4.5 95.7 1.0
CA A:CYS575 4.6 101.4 1.0
C A:ALA574 4.6 99.8 1.0
O A:HIS582 4.6 92.8 1.0
CA A:ALA574 4.8 99.8 1.0
CA A:CYS580 4.9 95.7 1.0
N A:ARG573 5.0 95.7 1.0

Zinc binding site 4 out of 6 in 7ok0

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A


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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:124.2
occ:1.00
 ND1 B:HIS1081 2.1 113.0 1.0
SG B:CYS1063 2.3 104.5 1.0
SG B:CYS1060 2.3 106.2 1.0
SG B:CYS1078 2.3 114.6 1.0
CE1 B:HIS1081 2.8 113.0 1.0
CB B:CYS1060 2.9 106.2 1.0
CG B:HIS1081 3.1 113.0 1.0
CB B:CYS1063 3.4 104.5 1.0
CG2 B:VAL1080 3.5 111.9 1.0
CB B:HIS1081 3.6 113.0 1.0
CB B:CYS1078 3.8 114.6 1.0
N B:CYS1063 3.8 104.5 1.0
NE2 B:HIS1081 3.8 113.0 1.0
CD2 B:HIS1081 4.0 113.0 1.0
N B:HIS1081 4.1 113.0 1.0
CA B:CYS1063 4.2 104.5 1.0
OG B:SER1085 4.2 114.7 1.0
CA B:CYS1060 4.4 106.2 1.0
CA B:HIS1081 4.5 113.0 1.0
CB B:SER1085 4.7 114.7 1.0
N B:GLY1064 4.8 101.3 1.0
CB B:VAL1080 4.9 111.9 1.0
C B:GLN1062 4.9 108.2 1.0
N B:GLN1062 5.0 108.2 1.0
CB B:GLN1062 5.0 108.2 1.0
C B:CYS1063 5.0 104.5 1.0

Zinc binding site 5 out of 6 in 7ok0

Go back to Zinc Binding Sites List in 7ok0
Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A


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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:66.9
occ:1.00
 SG N:CYS10 2.3 49.4 1.0
SG N:CYS44 2.3 48.2 1.0
SG N:CYS45 2.3 48.1 1.0
SG N:CYS7 2.3 45.7 1.0
CB N:CYS7 3.2 45.7 1.0
N N:CYS45 3.4 48.1 1.0
CB N:CYS44 3.5 48.2 1.0
CB N:CYS45 3.7 48.1 1.0
CB N:CYS10 3.8 49.4 1.0
CA N:CYS45 3.9 48.1 1.0
C N:CYS44 3.9 48.2 1.0
N N:CYS10 4.0 49.4 1.0
O N:CYS10 4.2 49.4 1.0
CA N:CYS44 4.3 48.2 1.0
CA N:CYS10 4.4 49.4 1.0
NE N:ARG42 4.5 48.5 1.0
C N:CYS10 4.6 49.4 1.0
O N:CYS44 4.7 48.2 1.0
CA N:CYS7 4.7 45.7 1.0
CB N:ALA12 4.8 46.7 1.0
CB N:THR9 4.8 45.9 1.0
N N:CYS44 4.9 48.2 1.0
CB N:ARG42 4.9 48.5 1.0

Zinc binding site 6 out of 6 in 7ok0

Go back to Zinc Binding Sites List in 7ok0
Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A


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 Sulfolobus Acidocaldarius Rna Polymerase at 2.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:123.4
occ:1.00
 SG P:CYS29 2.3 109.2 1.0
SG P:CYS6 2.3 96.9 1.0
SG P:CYS26 2.3 103.5 1.0
CB P:CYS6 2.8 96.9 1.0
CB P:CYS29 3.4 109.2 1.0
CG P:GLU12 3.6 101.2 1.0
CB P:CYS26 3.6 103.5 1.0
N P:CYS29 3.7 109.2 1.0
CA P:CYS29 4.2 109.2 1.0
CB P:TYR28 4.3 109.5 1.0
CB P:GLU12 4.3 101.2 1.0
CA P:CYS6 4.3 96.9 1.0
CD P:GLU12 4.6 101.2 1.0
C P:TYR28 4.6 109.5 1.0
CA P:TYR28 4.8 109.5 1.0
N P:TYR28 4.9 109.5 1.0
CA P:CYS26 5.0 103.5 1.0
OE2 P:GLU12 5.0 101.2 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 08:33:32 2024

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