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Zinc in PDB 6vjs: Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex

Enzymatic activity of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex

All present enzymatic activity of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex, PDB code: 6vjs was solved by K.S.Murakami, V.Molodtsov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.09 / 4.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.077, 205.501, 309.880, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27.6

Other elements in 6vjs:

The structure of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex (pdb code 6vjs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex, PDB code: 6vjs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6vjs

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Zinc binding site 1 out of 4 in the Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:0.5
occ:1.00
 SG D:CYS72 2.2 0.8 1.0
SG D:CYS70 2.2 0.9 1.0
SG D:CYS85 2.3 0.8 1.0
CB D:CYS85 3.0 0.8 1.0
CB D:CYS70 3.5 0.8 1.0
N D:GLY73 3.8 0.9 1.0
CB D:CYS72 3.8 0.2 1.0
N D:CYS72 3.9 0.6 1.0
SG D:CYS88 3.9 0.5 1.0
N D:LYS74 4.1 0.1 1.0
CA D:CYS72 4.3 0.5 1.0
N D:LEU71 4.4 0.8 1.0
CA D:CYS85 4.5 0.8 1.0
C D:CYS72 4.5 1.0 1.0
N D:CYS88 4.5 0.6 1.0
CB D:LYS74 4.6 0.5 1.0
CB D:LYS87 4.6 0.2 1.0
CA D:GLY73 4.7 0.2 1.0
N D:GLY89 4.8 0.4 1.0
CA D:CYS70 4.8 0.5 1.0
C D:GLY73 4.8 0.4 1.0
C D:CYS70 4.9 0.0 1.0
CA D:LYS74 4.9 0.8 1.0
CD1 D:TYR75 4.9 0.7 1.0
C D:LEU71 4.9 0.8 1.0
CB D:CYS88 5.0 0.0 1.0
N D:LYS87 5.0 0.0 1.0

Zinc binding site 2 out of 4 in 6vjs

Go back to Zinc Binding Sites List in 6vjs
Zinc binding site 2 out of 4 in the Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:0.4
occ:1.00
 SG D:CYS814 2.1 0.8 1.0
SG D:CYS888 2.2 0.8 1.0
SG D:CYS895 2.3 0.5 1.0
SG D:CYS898 2.4 0.0 1.0
CB D:CYS888 3.0 0.7 1.0
CA D:CYS888 3.1 0.2 1.0
CB D:CYS898 3.2 0.6 1.0
CB D:CYS895 3.3 0.8 1.0
CB D:CYS814 3.9 0.4 1.0
NH2 D:ARG883 4.0 0.2 1.0
C D:CYS888 4.0 0.5 1.0
N D:CYS895 4.1 1.0 1.0
CA D:CYS895 4.2 0.1 1.0
N D:CYS888 4.3 0.4 1.0
N D:CYS814 4.4 0.6 1.0
CA D:CYS898 4.4 0.6 1.0
N D:CYS898 4.5 0.2 1.0
N D:ASP889 4.5 0.1 1.0
O D:CYS888 4.6 0.9 1.0
CA D:CYS814 4.6 0.7 1.0
O D:CYS895 4.7 0.6 1.0
CB D:THR890 4.7 1.0 1.0
N D:THR890 4.8 0.2 1.0
C D:CYS895 4.8 0.2 1.0
NE D:ARG883 4.9 0.8 1.0
CZ D:ARG883 4.9 0.2 1.0

Zinc binding site 3 out of 4 in 6vjs

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Zinc binding site 3 out of 4 in the Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1501

b:0.8
occ:1.00
 SG I:CYS85 2.3 0.8 1.0
SG I:CYS72 2.3 0.0 1.0
SG I:CYS70 2.6 0.2 1.0
SG I:CYS88 2.7 0.6 1.0
CB I:CYS85 2.9 0.8 1.0
CB I:CYS72 3.7 0.4 1.0
CB I:CYS70 3.8 0.9 1.0
N I:CYS88 3.9 0.0 1.0
N I:CYS72 4.0 0.1 1.0
CB I:CYS88 4.1 0.8 1.0
CB I:LYS87 4.2 0.9 1.0
CA I:CYS72 4.4 0.6 1.0
CA I:CYS85 4.4 0.2 1.0
N I:GLY73 4.4 0.6 1.0
CA I:CYS88 4.5 0.6 1.0
N I:LYS74 4.6 0.4 1.0
CB I:LYS74 4.6 1.0 1.0
N I:LYS87 4.6 0.9 1.0
C I:LYS87 4.7 0.7 1.0
N I:LEU71 4.7 0.8 1.0
CA I:LYS87 4.8 0.9 1.0
CD1 I:TYR75 4.8 0.1 1.0
C I:CYS88 4.9 0.1 1.0
N I:GLU86 4.9 0.1 1.0
C I:CYS72 5.0 0.4 1.0

Zinc binding site 4 out of 4 in 6vjs

Go back to Zinc Binding Sites List in 6vjs
Zinc binding site 4 out of 4 in the Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Escherichia Coli Rna Polymerase and Ureidothiophene-2-Carboxylic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1502

b:0.8
occ:1.00
 SG I:CYS888 2.2 0.0 1.0
SG I:CYS898 2.4 0.9 1.0
CB I:CYS898 2.5 0.5 1.0
CB I:CYS895 2.5 0.3 1.0
CB I:CYS888 3.0 0.9 1.0
SG I:CYS895 3.3 0.4 1.0
CA I:CYS895 3.5 0.3 1.0
N I:CYS895 3.5 0.8 1.0
N I:CYS898 3.6 0.8 1.0
CA I:CYS898 3.7 0.9 1.0
CA I:CYS888 3.9 0.8 1.0
O I:CYS895 3.9 0.5 1.0
SG I:CYS814 3.9 0.6 1.0
C I:CYS895 4.0 0.5 1.0
NH2 I:ARG883 4.1 0.6 1.0
C I:CYS888 4.8 0.7 1.0
C I:CYS898 4.8 0.2 1.0
C I:VAL894 4.8 0.8 1.0
C I:HIS897 4.9 0.8 1.0
N I:CYS888 5.0 0.1 1.0

Reference:

J.Haupenthal, Y.Kautz, W.A.M.Elgaher, L.Patzold, T.Rohrig, M.W.Laschke, T.Tschernig, A.K.H.Hirsch, V.Molodtsov, K.S.Murakami, R.W.Hartmann, M.Bischoff. Evaluation of Bacterial Rna Polymerase Inhibitors in A Staphylococcus Aureus -Based Wound Infection Model in SKH1 Mice. Acs Infect Dis. V. 6 2573 2020.
ISSN: ESSN 2373-8227
PubMed: 32886885
DOI: 10.1021/ACSINFECDIS.0C00034
Page generated: Tue Oct 29 09:04:11 2024

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