Atomistry » Zinc » PDB 6v77-6vpc » 6vjs
Atomistry »
  Zinc »
    PDB 6v77-6vpc »
      6vjs »

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

Go back to Zinc Binding Sites List in 6vjs
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

Go back to Zinc Binding Sites List in 6vjs
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy