Atomistry » Sodium » PDB 6lgy-6me0 » 6m1j
Atomistry »
  Sodium »
    PDB 6lgy-6me0 »
      6m1j »

Sodium in PDB 6m1j: The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X

Enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X

All present enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X:
5.6.2.2;

Protein crystallography data

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X, PDB code: 6m1j was solved by Z.H.Xu, Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.92 / 1.70
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 145.216, 160.743, 41.421, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.1

Other elements in 6m1j:

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X (pdb code 6m1j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X, PDB code: 6m1j:

Sodium binding site 1 out of 1 in 6m1j

Go back to Sodium Binding Sites List in 6m1j
Sodium binding site 1 out of 1 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:25.0
occ:1.00
 OG A:SER165 2.2 18.8 1.0
O A:ASN76 2.3 12.6 1.0
O A:HOH548 2.3 35.3 1.0
O A:HOH552 2.3 37.3 1.0
O A:GLY77 2.6 12.8 1.0
O A:SER165 2.6 14.6 1.0
C A:ASN76 3.0 10.5 1.0
C A:SER165 3.2 14.6 1.0
CB A:SER165 3.3 18.4 1.0
C A:GLY77 3.4 14.1 1.0
CA A:SER165 3.6 12.5 1.0
N A:GLY77 3.7 13.8 1.0
N A:SER165 3.7 18.3 1.0
O A:HOH469 3.8 21.1 1.0
O A:HOH554 3.8 32.7 1.0
CA A:GLY77 3.8 12.4 1.0
CA A:ASN76 3.9 10.3 1.0
O A:HOH592 4.0 45.9 1.0
O A:HOH492 4.1 29.8 1.0
N A:GLY166 4.1 12.3 1.0
CB A:ASN76 4.2 13.6 1.0
N A:ARG78 4.4 11.1 1.0
O A:HOH579 4.6 42.3 1.0
CA A:GLY166 4.6 12.0 1.0
O A:TYR57 4.7 18.5 1.0
CA A:ARG78 4.8 12.5 1.0
CG A:ASN76 4.8 16.1 1.0
C A:GLY164 5.0 32.0 1.0

Reference:

Y.Hu, H.Shi, M.Zhou, Q.Ren, W.Zhu, W.Zhang, Z.Zhang, C.Zhou, Y.Liu, X.Ding, H.C.Shen, S.F.Yan, F.Dey, W.Wu, G.Zhai, Z.Zhou, Z.Xu, Y.Ji, H.Lv, T.Jiang, W.Wang, Y.Xu, M.Vercruysse, X.Yao, Y.Mao, X.Yu, K.Bradley, X.Tan. Discovery of Pyrido[2,3-B]Indole Derivatives with Gram-Negative Activity Targeting Both Dna Gyrase and Topoisomerase IV. J.Med.Chem. V. 63 9623 2020.
ISSN: ISSN 0022-2623
PubMed: 32787097
DOI: 10.1021/ACS.JMEDCHEM.0C00768
Page generated: Tue Oct 8 11:48:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy