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Sodium in PDB 7okc: Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1

Enzymatic activity of Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1

All present enzymatic activity of Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1:
2.3.1.129;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1, PDB code: 7okc was solved by M.D.Ryan, A.L.Parkes, M.Southey, O.A.Andersen, M.Zahn, J.Barker, B.L.M.Dejonge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.94 / 1.84
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 96.086, 96.086, 96.086, 90, 90, 90
R / Rfree (%) 17.3 / 21.8

Other elements in 7okc:

The structure of Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1 (pdb code 7okc). 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 Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1, PDB code: 7okc:

Sodium binding site 1 out of 1 in 7okc

Go back to Sodium Binding Sites List in 7okc
Sodium binding site 1 out of 1 in the Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Escherichia Coli Lpxa in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:39.6
occ:1.00
 O A:HOH1255 2.5 54.6 1.0
O A:SER256 2.5 30.1 1.0
O A:PHE253 2.9 35.4 1.0
O A:ALA254 3.3 36.9 1.0
C A:SER256 3.7 31.5 1.0
C A:ALA254 3.8 35.4 1.0
C A:PHE253 4.0 35.4 1.0
N A:SER256 4.0 31.9 1.0
CA A:ALA254 4.2 36.5 1.0
O A:HOH1235 4.3 44.8 1.0
CA A:SER256 4.4 30.5 1.0
C A:ARG255 4.4 32.0 1.0
N A:ARG255 4.4 32.9 1.0
N A:ALA254 4.6 35.6 1.0
O A:HOH1161 4.7 37.9 1.0
N A:THR257 4.7 31.3 1.0
CB A:SER256 4.7 30.4 1.0
O A:HOH1162 4.8 36.1 1.0
CA A:ARG255 4.9 32.2 1.0
O A:ARG255 5.0 32.0 1.0

Reference:

M.D.Ryan, A.L.Parkes, D.Corbett, A.P.Dickie, M.Southey, O.A.Andersen, D.B.Stein, O.R.Barbeau, A.Sanzone, P.Thommes, J.Barker, R.Cain, C.Compper, M.Dejob, A.Dorali, D.Etheridge, S.Evans, A.Faulkner, E.Gadouleau, T.Gorman, D.Haase, M.Holbrow-Wilshaw, T.Krulle, X.Li, C.Lumley, B.Mertins, S.Napier, R.Odedra, K.Papadopoulos, V.Roumpelakis, K.Spear, E.Trimby, J.Williams, M.Zahn, A.D.Keefe, Y.Zhang, H.T.Soutter, P.A.Centrella, M.A.Clark, J.W.Cuozzo, C.E.Dumelin, B.Deng, A.Hunt, E.A.Sigel, D.M.Troast, B.L.M.Dejonge. Discovery of Novel Udp- N -Acetylglucosamine Acyltransferase (Lpxa) Inhibitors with Activity Against Pseudomonas Aeruginosa . J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34569791
DOI: 10.1021/ACS.JMEDCHEM.1C00888
Page generated: Tue Oct 8 18:20:31 2024

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