Atomistry » Sodium » PDB 5mft-5mse » 5mox
Atomistry »
  Sodium »
    PDB 5mft-5mse »
      5mox »

Sodium in PDB 5mox: Oxa-10 Avibactam Complex with Bound CO2

Enzymatic activity of Oxa-10 Avibactam Complex with Bound CO2

All present enzymatic activity of Oxa-10 Avibactam Complex with Bound CO2:
3.5.2.6;

Protein crystallography data

The structure of Oxa-10 Avibactam Complex with Bound CO2, PDB code: 5mox was solved by J.Brem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.76 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.751, 96.635, 126.363, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Oxa-10 Avibactam Complex with Bound CO2 (pdb code 5mox). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Oxa-10 Avibactam Complex with Bound CO2, PDB code: 5mox:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5mox

Go back to Sodium Binding Sites List in 5mox
Sodium binding site 1 out of 2 in the Oxa-10 Avibactam Complex with Bound CO2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Oxa-10 Avibactam Complex with Bound CO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:23.5
occ:1.00
O A:HOH695 3.0 38.0 1.0
O A:HOH713 3.0 36.7 1.0
NE A:ARG250 3.1 11.7 1.0
NH1 A:ARG250 3.3 14.2 1.0
CZ A:ARG250 3.7 11.2 1.0
CD A:LYS251 3.8 28.7 1.0
CA A:PRO248 3.9 14.1 1.0
O A:LEU247 4.1 13.6 1.0
CG A:ARG250 4.1 11.8 1.0
CG A:LYS251 4.1 22.7 1.0
CD A:ARG250 4.2 11.4 1.0
N A:PRO248 4.5 13.6 1.0
C A:LEU247 4.5 13.1 1.0
CB A:LYS251 4.6 19.0 1.0
CB A:PRO248 4.7 16.1 1.0
O A:PRO248 4.7 15.0 1.0
C A:PRO248 4.7 14.1 1.0
O A:HOH504 4.7 22.4 1.0
CG A:LEU247 4.9 14.9 1.0
CG2 A:THR206 5.0 13.8 1.0
NH2 A:ARG250 5.0 11.3 1.0

Sodium binding site 2 out of 2 in 5mox

Go back to Sodium Binding Sites List in 5mox
Sodium binding site 2 out of 2 in the Oxa-10 Avibactam Complex with Bound CO2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Oxa-10 Avibactam Complex with Bound CO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:25.7
occ:1.00
O B:HOH532 2.8 20.9 1.0
NZ B:LYS70 2.9 17.2 1.0
O B:HOH597 3.2 15.5 1.0
O B:HOH626 3.2 10.7 1.0
NE1 B:TRP154 3.3 17.9 1.0
CE B:LYS70 3.4 15.2 1.0
CG B:LYS70 3.5 12.0 1.0
O B:HOH633 3.8 21.6 1.0
CA B:SER67 4.0 11.1 1.0
CD B:LYS70 4.0 14.9 1.0
OG B:SER67 4.0 13.7 1.0
CE2 B:TRP154 4.1 15.3 1.0
CD1 B:TRP154 4.2 15.6 1.0
CZ2 B:TRP154 4.4 15.5 1.0
CB B:PHE120 4.4 12.2 1.0
CB B:SER67 4.5 12.7 1.0
O B:ALA66 4.6 11.8 1.0
N B:SER67 4.7 9.8 1.0
O B:SER67 4.8 10.2 1.0
CG2 B:VAL117 4.8 16.3 1.0
C B:SER67 4.8 10.3 1.0
CB B:LYS70 4.8 11.2 1.0
C B:ALA66 4.9 10.6 1.0
CA B:VAL117 4.9 16.2 1.0
CAN B:NXL301 4.9 14.3 1.0
N B:LYS70 5.0 9.1 1.0
CG B:PHE120 5.0 12.3 1.0

Reference:

C.T.Lohans, D.Y.Wang, C.Jorgensen, S.T.Cahill, I.J.Clifton, M.A.Mcdonough, H.P.Oswin, J.Spencer, C.Domene, T.D.W.Claridge, J.Brem, C.J.Schofield. (13)C-Carbamylation As A Mechanistic Probe For the Inhibition of Class D Beta-Lactamases By Avibactam and Halide Ions. Org. Biomol. Chem. V. 15 6024 2017.
ISSN: ESSN 1477-0539
PubMed: 28678295
DOI: 10.1039/C7OB01514C
Page generated: Mon Oct 7 22:44:05 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy