Calcium in PDB 8faj: Oxa-48-Na-1-157 Inhibitor Complex

All present enzymatic activity of Oxa-48-Na-1-157 Inhibitor Complex:
3.5.2.6;

The structure of Oxa-48-Na-1-157 Inhibitor Complex, PDB code: 8faj was solved by C.A.Smith, N.K.Stewart, M.Toth, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.32 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.564, 74.638, 97.608, 90, 90, 90
R / Rfree (%)	18.2 / 21.6

The structure of Oxa-48-Na-1-157 Inhibitor Complex also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Cadmium	(Cd)	2 atoms

The binding sites of Calcium atom in the Oxa-48-Na-1-157 Inhibitor Complex (pdb code 8faj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Oxa-48-Na-1-157 Inhibitor Complex, PDB code: 8faj:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Oxa-48-Na-1-157 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Oxa-48-Na-1-157 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:12.4 occ:1.00 NE2 A:HIS38 2.1 22.7 1.0 OE1 A:GLU256 2.2 27.5 1.0 OE2 A:GLU256 2.3 28.4 1.0 OE2 A:GLU37 2.4 29.6 1.0 O A:HOH526 2.6 24.5 1.0 CD A:GLU256 2.6 29.3 1.0 O A:HOH519 2.6 15.2 1.0 CD2 A:HIS38 3.0 18.8 1.0 CE1 A:HIS38 3.0 21.9 1.0 CD A:GLU37 3.3 27.1 1.0 CG A:GLU37 3.8 22.4 1.0 CD A:CD304 4.1 26.7 1.0 CG A:GLU256 4.1 20.2 1.0 O A:HOH454 4.1 26.4 1.0 ND1 A:HIS38 4.1 20.5 1.0 CG A:HIS38 4.2 21.4 1.0 OE1 A:GLU37 4.3 26.1 1.0 O A:HIS34 4.3 25.4 1.0 ND1 A:HIS34 4.5 26.3 1.0 CB A:HIS34 4.8 20.7 1.0 CB A:GLU256 4.9 24.4 1.0 CA A:HIS34 4.9 21.1 1.0 CG1 A:ILE253 5.0 21.8 1.0

Calcium binding site 2 out of 3 in the Oxa-48-Na-1-157 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Oxa-48-Na-1-157 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:31.6 occ:1.00 O A:HOH483 2.0 27.2 1.0 OE2 A:GLU89 2.2 28.7 1.0 O B:HOH443 2.3 35.7 1.0 O B:HOH458 2.5 22.9 1.0 CE1 A:HIS90 2.7 34.5 1.0 O B:HOH505 2.9 25.1 1.0 NE2 A:HIS90 3.2 39.3 1.0 CD A:GLU89 3.3 26.8 1.0 ND1 A:HIS90 3.8 35.9 1.0 CG A:GLU89 3.9 26.6 1.0 NZ B:LYS192 4.0 19.0 1.0 O A:HOH539 4.1 32.8 1.0 OE1 A:GLU89 4.2 24.7 1.0 O B:TYR177 4.2 18.2 1.0 NH1 B:ARG189 4.3 23.4 1.0 NE2 A:GLN193 4.3 20.6 1.0 O B:HOH427 4.4 28.7 1.0 CD2 A:HIS90 4.5 34.4 1.0 OE1 A:GLN193 4.5 21.8 1.0 O A:HOH542 4.5 26.4 1.0 CG A:HIS90 4.8 32.6 1.0 ND2 B:ASN179 4.8 29.8 1.0 NH2 B:ARG189 4.9 23.2 1.0 CD A:GLN193 4.9 22.4 1.0 CZ B:ARG189 4.9 23.7 1.0

Calcium binding site 3 out of 3 in the Oxa-48-Na-1-157 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Oxa-48-Na-1-157 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:25.4 occ:1.00 O B:HOH402 1.9 31.8 1.0 OE2 B:GLU147 2.1 31.9 1.0 O B:HOH409 2.2 32.5 1.0 OD1 B:ASP143 2.2 42.1 1.0 O B:HOH470 2.2 31.7 1.0 CD B:GLU147 3.1 34.6 1.0 CG B:ASP143 3.4 33.3 1.0 OE1 B:GLU147 3.4 31.5 1.0 CA B:ASP143 3.9 29.4 1.0 CB B:ASP143 4.0 26.7 1.0 CD B:CD303 4.2 56.4 1.0 O B:HIS140 4.2 32.6 1.0 OD2 B:ASP143 4.4 29.7 1.0 CG B:GLU147 4.5 27.4 1.0 N B:ASP143 4.8 28.2 1.0 C B:ASP143 4.8 26.1 1.0

C.A.Smith, N.K.Stewart, M.Toth, P.Quan, J.D.Buynak, S.B.Vakulenko. The C5 Alpha-Methyl-Substituted Carbapenem Na-1-157 Exhibits Potent Activity Against Klebsiella Spp. Isolates Producing Oxa-48-Type Carbapenemases. Acs Infect Dis. V. 9 1123 2023.
ISSN: ESSN 2373-8227
PubMed: 37130087
DOI: 10.1021/ACSINFECDIS.3C00059