Cadmium in PDB 6p99: Oxa-48 Carbapanemase, Ertapenem Complex

All present enzymatic activity of Oxa-48 Carbapanemase, Ertapenem Complex:
3.5.2.6;

The structure of Oxa-48 Carbapanemase, Ertapenem Complex, PDB code: 6p99 was solved by C.A.Smith, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.41 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.883, 76.822, 101.247, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.7

The structure of Oxa-48 Carbapanemase, Ertapenem Complex also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	3 atoms

The binding sites of Cadmium atom in the Oxa-48 Carbapanemase, Ertapenem Complex (pdb code 6p99). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Oxa-48 Carbapanemase, Ertapenem Complex, PDB code: 6p99:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Oxa-48 Carbapanemase, Ertapenem Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Oxa-48 Carbapanemase, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd506 b:56.3 occ:1.00 O A:HOH639 2.5 45.4 1.0 OE2 A:GLU147 2.6 45.6 1.0 OE1 A:GLU147 2.7 55.1 1.0 CD A:GLU147 3.0 46.2 1.0 CA A:CA504 4.0 37.7 1.0 OD1 A:ASP143 4.2 57.4 1.0 O A:HIS140 4.3 39.7 1.0 ND1 A:HIS140 4.3 52.1 1.0 CG A:GLU147 4.5 45.4 1.0 CG A:ASP143 4.9 58.0 1.0 CA A:HIS140 5.0 42.3 1.0

Cadmium binding site 2 out of 3 in the Oxa-48 Carbapanemase, Ertapenem Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Oxa-48 Carbapanemase, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd507 b:48.6 occ:1.00 NE2 A:HIS38 2.4 46.8 1.0 OE2 A:GLU256 2.5 43.7 1.0 O A:HOH625 2.5 51.0 1.0 OE2 A:GLU37 2.6 49.0 1.0 OE1 A:GLU256 2.7 46.4 1.0 CD A:GLU256 2.9 50.6 1.0 CE1 A:HIS38 3.1 49.8 1.0 CA A:CA505 3.5 28.5 1.0 CD A:GLU37 3.5 50.9 1.0 CD2 A:HIS38 3.5 46.3 1.0 OE1 A:GLU37 4.3 53.9 1.0 CG A:GLU37 4.3 48.9 1.0 ND1 A:HIS38 4.3 52.0 1.0 CB A:GLU37 4.4 51.4 1.0 CG A:GLU256 4.4 45.4 1.0 CG A:HIS38 4.6 45.2 1.0

Cadmium binding site 3 out of 3 in the Oxa-48 Carbapanemase, Ertapenem Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Oxa-48 Carbapanemase, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd508 b:0.9 occ:1.00 ND1 A:HIS90 3.1 60.1 1.0 ND1 B:HIS178 3.2 52.6 1.0 CE1 A:HIS90 3.7 55.6 1.0 CG A:HIS90 4.0 50.6 1.0 CE1 B:HIS178 4.1 56.7 1.0 CG B:HIS178 4.2 49.9 1.0 CA B:HIS178 4.3 42.8 1.0 CB B:HIS178 4.4 47.6 1.0 CB A:HIS90 4.5 46.6 1.0 O B:HIS178 4.6 40.8 1.0 NE2 A:HIS90 4.7 57.6 1.0 NZ B:LYS180 4.8 61.3 1.0 CD2 A:HIS90 4.9 55.4 1.0 C B:HIS178 4.9 41.2 1.0

C.A.Smith, N.K.Stewart, M.Toth, S.B.Vakulenko. Structural Insights Into the Mechanism of Carbapenemase Activity of the Oxa-48 Beta-Lactamase. Antimicrob.Agents Chemother. V. 63 2019.
ISSN: ESSN 1098-6596
PubMed: 31358584
DOI: 10.1128/AAC.01202-19