Cadmium in PDB 6p9c: Oxa-48 Carbapanemase, Doripenem Complex

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

The structure of Oxa-48 Carbapanemase, Doripenem Complex, PDB code: 6p9c 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)	36.51 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.604, 76.749, 101.188, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.1

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

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	3 atoms

The binding sites of Cadmium atom in the Oxa-48 Carbapanemase, Doripenem Complex (pdb code 6p9c). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Oxa-48 Carbapanemase, Doripenem Complex, PDB code: 6p9c:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:36.9 occ:1.00 NE2 A:HIS38 2.4 28.1 1.0 OE2 A:GLU37 2.5 35.8 1.0 OE1 A:GLU256 2.6 25.6 1.0 OE2 A:GLU256 2.6 44.4 1.0 CD A:GLU256 2.9 31.1 1.0 CE1 A:HIS38 3.2 30.8 1.0 CD A:GLU37 3.3 40.0 1.0 CA A:CA305 3.4 68.6 1.0 CD2 A:HIS38 3.4 30.1 1.0 CG A:GLU37 3.8 35.9 1.0 OE1 A:GLU37 4.3 48.5 1.0 ND1 A:HIS38 4.3 29.5 1.0 CG A:GLU256 4.4 28.4 1.0 CG A:HIS38 4.5 30.2 1.0 ND1 A:HIS34 4.8 38.6 1.0 O A:HIS34 4.9 40.8 1.0

Cadmium binding site 2 out of 2 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd306 b:32.5 occ:1.00 O B:HOH404 2.5 30.2 1.0 OD1 B:ASP143 2.5 25.7 1.0 O B:HOH401 2.6 38.0 1.0 O B:HOH423 2.8 30.0 1.0 CG B:ASP143 3.2 26.1 1.0 OD2 B:ASP143 3.3 27.2 1.0 OE1 B:GLU147 3.5 35.9 1.0 O B:GLY145 3.9 31.7 1.0 CA B:CA305 4.0 18.6 1.0 O B:HOH402 4.5 37.6 1.0 O B:ASP143 4.5 24.1 1.0 O B:HOH475 4.6 44.2 1.0 CB B:ASP143 4.7 23.0 1.0 CD B:GLU147 4.7 31.9 1.0 C B:ASP143 4.9 21.9 1.0 CA B:ASP143 5.0 25.4 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