Cadmium in PDB 6p97: Oxa-48 Carbapanemase, Imipenem Complex

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

The structure of Oxa-48 Carbapanemase, Imipenem Complex, PDB code: 6p97 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)	38.11 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.131, 76.210, 101.130, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.3

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

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	5 atoms

The binding sites of Cadmium atom in the Oxa-48 Carbapanemase, Imipenem Complex (pdb code 6p97). 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, Imipenem Complex, PDB code: 6p97:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Oxa-48 Carbapanemase, Imipenem 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, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:27.0 occ:1.00 NE2 A:HIS38 2.4 25.3 1.0 OE2 A:GLU37 2.4 25.7 1.0 OE1 A:GLU256 2.5 29.7 1.0 OE2 A:GLU256 2.5 26.6 1.0 CD A:GLU256 2.8 28.4 1.0 CE1 A:HIS38 3.2 22.0 1.0 CA A:CA304 3.3 27.7 1.0 CD A:GLU37 3.3 29.8 1.0 CD2 A:HIS38 3.3 24.5 1.0 CG A:GLU37 3.8 25.9 1.0 OE1 A:GLU37 4.2 29.7 1.0 CG A:GLU256 4.3 26.2 1.0 ND1 A:HIS38 4.3 23.8 1.0 CG A:HIS38 4.4 22.0 1.0 O A:HOH427 4.6 37.3 1.0 O A:HOH585 4.8 41.1 1.0 ND1 A:HIS34 4.9 27.6 1.0

Cadmium binding site 2 out of 2 in the Oxa-48 Carbapanemase, Imipenem 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, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd306 b:30.3 occ:1.00 O B:HOH403 2.4 29.9 1.0 OD1 B:ASP143 2.5 30.5 1.0 O B:HOH418 2.5 27.5 1.0 CG B:ASP143 3.3 25.3 1.0 OD2 B:ASP143 3.4 26.0 1.0 OE1 B:GLU147 3.6 34.8 1.0 CA B:CA304 3.8 19.1 1.0 O B:GLY145 3.9 28.9 1.0 O B:ASP143 4.4 23.4 1.0 O B:HOH534 4.6 41.6 1.0 CB B:ASP143 4.7 23.7 1.0 CD B:GLU147 4.8 33.6 1.0 C B:ASP143 4.9 21.9 1.0 O B:HOH504 4.9 31.1 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