Cadmium in PDB 6p96: Oxa-48 Carbapanemase, Apo Form

All present enzymatic activity of Oxa-48 Carbapanemase, Apo Form:
3.5.2.6;

The structure of Oxa-48 Carbapanemase, Apo Form, PDB code: 6p96 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 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.746, 76.827, 100.044, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.9

The structure of Oxa-48 Carbapanemase, Apo Form 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, Apo Form (pdb code 6p96). 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, Apo Form, PDB code: 6p96:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Oxa-48 Carbapanemase, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:25.8 occ:1.00 OE2 A:GLU147 2.4 22.8 1.0 O A:HOH419 2.5 26.9 1.0 O A:HOH500 2.6 30.9 1.0 OE1 A:GLU147 2.6 31.3 1.0 CD A:GLU147 2.9 28.0 1.0 CA A:CA303 3.6 14.2 1.0 OD1 A:ASP143 4.0 26.4 1.0 O A:HOH565 4.1 37.0 1.0 ND1 A:HIS140 4.1 28.7 1.0 CG A:GLU147 4.4 21.9 1.0 O A:HIS140 4.4 21.9 1.0 CG A:ASP143 4.7 22.6 1.0

Cadmium binding site 2 out of 2 in the Oxa-48 Carbapanemase, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:27.9 occ:1.00 NE2 A:HIS38 2.5 32.0 1.0 OE1 A:GLU256 2.5 30.8 1.0 OE2 A:GLU37 2.5 27.9 1.0 OE2 A:GLU256 2.5 27.9 1.0 CD A:GLU256 2.8 35.0 1.0 CD2 A:HIS38 3.3 30.1 1.0 CD A:GLU37 3.4 39.0 1.0 CE1 A:HIS38 3.4 31.1 1.0 CA A:CA304 3.5 25.0 1.0 CG A:GLU37 3.9 33.5 1.0 OE1 A:GLU37 4.3 43.9 1.0 CG A:GLU256 4.3 26.5 1.0 CG A:HIS38 4.5 25.7 1.0 ND1 A:HIS38 4.5 28.2 1.0 O A:HOH564 4.8 36.8 1.0 O A:HOH476 5.0 40.3 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