Cadmium in PDB 6p98: Oxa-48 Carbapanemase, Meropenem Complex

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

The structure of Oxa-48 Carbapanemase, Meropenem Complex, PDB code: 6p98 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)	36.57 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.132, 74.563, 97.974, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22

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

Chlorine	(Cl)	5 atoms
Calcium	(Ca)	3 atoms

The binding sites of Cadmium atom in the Oxa-48 Carbapanemase, Meropenem Complex (pdb code 6p98). 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, Meropenem Complex, PDB code: 6p98:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:51.6 occ:1.00 OE1 A:GLU37 2.6 23.1 1.0 O A:HOH506 2.6 12.1 1.0 O A:HOH550 2.6 22.5 1.0 OE2 A:GLU37 2.6 20.2 1.0 O A:HOH401 2.7 24.6 1.0 CD A:GLU37 2.9 27.4 1.0 OE2 A:GLU256 3.3 38.9 1.0 O A:HOH526 4.0 37.8 1.0 CA A:CA304 4.1 15.5 1.0 CG A:GLU37 4.4 23.8 1.0 CD A:GLU256 4.5 31.4 1.0 ND1 A:HIS34 4.6 22.9 1.0 CE1 A:HIS34 4.8 25.6 1.0

Cadmium binding site 2 out of 2 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd306 b:0.5 occ:1.00 O B:HOH402 2.6 36.7 1.0 OD1 B:ASP143 2.6 36.9 1.0 O B:HOH465 2.7 35.4 1.0 O B:HOH468 2.7 40.2 1.0 O B:HOH502 2.8 39.0 1.0 OD2 B:ASP143 3.0 33.1 1.0 CG B:ASP143 3.1 35.7 1.0 CA B:CA305 3.8 35.8 1.0 O B:ASP143 4.5 22.8 1.0 CB B:ASP143 4.6 26.4 1.0 O B:GLY145 4.6 30.5 1.0 OE1 B:GLU147 4.7 38.9 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