Calcium 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:

Cadmium	(Cd)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Oxa-48 Carbapanemase, Apo Form (pdb code 6p96). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Oxa-48 Carbapanemase, Apo Form, PDB code: 6p96:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Oxa-48 Carbapanemase, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Oxa-48 Carbapanemase, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:14.2 occ:1.00 OD1 A:ASP143 2.2 26.4 1.0 OE1 A:GLU147 2.2 31.3 1.0 O A:HOH425 2.3 24.4 1.0 CG A:ASP143 3.2 22.6 1.0 CD A:GLU147 3.2 28.0 1.0 OD2 A:ASP143 3.5 26.3 1.0 CD A:CD305 3.6 25.8 1.0 CG A:GLU147 4.0 21.9 1.0 OE2 A:GLU147 4.1 22.8 1.0 O A:HOH555 4.2 39.3 1.0 O A:GLY145 4.3 22.4 1.0 O A:HOH439 4.3 34.2 1.0 CB A:ASP143 4.5 20.6 1.0 CA A:ASP143 4.9 22.4 1.0

Calcium binding site 2 out of 3 in the Oxa-48 Carbapanemase, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Oxa-48 Carbapanemase, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:25.0 occ:1.00 ND1 A:HIS34 2.2 32.9 1.0 O A:HOH476 2.2 40.3 1.0 OE2 A:GLU37 2.3 27.9 1.0 O A:HOH564 2.4 36.8 1.0 OE2 A:GLU256 2.6 27.9 1.0 CE1 A:HIS34 2.8 30.2 1.0 CD A:GLU37 3.1 39.0 1.0 OE1 A:GLU37 3.3 43.9 1.0 CD A:GLU256 3.4 35.0 1.0 CG A:HIS34 3.4 29.8 1.0 CD A:CD306 3.5 27.9 1.0 CB A:HIS34 4.0 30.9 1.0 CG A:GLU256 4.1 26.5 1.0 NE2 A:HIS34 4.1 30.1 1.0 CB A:GLU256 4.1 24.8 1.0 OE1 A:GLU256 4.1 30.8 1.0 CA A:HIS34 4.2 28.6 1.0 CD2 A:HIS34 4.4 30.4 1.0 CG A:GLU37 4.6 33.5 1.0 O A:HOH431 4.7 34.7 1.0 N A:HIS34 4.9 25.6 1.0

Calcium binding site 3 out of 3 in the Oxa-48 Carbapanemase, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Oxa-48 Carbapanemase, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:17.4 occ:1.00 OE1 B:GLU37 2.3 38.6 1.0 O B:HOH401 2.3 37.7 1.0 ND1 B:HIS34 2.4 29.2 1.0 OE1 B:GLU256 2.4 42.0 1.0 CD B:GLU256 3.1 39.6 1.0 CD B:GLU37 3.1 39.2 1.0 CE1 B:HIS34 3.1 27.2 1.0 OE2 B:GLU37 3.3 42.3 1.0 CG B:HIS34 3.5 32.9 1.0 OE2 B:GLU256 3.7 49.1 1.0 CG B:GLU256 3.9 31.5 1.0 CB B:HIS34 3.9 32.5 1.0 CB B:GLU256 4.0 26.9 1.0 CA B:HIS34 4.0 29.7 1.0 NE2 B:HIS34 4.3 32.5 1.0 CG B:GLU37 4.5 38.0 1.0 CD2 B:HIS34 4.5 29.8 1.0 O B:HOH567 4.6 35.5 1.0 N B:HIS34 4.8 31.4 1.0 CE1 B:HIS38 4.8 33.8 1.0 CB B:GLU37 4.9 36.8 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