Calcium in PDB 6p99: Oxa-48 Carbapanemase, Ertapenem Complex

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

The structure of Oxa-48 Carbapanemase, Ertapenem Complex, PDB code: 6p99 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 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.883, 76.822, 101.247, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.7

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

Cadmium	(Cd)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Calcium atom in the Oxa-48 Carbapanemase, Ertapenem Complex (pdb code 6p99). 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, Ertapenem Complex, PDB code: 6p99:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Oxa-48 Carbapanemase, Ertapenem Complex


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, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:37.7 occ:1.00 OE1 A:GLU147 2.3 55.1 1.0 OD1 A:ASP143 2.4 57.4 1.0 CD A:GLU147 3.5 46.2 1.0 CG A:ASP143 3.5 58.0 1.0 OD2 A:ASP143 4.0 56.6 1.0 CD A:CD506 4.0 56.3 1.0 O A:GLY145 4.1 39.8 1.0 CG A:GLU147 4.2 45.4 1.0 OE2 A:GLU147 4.5 45.6 1.0 CB A:ASP143 4.7 43.9 1.0 CA A:ASP143 5.0 42.2 1.0

Calcium binding site 2 out of 3 in the Oxa-48 Carbapanemase, Ertapenem Complex


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, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:28.5 occ:1.00 ND1 A:HIS34 2.1 45.4 1.0 OE2 A:GLU37 2.2 49.0 1.0 OE1 A:GLU37 2.4 53.9 1.0 OE1 A:GLU256 2.4 46.4 1.0 O A:HOH625 2.4 51.0 1.0 CD A:GLU37 2.6 50.9 1.0 CE1 A:HIS34 2.8 43.3 1.0 CD A:GLU256 3.2 50.6 1.0 CG A:HIS34 3.3 47.6 1.0 CD A:CD507 3.5 48.6 1.0 CB A:HIS34 3.8 45.9 1.0 OE2 A:GLU256 3.9 43.7 1.0 NE2 A:HIS34 4.0 44.3 1.0 CB A:GLU256 4.1 42.3 1.0 CG A:GLU256 4.1 45.4 1.0 CA A:HIS34 4.2 47.8 1.0 CG A:GLU37 4.2 48.9 1.0 CD2 A:HIS34 4.3 43.2 1.0 N A:HIS34 4.9 42.0 1.0 CB A:GLU37 5.0 51.4 1.0

Calcium binding site 3 out of 3 in the Oxa-48 Carbapanemase, Ertapenem Complex


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, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:48.5 occ:1.00 OE1 B:GLU256 2.2 64.9 1.0 OE2 B:GLU37 2.2 66.0 1.0 OE1 B:GLU37 2.3 68.5 1.0 ND1 B:HIS34 2.4 61.1 1.0 CD B:GLU37 2.5 71.3 1.0 CD B:GLU256 3.0 72.2 1.0 CE1 B:HIS34 3.2 66.9 1.0 CG B:HIS34 3.5 64.9 1.0 OE2 B:GLU256 3.6 69.9 1.0 CB B:HIS34 3.8 65.3 1.0 O B:HOH402 3.9 60.8 1.0 CG B:GLU37 4.0 69.7 1.0 CG B:GLU256 4.0 61.0 1.0 CA B:HIS34 4.2 65.0 1.0 CB B:GLU256 4.2 53.9 1.0 NE2 B:HIS34 4.4 68.1 1.0 CD2 B:HIS34 4.5 62.2 1.0 CB B:GLU37 4.6 73.2 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