Calcium 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:

Cadmium	(Cd)	2 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Calcium atom in the Oxa-48 Carbapanemase, Meropenem Complex (pdb code 6p98). 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, Meropenem Complex, PDB code: 6p98:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:15.5 occ:1.00 OE2 A:GLU256 2.1 38.9 1.0 NE2 A:HIS38 2.1 22.1 1.0 OE1 A:GLU256 2.3 29.4 1.0 CD A:GLU256 2.3 31.4 1.0 O A:HOH544 2.5 24.4 1.0 O A:HOH506 2.6 12.1 1.0 OE2 A:GLU37 2.6 20.2 1.0 CD2 A:HIS38 3.1 19.8 1.0 CE1 A:HIS38 3.1 19.7 1.0 CD A:GLU37 3.4 27.4 1.0 CG A:GLU256 3.7 33.1 1.0 CG A:GLU37 3.9 23.8 1.0 CD A:CD306 4.1 51.6 1.0 O A:HOH401 4.2 24.6 1.0 CG A:HIS38 4.2 19.7 1.0 ND1 A:HIS38 4.2 19.9 1.0 O A:HIS34 4.2 26.9 1.0 OE1 A:GLU37 4.4 23.1 1.0 ND1 A:HIS34 4.5 22.9 1.0 CB A:GLU256 4.7 19.4 1.0 CG1 A:ILE253 4.8 23.2 1.0 CB A:HIS34 4.8 20.4 1.0 CA A:HIS34 4.9 20.9 1.0

Calcium binding site 2 out of 3 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:53.4 occ:1.00 OE1 A:GLU27 2.4 31.9 1.0 O A:HOH529 2.5 34.2 1.0 OE2 A:GLU27 2.5 51.0 1.0 CD A:GLU27 2.8 42.3 1.0 CG A:GLU27 4.3 33.1 1.0 N A:LEU59 4.3 22.0 1.0 CD1 A:LEU59 4.6 34.5 1.0 O A:HOH437 4.7 33.5 1.0 CB A:LEU59 4.8 25.3 1.0 OD1 A:ASN58 4.9 24.1 1.0 CA A:ASN58 4.9 19.9 1.0

Calcium binding site 3 out of 3 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:35.8 occ:1.00 OD1 B:ASP143 2.1 36.9 1.0 O B:HOH421 2.2 38.9 1.0 OE1 B:GLU147 2.4 38.9 1.0 CG B:ASP143 3.1 35.7 1.0 O B:HOH468 3.5 40.2 1.0 CD B:GLU147 3.6 31.7 1.0 CB B:ASP143 3.8 26.4 1.0 CD B:CD306 3.8 0.5 1.0 CA B:ASP143 3.9 27.3 1.0 OD2 B:ASP143 4.1 33.1 1.0 OE2 B:GLU147 4.1 39.2 1.0 ND1 B:HIS140 4.3 43.1 1.0 CE1 B:HIS140 4.4 36.1 1.0 O B:HIS140 4.5 31.2 1.0 CG B:GLU147 4.8 31.0 1.0 N B:ASP143 4.8 26.1 1.0 C B:ASP143 4.8 25.1 1.0 O B:HOH402 5.0 36.7 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