Calcium in PDB 6p9c: Oxa-48 Carbapanemase, Doripenem Complex

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

The structure of Oxa-48 Carbapanemase, Doripenem Complex, PDB code: 6p9c 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)	36.51 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.604, 76.749, 101.188, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.1

The structure of Oxa-48 Carbapanemase, Doripenem Complex 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, Doripenem Complex (pdb code 6p9c). 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, Doripenem Complex, PDB code: 6p9c:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:68.6 occ:1.00 ND1 A:HIS34 2.2 38.6 1.0 OE2 A:GLU37 2.3 35.8 1.0 CE1 A:HIS34 2.7 30.7 1.0 OE1 A:GLU256 3.0 25.6 1.0 CD A:GLU37 3.2 40.0 1.0 OE1 A:GLU37 3.3 48.5 1.0 CD A:GLU256 3.4 31.1 1.0 CD A:CD307 3.4 36.9 1.0 CG A:HIS34 3.5 32.4 1.0 OE2 A:GLU256 3.6 44.4 1.0 NE2 A:HIS34 4.0 35.8 1.0 CB A:HIS34 4.2 31.3 1.0 CB A:GLU256 4.3 28.7 1.0 CG A:GLU256 4.4 28.4 1.0 CA A:HIS34 4.4 36.3 1.0 CD2 A:HIS34 4.4 36.4 1.0 CG A:GLU37 4.6 35.9 1.0 N A:HIS34 5.0 33.5 1.0

Calcium binding site 2 out of 3 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:0.1 occ:1.00 OD2 A:ASP154 2.8 45.3 1.0 OD1 A:ASP154 3.2 34.2 1.0 CG A:ASP154 3.4 40.2 1.0 O A:HOH461 3.9 50.6 1.0 ND2 A:ASN152 4.7 40.5 1.0 NH1 A:ARG128 4.8 36.9 1.0 NE2 A:GLN124 4.8 37.0 1.0 CB A:ASP154 4.9 29.6 1.0 CG A:ASN152 5.0 37.3 1.0

Calcium binding site 3 out of 3 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:18.6 occ:1.00 O B:HOH452 2.1 17.3 1.0 O B:HOH446 2.3 35.4 1.0 OE1 B:GLU147 2.3 35.9 1.0 OE2 B:GLU147 2.9 39.6 1.0 OD1 B:ASP143 2.9 25.7 1.0 CD B:GLU147 2.9 31.9 1.0 CG B:ASP143 3.9 26.1 1.0 CD B:CD306 4.0 32.5 1.0 O B:HOH401 4.1 38.0 1.0 CG B:GLU147 4.4 35.2 1.0 CB B:ASP143 4.4 23.0 1.0 CA B:ASP143 4.5 25.4 1.0 O B:HIS140 4.6 24.7 1.0 OD2 B:ASP143 4.8 27.2 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