Calcium in PDB 6p97: Oxa-48 Carbapanemase, Imipenem Complex

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

The structure of Oxa-48 Carbapanemase, Imipenem Complex, PDB code: 6p97 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)	38.11 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.131, 76.210, 101.130, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.3

The structure of Oxa-48 Carbapanemase, Imipenem 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, Imipenem Complex (pdb code 6p97). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Oxa-48 Carbapanemase, Imipenem Complex, PDB code: 6p97:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Oxa-48 Carbapanemase, Imipenem 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, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:27.7 occ:1.00 ND1 A:HIS34 2.2 27.6 1.0 OE2 A:GLU37 2.3 25.7 1.0 O A:HOH427 2.4 37.3 1.0 O A:HOH585 2.5 41.1 1.0 OE2 A:GLU256 2.6 26.6 1.0 CE1 A:HIS34 2.7 26.2 1.0 CD A:GLU37 3.1 29.8 1.0 CD A:CD306 3.3 27.0 1.0 OE1 A:GLU37 3.3 29.7 1.0 CD A:GLU256 3.3 28.4 1.0 CG A:HIS34 3.4 27.1 1.0 OE1 A:GLU256 3.9 29.7 1.0 NE2 A:HIS34 4.0 27.3 1.0 CB A:HIS34 4.1 22.8 1.0 CB A:GLU256 4.1 21.7 1.0 CG A:GLU256 4.2 26.2 1.0 CA A:HIS34 4.3 26.9 1.0 CD2 A:HIS34 4.3 25.3 1.0 CG A:GLU37 4.5 25.9 1.0 O A:HOH459 4.7 27.9 1.0 N A:HIS34 5.0 25.3 1.0

Calcium binding site 2 out of 5 in the Oxa-48 Carbapanemase, Imipenem 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, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:58.3 occ:1.00 O A:HOH588 2.3 51.7 1.0 O A:HOH511 2.3 41.3 1.0 OD2 A:ASP154 2.4 34.6 1.0 O A:HOH582 2.5 49.9 1.0 O A:HOH578 2.5 45.9 1.0 OD1 A:ASP154 2.8 31.4 1.0 CG A:ASP154 3.0 31.7 1.0 O A:HOH576 4.1 38.8 1.0 O A:HOH567 4.3 39.5 1.0 O A:HOH563 4.4 38.8 1.0 NH2 A:ARG128 4.5 28.0 1.0 CB A:ASP154 4.5 26.0 1.0 ND2 A:ASN152 4.9 38.0 1.0

Calcium binding site 3 out of 5 in the Oxa-48 Carbapanemase, Imipenem 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, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:19.1 occ:1.00 OE1 B:GLU147 2.1 34.8 1.0 O B:HOH474 2.2 31.3 1.0 O B:HOH410 2.4 28.4 1.0 OD1 B:ASP143 2.6 30.5 1.0 CD B:GLU147 2.9 33.6 1.0 OE2 B:GLU147 3.1 36.3 1.0 CG B:ASP143 3.6 25.3 1.0 CD B:CD306 3.8 30.3 1.0 O B:HOH403 3.8 29.9 1.0 CB B:ASP143 4.1 23.7 1.0 ND1 B:HIS140 4.1 30.2 0.5 CA B:ASP143 4.2 22.9 1.0 CE1 B:HIS140 4.3 30.1 0.5 CG B:GLU147 4.3 30.9 1.0 OD2 B:ASP143 4.5 26.0 1.0 O B:HIS140 4.5 27.0 1.0

Calcium binding site 4 out of 5 in the Oxa-48 Carbapanemase, Imipenem Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Oxa-48 Carbapanemase, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:53.3 occ:0.62 CA B:CA305 0.0 53.3 0.6 CA B:CA305 2.4 48.1 0.4 OE1 B:GLU256 3.1 61.0 1.0 OE2 B:GLU256 3.2 60.7 1.0 CD B:GLU256 3.2 53.5 1.0 NE2 B:HIS38 4.0 53.0 1.0 CG B:GLU256 4.2 41.6 1.0 ND1 B:HIS34 4.7 48.3 1.0 CE1 B:HIS38 4.8 55.9 1.0 CD2 B:HIS38 4.8 49.5 1.0

Calcium binding site 5 out of 5 in the Oxa-48 Carbapanemase, Imipenem Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Oxa-48 Carbapanemase, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:48.1 occ:0.38 CA B:CA305 0.0 48.1 0.4 CA B:CA305 2.4 53.3 0.6 ND1 B:HIS34 2.5 48.3 1.0 OE2 B:GLU256 2.8 60.7 1.0 CE1 B:HIS34 3.2 47.1 1.0 CD B:GLU256 3.5 53.5 1.0 CG B:HIS34 3.6 43.9 1.0 CB B:HIS34 4.1 47.7 1.0 CA B:HIS34 4.2 48.2 1.0 OE1 B:GLU256 4.2 61.0 1.0 CG B:GLU256 4.2 41.6 1.0 CB B:GLU256 4.3 35.5 1.0 NE2 B:HIS34 4.4 49.7 1.0 CD2 B:HIS34 4.6 44.2 1.0 N B:HIS34 4.8 47.6 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