Calcium in PDB 1k6s: Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid

All present enzymatic activity of Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid:
3.5.2.6;

The structure of Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid, PDB code: 1k6s was solved by F.Kerff, E.Fonze, E.Sauvage, J.M.Frere, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.20 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.245, 95.787, 125.074, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.4

The binding sites of Calcium atom in the Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid (pdb code 1k6s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid, PDB code: 1k6s:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:29.8 occ:1.00 OE1 B:GLU190 2.0 33.0 1.0 O B:HOH357 2.1 22.8 1.0 NE2 A:HIS203 2.3 22.8 1.0 OE2 A:GLU227 2.4 37.2 1.0 OE1 A:GLU227 2.4 35.2 1.0 CD A:GLU227 2.8 36.4 1.0 CD B:GLU190 2.8 31.9 1.0 CE1 A:HIS203 2.9 20.8 1.0 OE2 B:GLU190 3.1 30.4 1.0 CD2 A:HIS203 3.5 22.9 1.0 O B:HOH356 3.9 34.0 1.0 O B:HOH366 3.9 41.4 1.0 CD2 A:LEU201 4.0 35.9 1.0 ND1 A:HIS203 4.1 22.4 1.0 CG B:GLU190 4.2 27.8 1.0 O A:HOH405 4.2 32.4 1.0 CG A:GLU227 4.3 36.4 1.0 CG A:HIS203 4.4 22.9 1.0 NE1 A:TRP225 4.5 19.6 1.0 O B:HOH367 4.6 35.9 1.0 CZ2 A:TRP225 4.9 20.2 1.0

Calcium binding site 2 out of 3 in the Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:57.4 occ:1.00 NH1 A:ARG250 2.8 24.9 1.0 O A:HOH488 3.0 41.3 1.0 O2 A:IAP300 3.0 16.8 1.0 NH2 A:ARG250 3.2 26.9 1.0 CZ A:ARG250 3.4 27.2 1.0 CB A:PHE208 3.6 17.7 1.0 N A:PHE208 4.0 16.6 1.0 C A:GLY207 4.1 18.1 1.0 OG1 A:THR206 4.1 21.6 1.0 B A:IAP300 4.2 16.2 1.0 C6 A:IAP300 4.2 18.4 1.0 O1 A:IAP300 4.3 16.6 1.0 O3 A:IAP300 4.4 29.1 1.0 O A:HOH422 4.4 31.4 1.0 CA A:GLY207 4.4 16.3 1.0 CA A:PHE208 4.5 17.0 1.0 N A:GLY207 4.5 14.7 1.0 O A:GLY207 4.6 16.9 1.0 C1 A:IAP300 4.6 19.0 1.0 CB A:THR206 4.6 18.5 1.0 CG A:PHE208 4.7 20.3 1.0 NE A:ARG250 4.7 23.6 1.0 C A:THR206 4.8 16.0 1.0 CD2 A:PHE208 4.9 20.3 1.0 CD2 A:LEU247 4.9 28.8 1.0 OG A:SER115 5.0 20.2 1.0

Calcium binding site 3 out of 3 in the Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Class D Beta-Lactamase Oxa-10 in Complex with A Phenylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:32.0 occ:1.00 O B:HOH355 2.1 39.2 1.0 OE1 A:GLU190 2.2 33.2 1.0 NE2 B:HIS203 2.2 25.2 1.0 OE1 B:GLU227 2.4 31.3 1.0 OE2 B:GLU227 2.4 32.0 1.0 CD B:GLU227 2.7 31.1 1.0 CD A:GLU190 3.0 32.9 1.0 CE1 B:HIS203 3.0 26.1 1.0 CD2 B:HIS203 3.2 22.9 1.0 OE2 A:GLU190 3.2 35.4 1.0 CD2 B:LEU201 3.8 29.6 1.0 O A:HOH332 4.0 22.6 1.0 O A:HOH401 4.1 35.0 1.0 ND1 B:HIS203 4.2 25.4 1.0 CG B:GLU227 4.3 28.5 1.0 CG B:HIS203 4.3 24.8 1.0 NE1 B:TRP225 4.3 26.1 1.0 O B:HOH361 4.3 39.1 1.0 CG A:GLU190 4.4 31.1 1.0 O A:HOH360 4.6 31.7 1.0 O A:HOH442 4.6 32.9 1.0 CG B:LEU201 4.8 30.6 1.0 CZ2 B:TRP225 5.0 24.8 1.0

F.Kerff, E.Fonze, E.Sauvage, J.M.Frere, P.Charlier. Crystal Structure of Class D Beta-Lactamase Oxa-10 in Complex with Different Substrates and One Inhibitor. To Be Published.