Calcium in PDB 5e2f: Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis:
3.5.2.6;

The structure of Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis, PDB code: 5e2f was solved by Y.Kim, G.Joachimiak, M.Endres, G.Babnigg, A.Joachimiak, Mcsg, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.11 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.699, 68.856, 153.979, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 15.2

The binding sites of Calcium atom in the Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis (pdb code 5e2f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis, PDB code: 5e2f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:16.5 occ:0.85 O A:HOH508 2.3 23.5 1.0 O A:HOH616 2.3 33.6 1.0 OE2 A:GLU42 2.3 18.4 1.0 O A:HOH462 2.4 21.9 1.0 OD2 A:ASP41 2.4 18.5 1.0 CG A:ASP41 3.5 17.6 1.0 CD A:GLU42 3.5 16.1 1.0 CB A:ASP41 3.9 16.0 1.0 CG A:GLU42 4.1 16.0 1.0 O A:HOH573 4.2 24.8 1.0 OD1 A:ASP257 4.4 22.0 1.0 NZ A:LYS261 4.4 16.2 1.0 O A:HOH495 4.5 22.9 1.0 OD2 A:ASP257 4.5 19.0 1.0 OE1 A:GLU42 4.5 18.1 1.0 OD1 A:ASP41 4.6 18.3 1.0 CD A:LYS261 4.6 15.3 1.0 C A:ASP41 4.7 14.8 1.0 N A:GLU42 4.7 13.8 1.0 CG A:ASP257 4.9 18.8 1.0 CE A:LYS261 4.9 15.2 1.0 CA A:ASP41 4.9 13.9 1.0 O A:ASP41 5.0 15.9 1.0 CA A:GLU42 5.0 14.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:32.8 occ:0.64 O A:HOH599 2.3 36.0 1.0 O A:ASP45 2.4 24.6 1.0 O A:HOH581 2.4 44.1 1.0 O A:HOH451 2.5 36.8 1.0 C A:ASP45 3.6 22.2 1.0 CA A:THR46 4.3 18.2 1.0 N A:THR46 4.4 18.9 1.0 CA A:ASP45 4.5 24.6 1.0 CB A:ASP45 4.6 29.6 1.0 OD2 A:ASP245 4.6 18.1 0.6 OD1 A:ASP245 4.7 17.3 0.6 OD2 A:ASP246 4.9 23.9 1.0 OG1 A:THR46 4.9 23.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca300 b:18.6 occ:0.77 OD2 B:ASP47 2.5 28.5 1.0 OD1 B:ASP47 2.5 22.9 1.0 CG B:ASP47 2.8 22.8 1.0 CB B:ASP47 4.4 20.6 1.0

Y.Kim, G.Joachimiak, M.Endres, G.Babnigg, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of Beta-Lactamase Class D From Bacillus Subtilis To Be Published.