Calcium in PDB 3r6v: Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate

All present enzymatic activity of Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate:
4.3.1.1;

The structure of Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate, PDB code: 3r6v was solved by G.Fibriansah, V.Puthan Veetil, G.J.Poelarends, A.-M.W.H.Thunnissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.73 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	75.853, 118.960, 141.414, 89.93, 89.93, 76.42
R / Rfree (%)	19.3 / 25

The binding sites of Calcium atom in the Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate (pdb code 3r6v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate, PDB code: 3r6v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate


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 Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca469 b:55.6 occ:1.00 O A:ALA393 2.5 32.2 1.0 OE1 A:GLU395 2.7 40.1 1.0 C A:ALA393 3.7 31.8 1.0 CD A:GLU395 3.8 38.3 1.0 OE2 A:GLU395 4.2 38.5 1.0 CA A:ASN394 4.3 32.3 1.0 N A:GLU395 4.4 33.1 1.0 N A:ASN394 4.4 32.0 1.0 OD1 A:ASN394 4.5 34.7 1.0 N A:ALA393 4.8 30.9 1.0 CA A:ALA393 4.8 31.1 1.0 C A:ASN394 4.9 32.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate


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 Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca469 b:43.8 occ:1.00 OE1 D:GLU395 2.5 41.8 1.0 O D:ALA393 2.7 31.8 1.0 CD D:GLU395 3.6 40.0 1.0 C D:ALA393 3.9 31.3 1.0 OE2 D:GLU395 4.1 40.5 1.0 N D:GLU395 4.5 32.1 1.0 CA D:ASN394 4.6 31.3 1.0 N D:ASN394 4.7 31.2 1.0 N D:ALA393 4.8 30.9 1.0 CA D:ALA393 4.9 31.1 1.0 OD1 D:ASN394 4.9 31.1 1.0 CG D:GLU395 5.0 36.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate


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 Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca469 b:67.2 occ:1.00 OE2 E:GLU395 2.6 43.6 1.0 O E:ALA393 2.7 33.9 1.0 CD E:GLU395 3.6 42.8 1.0 C E:ALA393 3.9 33.9 1.0 OE1 E:GLU395 3.9 43.4 1.0 CA E:ASN394 4.3 35.2 1.0 N E:GLU395 4.4 36.5 1.0 N E:ASN394 4.6 34.5 1.0 OD1 E:ASN394 4.6 37.8 1.0 C E:ASN394 5.0 35.8 1.0 CA E:ALA393 5.0 33.2 1.0 N E:ALA393 5.0 32.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Aspartase From Bacillus Sp. YM55-1 with Bound L- Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca469 b:49.4 occ:1.00 O H:ALA393 2.5 31.8 1.0 OE1 H:GLU395 2.6 39.3 1.0 OD1 D:ASP67 2.8 35.9 1.0 CG D:ASP67 3.6 32.9 1.0 CD H:GLU395 3.7 38.4 1.0 C H:ALA393 3.8 31.4 1.0 OD2 D:ASP67 3.8 35.0 1.0 OE2 H:GLU395 4.2 38.2 1.0 CA H:ASN394 4.4 31.0 1.0 N H:GLU395 4.4 32.3 1.0 OE2 D:GLU69 4.5 35.1 1.0 N H:ASN394 4.5 31.1 1.0 OD1 H:ASN394 4.8 29.8 1.0 N H:ALA393 4.8 31.2 1.0 CB D:ASP67 4.8 31.2 1.0 CA H:ALA393 4.8 31.3 1.0 CG H:GLU395 4.9 35.2 1.0 C H:ASN394 4.9 31.6 1.0

G.Fibriansah, V.P.Veetil, G.J.Poelarends, A.M.Thunnissen. Structural Basis For the Catalytic Mechanism of Aspartate Ammonia Lyase. Biochemistry V. 50 6053 2011.
ISSN: ISSN 0006-2960
PubMed: 21661762
DOI: 10.1021/BI200497Y