Calcium in PDB 5vep: Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F

All present enzymatic activity of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F:
2.6.1.63; 2.6.1.7; 4.4.1.13;

The structure of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F, PDB code: 5vep was solved by A.Wlodawer, Z.Dauter, W.Minor, R.Stanfield, P.Porebski, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.21 / 2.59
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.820, 91.820, 233.649, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 26.4

The binding sites of Calcium atom in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F (pdb code 5vep). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F, PDB code: 5vep:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:45.3 occ:0.50 OE1 A:GLN122 2.3 34.5 1.0 O A:HOH645 2.3 35.7 1.0 O A:HOH672 2.3 41.1 0.5 CD A:GLN122 3.4 33.9 1.0 O A:GLN122 4.0 32.7 1.0 CB A:GLN122 4.1 33.5 1.0 O A:HOH659 4.1 23.6 1.0 CG A:GLN122 4.1 33.6 1.0 NE2 A:GLN122 4.5 34.0 1.0 C A:GLN122 4.5 33.1 1.0 CA A:GLN122 4.9 33.5 1.0

Calcium binding site 2 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:45.9 occ:1.00 O A:HOH665 1.9 43.9 1.0 O A:HIS240 2.3 33.4 1.0 O A:HOH664 2.9 36.8 1.0 O A:HOH668 3.0 14.5 1.0 O A:HOH622 3.0 32.8 1.0 O A:ASP241 3.5 31.8 1.0 C A:HIS240 3.6 32.9 1.0 O A:SER207 3.9 34.9 1.0 C A:ASP241 4.2 32.1 1.0 O A:THR209 4.3 31.4 1.0 CB A:ASP241 4.4 33.2 1.0 N A:ASP241 4.5 32.7 1.0 CG2 A:THR242 4.5 30.4 1.0 CA A:HIS240 4.5 33.0 1.0 CA A:ASP241 4.5 32.5 1.0 CA A:SER207 4.6 34.3 1.0 CB A:HIS240 4.6 32.9 1.0 O A:SER206 4.6 34.5 1.0 C A:SER207 4.6 34.4 1.0

Calcium binding site 3 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:51.3 occ:1.00 OE2 A:GLU47 2.4 40.0 1.0 OE1 A:GLU47 2.9 40.2 1.0 ND2 A:ASN42 3.0 36.2 1.0 CD A:GLU47 3.0 39.8 1.0 O A:HOH671 3.1 22.2 1.0 O A:HOH632 3.8 41.4 1.0 CG A:ASN42 4.2 35.6 1.0 CG A:GLU47 4.5 38.6 1.0 OD1 A:ASN42 4.7 35.7 1.0

Calcium binding site 4 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2F within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:36.7 occ:1.00 O B:HOH639 2.2 30.1 1.0 O B:HOH673 2.4 32.5 1.0 O B:HIS240 2.4 34.7 1.0 O B:HOH687 2.4 33.4 1.0 O B:HOH668 2.5 24.3 1.0 O B:HOH647 2.8 26.8 1.0 C B:HIS240 3.6 34.4 1.0 CA B:HIS240 4.3 34.5 1.0 CA B:SER207 4.3 33.7 1.0 CB B:HIS240 4.5 34.5 1.0 O B:ASP241 4.6 32.8 1.0 O B:SER206 4.6 32.9 1.0 O B:SER207 4.6 34.4 1.0 N B:ASP241 4.6 33.8 1.0 ND1 B:HIS240 4.7 34.9 1.0 CB B:SER207 4.7 33.9 1.0 CB B:ASP241 4.7 33.9 1.0 C B:ASP241 4.8 32.9 1.0 C B:SER207 4.8 34.0 1.0 O B:THR209 4.9 30.7 1.0 CA B:ASP241 4.9 33.5 1.0 CG2 B:THR242 5.0 30.8 1.0

A.Wlodawer, Z.Dauter, P.J.Porebski, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp. Detect, Correct, Retract: How to Manage Incorrect Structural Models. Febs J. V. 285 444 2018.
ISSN: ISSN 1742-4658
PubMed: 29113027
DOI: 10.1111/FEBS.14320