Calcium in PDB 5veq: Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Y

All present enzymatic activity of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Y:
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 3E2Y, PDB code: 5veq 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)	29.58 / 2.26
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.567, 91.567, 232.536, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.1

The binding sites of Calcium atom in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Y (pdb code 5veq). 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 3E2Y, PDB code: 5veq:
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 3E2Y


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 3E2Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:28.2 occ:0.50 OE1 A:GLN122 2.3 31.3 1.0 O A:HOH648 2.3 30.0 1.0 O A:HOH814 2.6 12.0 0.5 O A:HOH643 3.0 33.9 1.0 CD A:GLN122 3.4 30.1 1.0 CG A:GLN122 4.0 30.5 1.0 CB A:GLN122 4.1 30.6 1.0 NE2 A:GLN122 4.4 30.5 1.0 O A:GLN122 4.4 29.3 1.0 C A:GLN122 4.7 29.8 1.0 CB A:ASP124 4.8 27.2 1.0 OD2 A:ASP124 4.9 27.5 1.0 N A:ASP124 5.0 27.2 1.0 OE1 A:GLU128 5.0 28.2 1.0

Calcium binding site 2 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Y


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 3E2Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:37.4 occ:1.00 O A:HIS240 2.4 31.4 1.0 O A:HOH794 2.4 45.4 1.0 O A:HOH615 2.4 34.0 1.0 O A:HOH714 2.4 30.7 1.0 O A:HOH659 2.6 28.5 1.0 O A:HOH657 2.7 32.8 1.0 O A:HOH797 2.8 37.1 1.0 C A:HIS240 3.5 31.2 1.0 CA A:HIS240 4.1 31.4 1.0 CB A:HIS240 4.2 31.1 1.0 O A:SER207 4.3 33.8 1.0 O A:ASP241 4.4 31.4 1.0 CA A:SER207 4.4 34.4 1.0 N A:ASP241 4.6 31.6 1.0 O A:SER206 4.7 33.7 1.0 C A:SER207 4.7 34.1 1.0 CB A:ASP241 4.7 31.7 1.0 C A:ASP241 4.8 31.2 1.0 O A:THR209 4.8 29.0 1.0 ND1 A:HIS240 4.9 31.4 1.0 CA A:ASP241 4.9 31.5 1.0

Calcium binding site 3 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Y


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 3E2Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:44.2 occ:1.00 O A:HOH711 2.4 35.9 1.0 OE1 A:GLU47 2.5 32.6 1.0 OE2 A:GLU47 2.6 32.4 1.0 OD1 A:ASN42 2.7 34.5 1.0 O A:HOH774 2.8 38.6 1.0 CD A:GLU47 3.0 32.2 1.0 CG A:ASN42 3.6 33.8 1.0 ND2 A:ASN42 3.9 33.3 1.0 O A:HOH767 4.0 46.0 1.0 O A:HOH791 4.1 42.1 1.0 CG A:GLU47 4.5 31.2 1.0 O A:HOH744 4.7 28.4 1.0 O A:HOH743 4.9 47.4 1.0 CB A:ASN42 5.0 33.5 1.0

Calcium binding site 4 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Y


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 3E2Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:33.3 occ:1.00 O B:HOH726 2.2 37.6 1.0 O B:HIS240 2.3 31.3 1.0 O B:HOH777 2.4 35.6 1.0 O B:HOH643 2.4 33.1 1.0 O B:HOH698 2.5 32.5 1.0 O B:HOH758 2.5 35.7 1.0 O B:HOH632 2.6 33.6 1.0 C B:HIS240 3.4 31.2 1.0 CA B:HIS240 4.1 31.4 1.0 CB B:HIS240 4.3 31.1 1.0 CA B:SER207 4.4 32.6 1.0 O B:ASP241 4.4 31.1 1.0 N B:ASP241 4.5 31.2 1.0 O B:HOH604 4.5 40.5 1.0 O B:SER206 4.6 31.6 1.0 O B:SER207 4.7 32.8 1.0 CB B:ASP241 4.7 32.1 1.0 ND1 B:HIS240 4.7 31.2 1.0 C B:ASP241 4.8 31.1 1.0 CA B:ASP241 4.8 31.5 1.0 O B:THR209 4.9 29.4 1.0 C B:SER207 4.9 32.6 1.0 CB B:SER207 4.9 33.0 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