Calcium in PDB 5ver: Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Z

All present enzymatic activity of Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Z:
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 3E2Z, PDB code: 5ver 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)	29.64 / 2.81
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.490, 91.490, 233.501, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 25.2

The binding sites of Calcium atom in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Z (pdb code 5ver). 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 3E2Z, PDB code: 5ver:
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 3E2Z


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 3E2Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:32.0 occ:0.50 O A:HOH825 2.0 31.2 1.0 OE1 A:GLN122 2.3 25.1 1.0 O A:HOH855 2.5 13.8 0.5 CD A:GLN122 3.5 32.1 1.0 O A:HOH824 3.5 11.9 1.0 CB A:GLN122 4.0 25.6 1.0 O A:GLN122 4.2 18.1 1.0 CG A:GLN122 4.2 28.4 1.0 NE2 A:GLN122 4.6 24.4 1.0 C A:GLN122 4.6 21.5 1.0 OE1 A:GLU128 4.8 36.3 1.0 N A:ASP124 4.9 24.7 1.0 OD2 A:ASP124 4.9 27.3 1.0 CA A:GLN122 5.0 24.7 1.0

Calcium binding site 2 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Z


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 3E2Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:33.5 occ:1.00 O A:HOH812 2.2 50.3 1.0 O A:HIS240 2.3 20.8 1.0 O A:HOH820 2.4 33.2 1.0 O A:HOH853 2.6 14.3 1.0 O A:HOH833 2.8 7.5 1.0 O A:HOH803 2.9 23.7 1.0 C A:HIS240 3.4 18.1 1.0 O A:ASP241 3.8 21.6 1.0 CA A:HIS240 4.2 19.9 1.0 CB A:HIS240 4.3 22.5 1.0 N A:ASP241 4.4 16.5 1.0 CB A:ASP241 4.4 18.7 1.0 C A:ASP241 4.4 21.3 1.0 CA A:SER207 4.5 31.1 1.0 O A:SER207 4.5 32.2 1.0 CA A:ASP241 4.6 17.3 1.0 CG2 A:THR242 4.8 17.4 1.0 O A:THR209 4.8 19.8 1.0 C A:SER207 4.9 32.2 1.0 O A:SER206 4.9 26.4 1.0

Calcium binding site 3 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Z


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 3E2Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:48.5 occ:1.00 OE2 A:GLU47 2.8 24.1 1.0 ND2 A:ASN42 2.9 37.4 1.0 OE1 A:GLU47 3.1 39.0 1.0 CD A:GLU47 3.3 26.6 1.0 CG A:ASN42 3.9 28.1 1.0 OD1 A:ASN42 4.2 29.8 1.0 O A:HOH845 4.7 41.8 1.0 CG A:GLU47 4.8 22.8 1.0

Calcium binding site 4 out of 4 in the Mouse Kynurenine Aminotransferase III, Re-Refinement of the Pdb Structure 3E2Z


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 3E2Z within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:32.6 occ:1.00 O B:HOH641 2.2 36.9 1.0 O B:HIS240 2.2 35.0 1.0 O B:HOH608 2.4 28.1 1.0 O B:HOH645 2.4 28.3 1.0 O B:HOH631 2.4 20.4 1.0 O B:HOH638 3.0 11.2 1.0 O B:HOH640 3.1 11.1 1.0 C B:HIS240 3.4 27.9 1.0 O B:ASP241 3.8 19.9 1.0 CA B:HIS240 4.2 27.1 1.0 CB B:ASP241 4.3 24.7 1.0 N B:ASP241 4.4 22.1 1.0 C B:ASP241 4.4 19.5 1.0 CB B:HIS240 4.5 26.5 1.0 CA B:ASP241 4.5 20.7 1.0 CG2 B:THR242 4.7 16.4 1.0 O B:THR209 4.8 16.2 1.0 CA B:SER207 4.8 29.4 1.0 O B:SER206 4.9 28.1 1.0 O B:SER207 5.0 24.0 1.0 ND1 B:HIS240 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