Sodium in PDB 4a6u: Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350

All present enzymatic activity of Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350:
2.6.1.18; 2.6.1.62;

The structure of Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350, PDB code: 4a6u was solved by D.T.Logan, M.Hakansson, K.Yengo, M.Svedendahl Humble, K.Engelmarkcassimjee, B.Walse, V.Abedi, H.-J.Federsel, P.Berglund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 1.69
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.170, 61.110, 60.240, 109.14, 85.59, 103.25
R / Rfree (%)	15.5 / 18

The binding sites of Sodium atom in the Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350 (pdb code 4a6u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350, PDB code: 4a6u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1460 b:20.5 occ:1.00 OG1 A:THR107 2.6 13.7 1.0 O A:THR107 2.6 17.2 1.0 O A:PRO108 2.6 15.0 1.0 O A:ALA104 2.6 18.1 1.0 O A:HOH2097 2.7 37.1 1.0 O A:HOH2091 2.9 41.5 1.0 C A:THR107 3.2 15.6 1.0 C A:PRO108 3.4 17.1 1.0 C A:ALA104 3.6 15.4 1.0 CB A:THR107 3.6 12.3 1.0 CA A:THR107 3.8 14.7 1.0 CA A:ALA104 3.9 14.2 1.0 N A:PRO108 3.9 16.9 1.0 N A:THR107 4.0 15.8 1.0 N A:ALA109 4.0 19.8 1.0 CA A:ALA109 4.2 23.6 1.0 CA A:PRO108 4.2 17.9 1.0 O A:HOH2098 4.5 15.0 1.0 CB A:ALA104 4.6 16.8 1.0 O A:LEU103 4.6 11.0 1.0 C A:ALA109 4.7 24.1 1.0 N A:PHE111 4.7 19.8 1.0 N A:GLU105 4.7 15.3 1.0 N A:GLY110 4.8 23.6 1.0 O A:HOH2102 4.8 33.0 1.0 CG2 A:THR107 4.9 11.4 1.0 OD1 A:ASP112 4.9 43.1 1.0 CB A:PHE111 5.0 13.5 1.0 O A:PHE111 5.0 28.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Omega Transaminase From Chromobacterium Violaceum in the Apo Form, Crystallised From Peg 3350 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1460 b:15.6 occ:1.00 O B:HOH2061 2.5 17.2 1.0 OG1 B:THR107 2.5 10.6 1.0 O B:THR107 2.5 12.1 1.0 O B:HOH2066 2.5 20.9 1.0 O B:ALA104 2.6 14.0 1.0 O B:PRO108 2.7 13.9 1.0 C B:THR107 3.0 11.4 1.0 C B:PRO108 3.3 14.7 1.0 C B:ALA104 3.5 12.4 1.0 CB B:THR107 3.5 10.3 1.0 CA B:THR107 3.7 11.3 1.0 N B:PRO108 3.8 13.8 1.0 CA B:ALA104 3.8 11.8 1.0 N B:THR107 3.8 13.4 1.0 N B:ALA109 3.9 15.6 1.0 CA B:PRO108 4.1 16.7 1.0 CA B:ALA109 4.1 16.3 1.0 O B:HOH2065 4.4 13.5 1.0 O B:LEU103 4.5 10.3 1.0 CB B:ALA104 4.5 12.6 1.0 O B:HOH2070 4.6 22.6 1.0 N B:GLU105 4.7 11.8 1.0 C B:ALA109 4.7 16.7 1.0 CG2 B:THR107 4.8 11.0 1.0 N B:PHE111 4.8 14.0 1.0 N B:GLY110 4.8 16.5 1.0 C B:VAL106 4.9 16.6 1.0 CB B:PHE111 5.0 12.9 1.0 O B:PHE111 5.0 23.2 1.0

M.Svedendahl Humble, K.Engelmark Cassimjee, M.Hakansson, Y.R.Kimbung, B.Walse, V.Abedi, H.-J.Federsel, P.Berglund, D.T.Logan. Crystal Structures of the Chromobacterium Violaceum Omega-Transaminase Reveal Major Structural Rearrangements Upon Binding of Coenzyme Plp. Febs J. V. 279 779 2012.
ISSN: ISSN 1742-464X
PubMed: 22268978
DOI: 10.1111/J.1742-4658.2011.08468.X