Sodium in PDB 4e3q: Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis

The structure of Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis, PDB code: 4e3q was solved by K.S.Midelfort, R.Kumar, S.Han, M.J.Karmilowicz, K.Mcconnell, D.K.Gehlhaar, A.Mistry, J.S.Chang, M.Anderson, A.Vilalobos, J.Minshull, S.Govindarajan, J.W.Wong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.79 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.071, 162.182, 180.398, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21

The binding sites of Sodium atom in the Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis (pdb code 4e3q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis, PDB code: 4e3q:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:33.4 occ:1.00 O A:SER104 2.3 29.4 1.0 O A:PHE106 2.4 32.8 1.0 O A:VAL101 2.5 27.8 1.0 O A:HOH693 2.5 34.4 1.0 O A:GLU102 2.5 28.5 1.0 O A:HOH765 2.5 41.4 1.0 C A:GLU102 3.2 29.7 1.0 C A:SER104 3.4 30.2 1.0 C A:PHE106 3.5 33.6 1.0 C A:VAL101 3.5 29.7 1.0 OG A:SER104 3.6 27.4 1.0 CA A:GLU102 3.6 28.3 1.0 N A:PHE106 3.8 29.0 1.0 N A:SER104 3.9 24.6 1.0 N A:GLU102 4.0 27.5 1.0 CA A:SER104 4.1 24.6 1.0 N A:VAL103 4.2 24.9 1.0 C A:PRO105 4.2 33.2 1.0 CA A:PHE106 4.3 29.1 1.0 C A:VAL103 4.3 28.8 1.0 N A:PRO105 4.4 28.0 1.0 CB A:SER104 4.4 24.9 1.0 CA A:PRO105 4.5 28.0 1.0 N A:ASP107 4.5 32.6 1.0 CA A:VAL103 4.7 25.6 1.0 CA A:ASP107 4.8 33.4 1.0 O A:PRO105 4.8 34.0 1.0 CA A:VAL101 4.8 25.5 1.0 O A:VAL103 4.9 28.2 1.0

Sodium binding site 2 out of 4 in the Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:31.9 occ:1.00 O B:HOH890 2.3 45.1 1.0 O B:PHE106 2.3 32.0 1.0 O B:SER104 2.4 29.1 1.0 O B:VAL101 2.5 26.4 1.0 O B:HOH796 2.5 40.2 1.0 O B:GLU102 2.6 28.9 1.0 C B:GLU102 3.2 29.1 1.0 C B:PHE106 3.5 31.5 1.0 C B:SER104 3.5 29.6 1.0 C B:VAL101 3.6 27.4 1.0 CA B:GLU102 3.6 24.8 1.0 OG B:SER104 3.6 26.4 1.0 N B:PHE106 3.8 25.9 1.0 N B:SER104 3.9 24.8 1.0 N B:GLU102 4.0 24.2 1.0 N B:VAL103 4.2 26.7 1.0 C B:PRO105 4.2 31.0 1.0 CA B:SER104 4.2 24.4 1.0 CA B:PHE106 4.2 25.9 1.0 C B:VAL103 4.4 29.2 1.0 N B:PRO105 4.5 27.6 1.0 N B:ASP107 4.5 30.5 1.0 CB B:SER104 4.5 24.6 1.0 CA B:PRO105 4.6 28.3 1.0 CA B:ASP107 4.7 31.9 1.0 CA B:VAL103 4.7 26.3 1.0 O B:PRO105 4.7 31.9 1.0 O B:HOH804 4.8 38.4 1.0 CA B:VAL101 4.9 25.6 1.0 O B:VAL103 5.0 27.4 1.0

Sodium binding site 3 out of 4 in the Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:35.6 occ:1.00 O C:HOH799 2.4 43.6 1.0 O C:SER104 2.4 29.7 1.0 O C:PHE106 2.4 35.4 1.0 O C:GLU102 2.4 28.0 1.0 O C:VAL101 2.5 29.4 1.0 O C:HOH826 2.6 44.2 1.0 C C:GLU102 3.1 30.9 1.0 C C:SER104 3.5 29.9 1.0 C C:VAL101 3.5 31.5 1.0 CA C:GLU102 3.6 29.7 1.0 C C:PHE106 3.6 36.7 1.0 OG C:SER104 3.7 30.6 1.0 N C:SER104 3.9 27.1 1.0 N C:PHE106 3.9 30.1 1.0 N C:GLU102 4.0 28.9 1.0 N C:VAL103 4.1 28.4 1.0 CA C:SER104 4.2 25.6 1.0 C C:VAL103 4.3 30.8 1.0 CA C:PHE106 4.3 30.6 1.0 C C:PRO105 4.3 33.9 1.0 N C:PRO105 4.5 28.8 1.0 CB C:SER104 4.5 28.3 1.0 N C:ASP107 4.6 36.3 1.0 CA C:PRO105 4.6 29.5 1.0 CA C:VAL103 4.6 27.8 1.0 CA C:ASP107 4.9 37.4 1.0 O C:HOH690 4.9 44.5 1.0 CA C:VAL101 4.9 28.4 1.0 O C:PRO105 5.0 34.5 1.0 O C:VAL103 5.0 30.6 1.0 CB C:GLU102 5.0 31.1 1.0

Sodium binding site 4 out of 4 in the Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pmp-Bound Form of Aminotransferase Crystal Structure From Vibrio Fluvialis within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:35.5 occ:1.00 O D:VAL101 2.4 28.9 1.0 O D:HOH687 2.4 38.6 1.0 O D:PHE106 2.4 34.1 1.0 O D:SER104 2.5 31.2 1.0 O D:GLU102 2.5 30.3 1.0 O D:HOH767 2.6 37.7 1.0 C D:GLU102 3.2 32.0 1.0 C D:VAL101 3.5 30.2 1.0 CA D:GLU102 3.6 29.3 1.0 C D:PHE106 3.6 35.0 1.0 C D:SER104 3.6 31.1 1.0 OG D:SER104 3.6 29.8 1.0 N D:SER104 3.9 26.9 1.0 N D:GLU102 3.9 28.3 1.0 N D:PHE106 4.0 30.1 1.0 N D:VAL103 4.1 29.0 1.0 CA D:SER104 4.3 26.3 1.0 CA D:PHE106 4.4 29.7 1.0 C D:PRO105 4.4 34.4 1.0 C D:VAL103 4.4 30.4 1.0 N D:PRO105 4.6 28.5 1.0 CB D:SER104 4.6 27.6 1.0 N D:ASP107 4.6 34.7 1.0 CA D:PRO105 4.7 28.9 1.0 CA D:VAL103 4.7 28.4 1.0 CA D:ASP107 4.8 35.5 1.0 CA D:VAL101 4.8 26.6 1.0 O D:HOH794 4.8 48.0 1.0 CG1 D:VAL101 4.9 31.1 1.0 O D:PRO105 4.9 35.2 1.0 C D:ASP107 5.0 37.1 1.0

K.S.Midelfort, R.Kumar, S.Han, M.J.Karmilowicz, K.Mcconnell, D.K.Gehlhaar, A.Mistry, J.S.Chang, M.Anderson, A.Villalobos, J.Minshull, S.Govindarajan, J.W.Wong. Redesigning and Characterizing the Substrate Specificity and Activity of Vibrio Fluvialis Aminotransferase For the Synthesis of Imagabalin. Protein Eng.Des.Sel. V. 26 25 2013.
ISSN: ISSN 1741-0126
PubMed: 23012440
DOI: 10.1093/PROTEIN/GZS065