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Sodium in PDB 4e3r: Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis

Protein crystallography data

The structure of Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis, PDB code: 4e3r 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) 29.88 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.980, 161.940, 179.270, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19

Sodium Binding Sites:

The binding sites of Sodium atom in the Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis (pdb code 4e3r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis, PDB code: 4e3r:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4e3r

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Sodium binding site 1 out of 4 in the Plp-Bound Aminotransferase Mutant 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 Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:24.5
occ:1.00
 O A:PHE106 2.3 22.2 1.0
O A:SER104 2.4 18.4 1.0
O A:HOH718 2.4 34.5 1.0
O A:HOH735 2.4 36.7 1.0
O A:VAL101 2.5 19.9 1.0
O A:GLU102 2.6 20.2 1.0
C A:GLU102 3.2 20.9 1.0
C A:PHE106 3.4 23.5 1.0
C A:SER104 3.5 20.4 1.0
C A:VAL101 3.6 21.0 1.0
CA A:GLU102 3.6 19.4 1.0
OG A:SER104 3.6 19.4 1.0
N A:PHE106 3.9 18.6 1.0
O A:HOH900 3.9 55.3 1.0
N A:SER104 4.0 16.9 1.0
N A:GLU102 4.0 18.7 1.0
N A:VAL103 4.2 16.8 1.0
C A:PRO105 4.2 22.8 1.0
CA A:SER104 4.2 16.8 1.0
CA A:PHE106 4.2 18.9 1.0
N A:ASP107 4.4 22.6 1.0
C A:VAL103 4.4 21.1 1.0
N A:PRO105 4.5 19.0 1.0
CB A:SER104 4.5 16.9 1.0
CA A:PRO105 4.5 19.9 1.0
CA A:ASP107 4.6 23.9 1.0
CA A:VAL103 4.7 16.3 1.0
O A:PRO105 4.7 22.4 1.0
CA A:VAL101 4.9 15.4 1.0
C A:ASP107 5.0 25.8 1.0

Sodium binding site 2 out of 4 in 4e3r

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Sodium binding site 2 out of 4 in the Plp-Bound Aminotransferase Mutant 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 Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:25.1
occ:1.00
 O B:PHE106 2.3 21.8 1.0
O B:GLU102 2.4 21.4 1.0
O B:VAL101 2.4 18.8 1.0
O B:SER104 2.5 22.6 1.0
O B:HOH697 2.5 27.9 1.0
O B:HOH689 2.5 39.1 1.0
C B:GLU102 3.1 22.4 1.0
C B:PHE106 3.5 23.3 1.0
C B:VAL101 3.5 19.8 1.0
C B:SER104 3.5 22.2 1.0
CA B:GLU102 3.5 19.9 1.0
OG B:SER104 3.6 20.3 1.0
N B:PHE106 3.9 19.3 1.0
N B:SER104 3.9 16.1 1.0
N B:GLU102 4.0 18.8 1.0
N B:VAL103 4.1 16.9 1.0
CA B:SER104 4.2 16.5 1.0
CA B:PHE106 4.3 19.3 1.0
C B:PRO105 4.3 22.8 1.0
C B:VAL103 4.3 20.7 1.0
O B:HOH954 4.5 57.8 1.0
N B:PRO105 4.5 21.5 1.0
CB B:SER104 4.5 17.5 1.0
N B:ASP107 4.5 21.1 1.0
CA B:PRO105 4.6 20.9 1.0
CA B:VAL103 4.7 16.9 1.0
CA B:ASP107 4.7 22.4 1.0
O B:HOH895 4.8 44.3 1.0
CA B:VAL101 4.8 14.8 1.0
O B:PRO105 4.9 21.5 1.0
O B:VAL103 5.0 18.5 1.0
CB B:GLU102 5.0 22.3 1.0

Sodium binding site 3 out of 4 in 4e3r

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Sodium binding site 3 out of 4 in the Plp-Bound Aminotransferase Mutant 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 Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:29.8
occ:1.00
 O C:SER104 2.3 24.1 1.0
O C:PHE106 2.3 25.9 1.0
O C:VAL101 2.4 25.1 1.0
O C:HOH801 2.5 37.0 1.0
O C:GLU102 2.6 24.9 1.0
C C:GLU102 3.2 25.7 1.0
C C:SER104 3.3 24.2 1.0
C C:PHE106 3.4 26.7 1.0
OG C:SER104 3.5 26.0 1.0
C C:VAL101 3.5 25.8 1.0
CA C:GLU102 3.6 24.1 1.0
N C:PHE106 3.8 21.9 1.0
N C:SER104 3.8 19.9 1.0
N C:GLU102 4.0 23.5 1.0
CA C:SER104 4.1 19.2 1.0
N C:VAL103 4.1 22.2 1.0
O C:HOH905 4.1 60.3 1.0
C C:PRO105 4.2 25.6 1.0
CA C:PHE106 4.2 21.1 1.0
C C:VAL103 4.3 24.3 1.0
N C:PRO105 4.3 22.1 1.0
CB C:SER104 4.4 19.9 1.0
CA C:PRO105 4.4 22.2 1.0
N C:ASP107 4.5 25.9 1.0
CA C:VAL103 4.6 21.1 1.0
CA C:ASP107 4.7 27.1 1.0
O C:PRO105 4.8 24.1 1.0
CA C:VAL101 4.8 20.2 1.0
O C:VAL103 4.9 22.7 1.0
CB C:PHE106 4.9 22.0 1.0
O C:HOH950 5.0 58.6 1.0

Sodium binding site 4 out of 4 in 4e3r

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Sodium binding site 4 out of 4 in the Plp-Bound Aminotransferase Mutant 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 Plp-Bound Aminotransferase Mutant Crystal Structure From Vibrio Fluvialis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:30.1
occ:1.00
 O D:PHE106 2.3 25.8 1.0
O D:SER104 2.4 23.3 1.0
O D:HOH652 2.4 34.6 1.0
O D:VAL101 2.5 21.4 1.0
O D:HOH669 2.5 35.2 1.0
O D:GLU102 2.6 24.5 1.0
C D:GLU102 3.2 24.0 1.0
C D:SER104 3.4 24.8 1.0
OG D:SER104 3.5 21.9 1.0
C D:PHE106 3.5 27.3 1.0
C D:VAL101 3.6 23.0 1.0
CA D:GLU102 3.6 20.3 1.0
N D:SER104 3.8 20.1 1.0
N D:PHE106 3.9 21.7 1.0
N D:GLU102 4.0 21.1 1.0
CA D:SER104 4.1 18.7 1.0
N D:VAL103 4.1 20.1 1.0
C D:PRO105 4.2 26.7 1.0
CA D:PHE106 4.2 21.5 1.0
C D:VAL103 4.3 22.4 1.0
CB D:SER104 4.3 20.6 1.0
N D:PRO105 4.4 22.9 1.0
N D:ASP107 4.5 26.0 1.0
CA D:PRO105 4.6 23.1 1.0
CA D:VAL103 4.7 19.4 1.0
CA D:ASP107 4.7 26.5 1.0
O D:PRO105 4.8 26.7 1.0
O D:VAL103 4.9 21.1 1.0
O D:HOH890 4.9 47.7 1.0
CA D:VAL101 4.9 18.0 1.0

Reference:

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
Page generated: Sun Aug 17 19:05:39 2025

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