Atomistry » Sodium » PDB 4dy7-4egs » 4e3q
Atomistry »
  Sodium »
    PDB 4dy7-4egs »
      4e3q »

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

Protein crystallography data

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

Sodium Binding Sites:

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 4e3q

Go back to Sodium Binding Sites List in 4e3q
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 4e3q

Go back to Sodium Binding Sites List in 4e3q
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 4e3q

Go back to Sodium Binding Sites List in 4e3q
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 4e3q

Go back to Sodium Binding Sites List in 4e3q
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

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: Tue Dec 15 06:38:20 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy