Atomistry » Sodium » PDB 3zux-4adj » 4adb
Atomistry »
  Sodium »
    PDB 3zux-4adj »
      4adb »

Sodium in PDB 4adb: Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli

Enzymatic activity of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli

All present enzymatic activity of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli:
2.6.1.17; 2.6.1.81;

Protein crystallography data

The structure of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli, PDB code: 4adb was solved by J.Newman, T.S.Peat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.05 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.708, 118.428, 109.792, 90.00, 96.69, 90.00
R / Rfree (%) 17.085 / 21.885

Other elements in 4adb:

The structure of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli (pdb code 4adb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli, PDB code: 4adb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4adb

Go back to Sodium Binding Sites List in 4adb
Sodium binding site 1 out of 4 in the Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1405

b:23.2
occ:1.00
 O A:HOH2090 2.1 31.7 1.0
O A:ILE91 2.3 23.2 1.0
O A:ALA96 2.4 24.2 1.0
O A:THR94 2.4 22.2 1.0
O A:HOH2093 2.5 21.9 1.0
C A:ILE91 3.3 22.8 1.0
C A:ALA96 3.5 22.7 1.0
C A:THR94 3.6 23.1 1.0
C A:PHE95 3.8 22.7 1.0
N A:ALA96 3.8 19.5 1.0
CG2 A:ILE91 3.9 18.0 1.0
CA A:ILE91 4.0 20.9 1.0
O A:PHE95 4.1 20.6 1.0
CA A:ALA96 4.3 21.5 1.0
CA A:PHE95 4.3 20.9 1.0
O A:HOH2091 4.3 29.7 1.0
N A:THR94 4.3 19.1 1.0
N A:ASP92 4.4 20.0 1.0
N A:PHE95 4.4 22.5 1.0
O A:HOH2095 4.5 22.2 1.0
OD1 A:ASP97 4.5 30.8 1.0
CB A:ILE91 4.6 21.7 1.0
N A:ASP97 4.6 21.3 1.0
CA A:THR94 4.6 21.6 1.0
CA A:ASP92 4.6 23.5 1.0
C A:ASP92 4.7 24.8 1.0
OG1 A:THR94 4.7 22.0 1.0
O A:ASP92 4.8 23.5 1.0
CA A:ASP97 4.9 21.3 1.0

Sodium binding site 2 out of 4 in 4adb

Go back to Sodium Binding Sites List in 4adb
Sodium binding site 2 out of 4 in the Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1405

b:21.7
occ:1.00
 O B:ALA96 2.3 18.5 1.0
O B:ILE91 2.4 18.3 1.0
O B:HOH2064 2.4 21.3 1.0
O B:THR94 2.4 18.9 1.0
O B:HOH2062 2.4 34.5 1.0
C B:ALA96 3.4 19.4 1.0
C B:ILE91 3.4 20.6 1.0
C B:PHE95 3.5 20.4 1.0
N B:ALA96 3.6 21.4 1.0
C B:THR94 3.6 19.8 1.0
O B:PHE95 3.7 19.8 1.0
CG2 B:ILE91 3.9 17.3 1.0
CA B:ILE91 4.0 16.8 1.0
CA B:ALA96 4.0 18.5 1.0
CA B:PHE95 4.1 19.1 1.0
N B:PHE95 4.3 20.2 1.0
O B:HOH2066 4.4 21.8 1.0
N B:ASP97 4.4 19.9 1.0
N B:THR94 4.5 20.7 1.0
OD1 B:ASP97 4.5 22.7 1.0
CB B:ILE91 4.5 18.0 1.0
N B:ASP92 4.5 22.0 1.0
OG1 B:THR94 4.6 20.1 1.0
CA B:THR94 4.7 19.9 1.0
CB B:ALA96 4.8 17.1 1.0
CA B:ASP97 4.8 19.9 1.0
CA B:ASP92 4.8 22.3 1.0
C B:ASP92 4.9 24.8 1.0
O B:ASP92 5.0 25.6 1.0

Sodium binding site 3 out of 4 in 4adb

Go back to Sodium Binding Sites List in 4adb
Sodium binding site 3 out of 4 in the Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1405

b:27.9
occ:1.00
 O C:HOH2063 2.2 26.0 1.0
O C:THR94 2.4 26.2 1.0
O C:ILE91 2.4 26.1 1.0
O C:ALA96 2.4 25.6 1.0
O C:HOH2065 2.6 27.8 1.0
C C:ILE91 3.5 25.5 1.0
C C:ALA96 3.5 25.3 1.0
C C:THR94 3.6 24.4 1.0
N C:ALA96 3.6 26.4 1.0
C C:PHE95 3.7 28.1 1.0
O C:PHE95 4.0 30.8 1.0
CA C:ILE91 4.0 25.8 1.0
CG2 C:ILE91 4.1 25.4 1.0
CA C:ALA96 4.2 26.4 1.0
CA C:PHE95 4.2 26.1 1.0
N C:PHE95 4.4 25.2 1.0
N C:THR94 4.5 23.4 1.0
O C:HOH2067 4.5 31.6 1.0
N C:ASP92 4.6 24.2 1.0
OG1 C:THR94 4.6 24.9 1.0
N C:ASP97 4.6 24.6 1.0
CA C:THR94 4.6 24.0 1.0
OD1 C:ASP97 4.6 28.6 1.0
CB C:ILE91 4.6 24.3 1.0
CA C:ASP92 4.8 27.7 1.0
C C:ASP92 4.9 27.1 1.0
CA C:ASP97 4.9 25.9 1.0
CB C:ALA96 5.0 25.6 1.0

Sodium binding site 4 out of 4 in 4adb

Go back to Sodium Binding Sites List in 4adb
Sodium binding site 4 out of 4 in the Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1405

b:36.9
occ:1.00
 O D:ILE91 2.5 35.0 1.0
O D:THR94 2.5 31.3 1.0
O D:ALA96 2.6 31.9 1.0
C D:ILE91 3.6 35.1 1.0
C D:ALA96 3.6 34.5 1.0
C D:THR94 3.7 30.6 1.0
C D:PHE95 3.7 34.1 1.0
N D:ALA96 3.8 38.0 1.0
O D:PHE95 3.9 33.2 1.0
CG2 D:ILE91 4.0 29.6 1.0
CA D:PHE95 4.2 30.2 1.0
CA D:ILE91 4.2 34.1 1.0
CA D:ALA96 4.3 36.5 1.0
N D:PHE95 4.4 28.1 1.0
OD1 D:ASP97 4.5 34.3 1.0
N D:THR94 4.6 34.2 1.0
N D:ASP92 4.6 29.6 1.0
N D:ASP97 4.6 34.4 1.0
CA D:THR94 4.8 32.5 1.0
CB D:ILE91 4.8 31.9 1.0
OG1 D:THR94 4.9 39.1 1.0
O D:ASP92 4.9 45.1 1.0
CA D:ASP92 4.9 34.0 1.0
CA D:ASP97 5.0 36.1 1.0
C D:ASP92 5.0 40.7 1.0

Reference:

J.Newman, S.Seabrook, R.Surjadi, C.C.Williams, D.Lucent, M.Wilding, C.Scott, T.S.Peat. Determination of the Structure of the Catabolic N- Succinylornithine Transaminase (Astc) From Escherichia Coli. Plos One V. 8 58298 2013.
ISSN: ISSN 1932-6203
PubMed: 23484010
DOI: 10.1371/JOURNAL.PONE.0058298
Page generated: Mon Oct 7 14:19:47 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy