Sodium in PDB 4adc: 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;

The structure of Structural and Functional Study of Succinyl-Ornithine Transaminase From E. Coli, PDB code: 4adc 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)	108.69 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.370, 118.277, 109.457, 90.00, 96.80, 90.00
R / Rfree (%)	17.023 / 21.294

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

Magnesium

(Mg)

1 atom

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

Sodium binding site 1 out of 2 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 B:Na1404 b:21.4 occ:1.00 O B:ILE91 2.4 17.6 1.0 O B:HOH2049 2.4 18.6 1.0 O B:THR94 2.4 17.4 1.0 O B:HOH2048 2.4 24.7 1.0 O B:ALA96 2.6 18.6 1.0 C B:ILE91 3.5 17.6 1.0 C B:THR94 3.6 18.4 1.0 C B:ALA96 3.6 18.4 1.0 C B:PHE95 3.7 17.7 1.0 N B:ALA96 3.8 16.7 1.0 O B:PHE95 3.8 15.7 1.0 CG2 B:ILE91 4.0 15.0 1.0 CA B:ILE91 4.0 16.0 1.0 CA B:PHE95 4.1 16.6 1.0 CA B:ALA96 4.2 15.3 1.0 N B:PHE95 4.3 16.6 1.0 N B:THR94 4.4 19.4 1.0 N B:ASP92 4.5 18.9 1.0 CA B:THR94 4.6 17.1 1.0 CB B:ILE91 4.6 16.0 1.0 C B:ASP92 4.7 21.9 1.0 OD1 B:ASP97 4.7 19.5 1.0 O B:ASP92 4.7 25.0 1.0 CA B:ASP92 4.7 20.5 1.0 N B:ASP97 4.8 18.5 1.0 O B:HOH2050 4.8 18.0 1.0 OG1 B:THR94 4.9 17.6 1.0

Sodium binding site 2 out of 2 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 C:Na1404 b:25.2 occ:1.00 O C:HOH2055 2.3 24.3 1.0 O C:ALA96 2.4 20.0 1.0 O C:ILE91 2.5 22.2 1.0 O C:THR94 2.5 29.5 1.0 O C:HOH2056 2.5 25.3 1.0 C C:ALA96 3.6 22.4 1.0 C C:ILE91 3.6 23.0 1.0 C C:THR94 3.7 23.7 1.0 C C:PHE95 3.7 26.8 1.0 N C:ALA96 3.8 25.9 1.0 O C:PHE95 4.0 28.6 1.0 CG2 C:ILE91 4.1 21.1 1.0 CA C:PHE95 4.2 24.8 1.0 CA C:ILE91 4.2 22.7 1.0 CA C:ALA96 4.2 23.4 1.0 N C:PHE95 4.3 24.6 1.0 OD1 C:ASP97 4.5 29.4 1.0 N C:THR94 4.5 19.6 1.0 OG1 C:THR94 4.6 19.6 1.0 N C:ASP97 4.6 24.5 1.0 N C:ASP92 4.7 23.2 1.0 CA C:THR94 4.7 22.6 1.0 CB C:ILE91 4.8 21.1 1.0 CA C:ASP92 4.9 25.9 1.0 C C:ASP92 4.9 26.3 1.0 CA C:ASP97 4.9 24.2 1.0 O C:ASP92 5.0 24.3 1.0

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