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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: Tue Dec 15 06:32:41 2020

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