Sodium in PDB 3njh: D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.

The structure of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis., PDB code: 3njh was solved by J.Osipiuk, R.Mulligan, M.Bargassa, F.Collart, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.30 / 1.94
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	97.986, 97.986, 65.844, 90.00, 90.00, 120.00
R / Rfree (%)	12.7 / 15.2

The structure of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. (pdb code 3njh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis., PDB code: 3njh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:31.5 occ:1.00 O A:HOH178 2.0 40.0 1.0 O A:HOH261 2.1 28.5 1.0 O A:HOH177 2.3 33.4 1.0 O A:HOH260 2.3 30.9 1.0 O A:HOH263 2.4 21.8 1.0 O A:THR106 2.6 18.4 1.0 O A:HOH164 3.1 26.6 1.0 C A:THR106 3.7 18.2 1.0 O A:ALA107 4.1 15.9 1.0 O A:HOH134 4.4 26.7 1.0 C A:ALA107 4.4 17.2 1.0 CA A:THR106 4.6 18.0 1.0 N A:ALA107 4.6 17.2 1.0 CA A:ALA107 4.6 17.4 1.0 CB A:THR106 4.9 18.4 1.0

Sodium binding site 2 out of 2 in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:38.8 occ:1.00 O C:HOH232 1.9 39.6 1.0 O C:HOH214 2.1 39.2 1.0 O C:HOH248 2.3 38.0 1.0 O C:HOH272 2.3 27.8 1.0 O C:HOH276 2.6 23.1 1.0 O C:THR106 2.6 19.3 1.0 O C:HOH233 2.7 26.8 1.0 C C:THR106 3.8 19.3 1.0 O C:HOH146 4.0 18.8 1.0 O C:ALA107 4.2 17.3 1.0 C C:ALA107 4.3 18.2 1.0 CA C:ALA107 4.5 18.4 1.0 N C:ALA107 4.6 18.5 1.0 O C:HOH203 4.7 30.8 1.0 CA C:THR106 4.8 20.6 1.0 N C:ASN108 4.8 17.8 1.0

J.Osipiuk, R.Mulligan, M.Bargassa, J.E.Hamilton, M.A.Cunningham, A.Joachimiak. Characterization of Member of DUF1888 Protein Family, Self-Cleaving and Self-Assembling Endopeptidase. J.Biol.Chem. V. 287 19452 2012.
ISSN: ISSN 0021-9258
PubMed: 22493430
DOI: 10.1074/JBC.M112.358069