Sodium in PDB 4k28: 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+

The structure of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+, PDB code: 4k28 was solved by C.Garcia, J.Peek, P.Petit, D.Christendat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.22 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.437, 76.688, 153.333, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.8

The structure of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Sodium atom in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ (pdb code 4k28). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+, PDB code: 4k28:

Sodium binding site 1 out of 1 in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:24.8 occ:1.00 N B:LYS71 3.3 26.7 1.0 CB B:LYS71 3.4 27.3 1.0 C B:PRO69 3.5 29.5 1.0 CA B:PRO69 3.6 30.3 1.0 CG B:LYS71 3.6 29.7 1.0 N B:TYR70 3.6 26.8 1.0 CA B:VAL68 3.6 30.3 1.0 CB B:VAL68 3.9 31.0 1.0 O B:PRO69 3.9 31.0 1.0 CA B:LYS71 4.0 25.9 1.0 CD B:LYS71 4.1 32.0 1.0 O B:HOH491 4.2 47.8 1.0 N B:VAL68 4.3 30.3 1.0 C B:TYR70 4.4 25.1 1.0 O B:THR67 4.4 25.6 1.0 CG1 B:VAL68 4.5 32.8 1.0 CA B:TYR70 4.5 24.1 1.0 N B:PRO69 4.5 29.1 1.0 O B:HOH425 4.6 27.2 1.0 C B:VAL68 4.6 28.4 1.0 C B:THR67 4.6 27.1 1.0 N B:GLN72 4.7 23.3 1.0 CB B:PRO69 4.7 32.2 1.0 O B:HOH445 4.8 31.7 1.0 C B:LYS71 4.9 27.1 1.0 CE B:LYS71 5.0 37.8 1.0

J.Peek, C.Garcia, J.Lee, D.Christendat. Insights Into the Function of RIFI2: Structural and Biochemical Investigation of A New Shikimate Dehydrogenase Family Protein. Biochim.Biophys.Acta V.1834 516 2013.
ISSN: ISSN 0006-3002
PubMed: 23142411
DOI: 10.1016/J.BBAPAP.2012.10.016