Sodium in PDB 4q3n: Crystal Structure of Mgs-M5, A Lactate Dehydrogenase Enzyme From A Medee Basin Deep-Sea Metagenome Library

The structure of Crystal Structure of Mgs-M5, A Lactate Dehydrogenase Enzyme From A Medee Basin Deep-Sea Metagenome Library, PDB code: 4q3n was solved by P.J.Stogios, X.Xu, H.Cui, M.Alcaide, M.Ferrer, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.31 / 1.97
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.818, 92.818, 203.804, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.4

The structure of Crystal Structure of Mgs-M5, A Lactate Dehydrogenase Enzyme From A Medee Basin Deep-Sea Metagenome Library also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Mgs-M5, A Lactate Dehydrogenase Enzyme From A Medee Basin Deep-Sea Metagenome Library (pdb code 4q3n). 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 Crystal Structure of Mgs-M5, A Lactate Dehydrogenase Enzyme From A Medee Basin Deep-Sea Metagenome Library, PDB code: 4q3n:

Sodium binding site 1 out of 1 in the Crystal Structure of Mgs-M5, A Lactate Dehydrogenase Enzyme From A Medee Basin Deep-Sea Metagenome Library


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mgs-M5, A Lactate Dehydrogenase Enzyme From A Medee Basin Deep-Sea Metagenome Library within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:37.3 occ:1.00 O A:ILE204 2.3 34.4 1.0 O A:ILE198 2.3 37.2 1.0 O A:HOH709 2.3 37.5 1.0 O A:HOH708 2.4 50.7 1.0 O A:MET201 2.5 36.4 1.0 O A:HOH711 2.7 48.5 1.0 C A:ILE204 3.4 35.6 1.0 C A:ILE198 3.4 38.1 1.0 C A:MET201 3.5 38.1 1.0 CA A:ILE198 3.9 35.6 1.0 CG2 A:ILE198 3.9 40.2 1.0 OG A:SER205 4.0 39.1 0.5 CA A:SER205 4.1 37.1 0.5 CA A:SER205 4.1 36.9 0.5 CA A:ASP202 4.2 44.7 1.0 N A:SER205 4.2 35.8 1.0 N A:ILE204 4.2 36.5 1.0 N A:ASP202 4.2 40.0 1.0 O A:HOH710 4.3 54.4 1.0 C A:ASP202 4.4 41.9 1.0 CA A:ILE204 4.4 33.7 1.0 O A:ASP202 4.5 41.5 1.0 N A:ASP199 4.5 41.6 1.0 N A:MET201 4.6 35.6 1.0 CB A:ILE198 4.6 38.5 1.0 CB A:SER205 4.6 38.1 0.5 CA A:MET201 4.6 35.7 1.0 CB A:SER205 4.7 37.5 0.5 O A:HOH554 4.7 43.5 1.0 CA A:ASP199 4.8 45.0 1.0 C A:ASP199 4.8 42.8 1.0 CG2 A:ILE204 4.8 29.8 1.0 O A:VAL197 4.9 32.4 1.0 N A:GLU203 5.0 34.8 1.0

M.Alcaide, P.J.Stogios, A.Lafraya, A.Tchigvintsev, R.Flick, R.Bargiela, T.N.Chernikova, O.N.Reva, T.Hai, C.C.Leggewie, N.Katzke, V.La Cono, R.Matesanz, M.Jebbar, K.E.Jaeger, M.M.Yakimov, A.F.Yakunin, P.N.Golyshin, O.V.Golyshina, A.Savchenko, M.Ferrer. Pressure Adaptation Is Linked to Thermal Adaptation in Salt-Saturated Marine Habitats. Environ Microbiol 2014.
PubMed: 25330254
DOI: 10.1111/1462-2920.12660