Sodium in PDB 6dam: Crystal Structure of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylomicrobium Buryatense 5G

The structure of Crystal Structure of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylomicrobium Buryatense 5G, PDB code: 6dam was solved by Y.Deng, S.Y.Ro, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.67 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	55.347, 92.283, 191.772, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.2

The structure of Crystal Structure of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylomicrobium Buryatense 5G also contains other interesting chemical elements:

Lanthanum

(La)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylomicrobium Buryatense 5G (pdb code 6dam). 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 Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylomicrobium Buryatense 5G, PDB code: 6dam:

Sodium binding site 1 out of 1 in the Crystal Structure of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylomicrobium Buryatense 5G


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 Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylomicrobium Buryatense 5G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:30.0 occ:1.00 O A:GLY246 2.7 23.8 1.0 N A:SER249 2.7 24.5 1.0 OG A:SER249 2.9 29.5 1.0 OD1 A:ASP224 2.9 25.3 1.0 CB A:SER249 3.2 23.4 1.0 N A:ASP248 3.3 29.0 1.0 CA A:SER249 3.5 24.9 1.0 C A:LYS247 3.6 26.9 1.0 OD2 A:ASP224 3.7 30.1 1.0 C A:ASP248 3.7 27.9 1.0 CG A:ASP224 3.7 28.2 1.0 O A:HOH829 3.7 25.9 1.0 CA A:ASP248 3.8 29.4 1.0 C A:GLY246 3.8 28.8 1.0 CA A:LYS247 3.8 30.7 1.0 CG2 A:ILE229 3.9 22.4 1.0 O A:HOH908 3.9 22.1 1.0 CG1 A:VAL245 4.2 21.5 1.0 O A:LYS247 4.2 25.9 1.0 N A:LYS247 4.3 26.9 1.0 O A:HOH1126 4.5 18.7 1.0 C A:SER249 4.7 26.0 1.0 N A:SER250 4.7 23.4 1.0 CB A:ILE229 4.8 21.3 1.0 O A:ASP248 4.8 28.0 1.0 CB A:PRO231 4.9 26.2 1.0 CG A:PRO231 4.9 28.4 1.0 CA A:PRO231 4.9 26.1 1.0

Y.W.Deng, S.Y.Ro, A.C.Rosenzweig. Structure and Function of the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From the Methanotroph Methylomicrobium Buryatense 5GB1C. J. Biol. Inorg. Chem. V. 23 1037 2018.
ISSN: ESSN 1432-1327
PubMed: 30132076
DOI: 10.1007/S00775-018-1604-2