Sodium in PDB 5k9h: Crystal Structure of A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium

The structure of Crystal Structure of A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium, PDB code: 5k9h was solved by E.L.Summers, V.L.Arcus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.99 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.671, 78.308, 134.529, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.9

The binding sites of Sodium atom in the Crystal Structure of A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium (pdb code 5k9h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium, PDB code: 5k9h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium


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 A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na628 b:41.9 occ:1.00 O A:LEU439 3.3 19.8 1.0 O A:HOH730 4.1 21.6 1.0 C A:LEU439 4.1 18.7 1.0 OE1 A:GLU448 4.2 13.6 1.0 OG A:SER280 4.2 12.7 1.0 CB A:SER280 4.2 10.3 1.0 CD A:GLU448 4.4 11.4 1.0 N A:SCN618 4.4 39.9 1.0 CB A:LEU439 4.5 15.0 1.0 CG A:GLU448 4.6 15.7 1.0 O A:HOH1220 4.8 33.6 1.0 OE2 A:GLU448 4.8 12.3 1.0 CA A:THR440 4.8 14.7 1.0 N A:THR440 4.8 17.2 1.0 O A:HOH931 4.8 9.3 1.0 CA A:LEU439 5.0 16.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Glycoside Hydrolase 29 Family Member From An Unknown Rumen Bacterium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na629 b:35.9 occ:1.00 N A:SCN621 2.9 24.8 1.0 O A:ARG211 3.2 14.9 1.0 O A:HOH959 3.3 37.9 1.0 O A:HOH760 3.4 25.1 1.0 C A:SCN621 3.7 30.7 1.0 NH2 A:ARG196 3.8 23.8 1.0 OD1 A:ASP213 4.1 19.0 1.0 C A:ARG211 4.2 16.8 1.0 C A:GLY212 4.5 14.0 1.0 CE1 A:HIS234 4.5 22.3 1.0 CA A:GLY212 4.6 13.0 1.0 O A:GLY212 4.7 13.1 1.0 CD2 A:TYR192 4.7 15.6 1.0 N A:GLY212 4.8 11.4 1.0 CE2 A:TYR192 4.8 13.1 1.0 ND1 A:HIS234 4.9 23.5 1.0 N A:ASP213 4.9 11.6 1.0 O A:HOH713 5.0 29.9 1.0

E.L.Summers, C.D.Moon, R.Atua, V.L.Arcus. The Structure of A Glycoside Hydrolase 29 Family Member From A Rumen Bacterium Reveals Unique, Dual Carbohydrate-Binding Domains. Acta Crystallogr.,Sect.F V. 72 750 2016.
ISSN: ESSN 2053-230X
PubMed: 27710940
DOI: 10.1107/S2053230X16014072