Sodium in PDB 5vma: Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine

The structure of Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine, PDB code: 5vma was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.891, 98.891, 216.799, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19.6

The structure of Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine (pdb code 5vma). 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 Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine, PDB code: 5vma:

Sodium binding site 1 out of 1 in the Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na806 b:27.2 occ:0.82 OD1 A:ASN165 2.4 29.4 1.0 OG A:SER167 2.5 24.9 1.0 N A:SER167 3.1 17.2 1.0 C A:ASN165 3.3 16.4 1.0 CB A:SER167 3.4 20.0 1.0 CG A:ASN165 3.4 24.1 1.0 N A:PRO166 3.4 16.5 1.0 CA A:ASN165 3.5 17.0 1.0 O A:ASN165 3.7 13.3 1.0 CA A:SER167 3.8 19.3 1.0 CD A:PRO166 3.8 16.1 1.0 CB A:ASN165 3.9 21.3 1.0 OD1 A:ASN90 4.1 30.5 0.5 C A:PRO166 4.1 17.6 1.0 N A:HIS168 4.2 16.9 1.0 CA A:PRO166 4.3 16.8 1.0 C A:SER167 4.3 18.8 1.0 CD2 A:HIS168 4.5 18.8 1.0 ND2 A:ASN165 4.6 26.5 1.0 NE2 A:HIS168 4.7 19.7 1.0 N A:ASN165 4.8 17.1 1.0 CG A:HIS168 4.9 18.1 1.0 CG A:ASN90 4.9 31.2 0.5

P.M.Alahuhta, V.V.Lunin. Bacillus Pumilus Family 48 Glycoside Hydrolase in Complex with Cellobio-Derived Isofagomine To Be Published.