Calcium 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:

Sodium

(Na)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine, PDB code: 5vma:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca804 b:17.1 occ:0.68 O A:GLN181 2.3 11.5 1.0 OD2 A:ASP405 2.3 13.8 1.0 O A:HOH1034 2.3 16.4 1.0 OE2 A:GLU186 2.4 12.4 1.0 OE1 A:GLN181 2.5 16.2 1.0 OE1 A:GLU186 2.8 11.1 1.0 O A:HOH1313 2.9 22.3 1.0 CD A:GLU186 3.0 11.0 1.0 CG A:ASP405 3.4 14.5 1.0 C A:GLN181 3.4 13.2 1.0 CD A:GLN181 3.6 15.6 1.0 CB A:ASP405 3.8 15.3 1.0 CB A:GLN181 3.8 13.7 1.0 CA A:GLN181 3.9 13.4 1.0 O A:HOH1275 4.0 38.0 1.0 O A:HOH1371 4.1 27.9 0.5 NH1 A:ARG597 4.2 14.6 1.0 N A:SER183 4.2 11.3 1.0 CG A:GLN181 4.3 13.8 1.0 OD1 A:ASP405 4.5 15.0 1.0 CG A:GLU186 4.5 9.5 1.0 N A:GLU182 4.5 10.9 1.0 OG A:SER183 4.6 12.7 1.0 OE1 A:GLU602 4.6 16.2 1.0 NE2 A:GLN181 4.7 12.8 1.0 CB A:SER183 4.7 11.4 1.0 CA A:GLU182 4.8 11.0 1.0 C A:GLU182 5.0 11.1 1.0

Calcium binding site 2 out of 2 in the Structure of B. Pumilus GH48 in Complex with A Cellobio-Derived Isofagomine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 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:Ca805 b:24.9 occ:0.47 O A:HOH1199 2.2 36.2 1.0 O A:ILE83 2.3 11.8 1.0 O A:GLU79 2.4 14.2 1.0 O A:VAL85 2.5 31.0 1.0 O A:HOH1090 2.8 17.0 1.0 OE1 A:GLU92 3.2 23.6 1.0 O A:LYS80 3.4 15.7 1.0 C A:ILE83 3.5 12.4 1.0 C A:VAL85 3.6 29.1 1.0 C A:GLU79 3.6 16.2 1.0 N A:VAL85 3.6 19.3 1.0 C A:LYS80 3.8 16.4 1.0 CA A:LYS80 4.1 16.9 1.0 CA A:PRO84 4.2 14.2 1.0 N A:PRO84 4.3 13.6 1.0 N A:LYS80 4.3 17.2 1.0 OH A:TYR172 4.3 13.8 1.0 CA A:VAL85 4.3 23.9 1.0 CD A:GLU92 4.3 21.1 1.0 C A:PRO84 4.3 16.9 1.0 N A:ASN86 4.5 39.9 1.0 N A:ILE83 4.5 11.3 1.0 CA A:ILE83 4.5 11.6 1.0 N A:TYR81 4.6 16.2 1.0 CG2 A:VAL85 4.6 33.3 1.0 OE2 A:GLU92 4.6 20.7 1.0 CA A:ASN86 4.7 52.2 1.0 CA A:GLU79 4.7 16.8 1.0 CB A:ILE83 4.7 11.6 1.0 OD1 A:ASN86 4.9 49.0 1.0

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