Sodium in PDB 3bc9: Alpha-Amylase B in Complex with Acarbose

All present enzymatic activity of Alpha-Amylase B in Complex with Acarbose:
3.2.1.1;

The structure of Alpha-Amylase B in Complex with Acarbose, PDB code: 3bc9 was solved by T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	227.850, 77.240, 50.380, 90.00, 98.63, 90.00
R / Rfree (%)	15.1 / 17.8

The structure of Alpha-Amylase B in Complex with Acarbose also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Alpha-Amylase B in Complex with Acarbose (pdb code 3bc9). 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 Alpha-Amylase B in Complex with Acarbose, PDB code: 3bc9:

Sodium binding site 1 out of 1 in the Alpha-Amylase B in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Alpha-Amylase B in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:11.0 occ:1.00 OD2 A:ASP319 2.3 12.0 1.0 OD2 A:ASP313 2.3 12.0 1.0 OD2 A:ASP283 2.3 10.0 1.0 O A:VAL320 2.4 11.0 1.0 OD2 A:ASP305 2.6 10.9 1.0 CG A:ASP313 3.0 11.3 1.0 OD1 A:ASP313 3.1 11.8 1.0 CG A:ASP305 3.2 10.8 1.0 CG A:ASP283 3.3 10.6 1.0 CG A:ASP319 3.4 13.5 1.0 C A:VAL320 3.4 10.7 1.0 O A:HOH1023 3.5 13.1 1.0 O A:HOH1029 3.8 12.5 1.0 CB A:ASP283 3.8 11.4 1.0 CA A:ASP321 3.9 11.3 1.0 OD1 A:ASP305 3.9 11.2 1.0 CB A:ASP305 4.0 12.6 1.0 N A:ASP321 4.1 10.9 1.0 OD1 A:ASP319 4.2 11.8 1.0 CA A:CA702 4.3 10.6 1.0 N A:ASP305 4.3 10.9 1.0 O A:ASP319 4.4 11.0 1.0 N A:TYR322 4.4 11.9 1.0 CB A:ASP313 4.4 9.1 1.0 OD1 A:ASP283 4.5 12.2 1.0 C A:ASP319 4.5 10.6 1.0 CA A:CA701 4.5 11.4 1.0 N A:VAL320 4.5 10.7 1.0 CB A:ASP319 4.5 12.2 1.0 CA A:VAL320 4.6 10.6 1.0 CE3 A:TRP304 4.7 12.8 1.0 C A:ASP321 4.7 11.7 1.0 CA A:ASP305 4.8 10.9 1.0 N A:ASP283 4.9 11.4 1.0 CB A:ASP321 4.9 12.6 1.0 CA A:ASP283 5.0 12.6 1.0 OD1 A:ASP321 5.0 11.6 1.0

T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne. Crystal Structure of the Polyextremophilic Alpha-Amylase Amyb From Halothermothrix Orenii: Details of A Productive Enzyme-Substrate Complex and An N Domain with A Role in Binding Raw Starch J.Mol.Biol. V. 378 850 2008.
ISSN: ISSN 0022-2836
PubMed: 18387632
DOI: 10.1016/J.JMB.2008.02.041