Sodium in PDB 3bcf: Alpha-Amylase B From Halothermothrix Orenii

All present enzymatic activity of Alpha-Amylase B From Halothermothrix Orenii:
3.2.1.1;

The structure of Alpha-Amylase B From Halothermothrix Orenii, PDB code: 3bcf 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 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	226.620, 77.820, 50.330, 90.00, 99.38, 90.00
R / Rfree (%)	19.1 / 22.9

The structure of Alpha-Amylase B From Halothermothrix Orenii also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Alpha-Amylase B From Halothermothrix Orenii (pdb code 3bcf). 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 From Halothermothrix Orenii, PDB code: 3bcf:

Sodium binding site 1 out of 1 in the Alpha-Amylase B From Halothermothrix Orenii


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 From Halothermothrix Orenii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:29.8 occ:1.00 OD2 A:ASP283 2.3 33.6 1.0 OD2 A:ASP313 2.3 35.4 1.0 OD2 A:ASP319 2.3 32.2 1.0 O A:VAL320 2.3 34.5 1.0 OD2 A:ASP305 2.3 36.5 1.0 OD1 A:ASP313 3.0 31.0 1.0 CG A:ASP313 3.0 35.4 1.0 CG A:ASP305 3.1 38.0 1.0 CG A:ASP283 3.3 35.4 1.0 C A:VAL320 3.4 35.1 1.0 CG A:ASP319 3.5 33.7 1.0 CB A:ASP283 3.7 34.2 1.0 O A:HOH707 3.7 33.3 1.0 CA A:ASP321 3.8 37.1 1.0 OD1 A:ASP305 3.8 39.7 1.0 CB A:ASP305 4.0 38.5 1.0 N A:ASP321 4.0 35.1 1.0 O A:HOH727 4.0 31.9 1.0 N A:ASP305 4.3 35.7 1.0 O A:ASP319 4.3 32.2 1.0 N A:TYR322 4.3 36.2 1.0 OD1 A:ASP319 4.3 28.3 1.0 OD1 A:ASP283 4.4 31.0 1.0 CA A:CA701 4.4 35.0 1.0 CA A:CA702 4.4 30.0 1.0 CB A:ASP313 4.5 32.8 1.0 C A:ASP319 4.5 33.8 1.0 CB A:ASP319 4.5 33.4 1.0 N A:VAL320 4.6 34.2 1.0 CA A:VAL320 4.6 34.6 1.0 C A:ASP321 4.6 37.2 1.0 CE3 A:TRP304 4.7 35.6 1.0 CA A:ASP305 4.8 37.3 1.0 CB A:ASP321 4.8 39.1 1.0 N A:ASP283 4.9 36.2 1.0 CA A:ASP283 4.9 35.0 1.0 OD1 A:ASP321 4.9 32.9 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