Sodium in PDB 2die: Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378

All present enzymatic activity of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378:
3.2.1.1;

The structure of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378, PDB code: 2die was solved by T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, S.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.577, 41.467, 74.855, 90.00, 92.24, 90.00
R / Rfree (%)	17.7 / 23.1

The structure of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 (pdb code 2die). 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 Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378, PDB code: 2die:

Sodium binding site 1 out of 1 in the Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na781 b:14.5 occ:1.00 OD1 A:ASP205 2.3 10.9 1.0 OD2 A:ASP163 2.3 4.5 1.0 OD2 A:ASP199 2.5 8.4 1.0 O A:ILE206 2.6 6.0 1.0 OD1 A:ASP188 2.7 9.4 1.0 OD1 A:ASP199 2.8 9.2 1.0 CG A:ASP199 3.0 9.9 1.0 CG A:ASP188 3.2 8.9 1.0 CG A:ASP163 3.3 8.0 1.0 CG A:ASP205 3.4 9.5 1.0 O A:HOH707 3.5 5.0 1.0 C A:ILE206 3.6 6.6 1.0 CB A:ASP163 3.6 6.7 1.0 OD2 A:ASP188 3.7 11.0 1.0 O A:HOH611 3.9 3.2 1.0 CA A:ASP207 3.9 7.1 1.0 OD2 A:ASP205 4.0 12.1 1.0 CB A:ASP188 4.1 9.7 1.0 CA A:CA779 4.1 6.8 1.0 N A:ASP207 4.1 8.0 1.0 N A:ASP188 4.3 8.3 1.0 N A:MET208 4.3 9.3 1.0 OD1 A:ASP163 4.4 8.4 1.0 CA A:CA778 4.4 10.7 1.0 CB A:ASP199 4.4 8.6 1.0 CB A:ASP205 4.5 8.1 1.0 N A:ILE206 4.5 8.2 1.0 C A:ASP205 4.6 8.9 1.0 CA A:ILE206 4.7 6.5 1.0 C A:ASP207 4.7 7.5 1.0 CE3 A:TRP187 4.8 7.7 1.0 O A:ASP205 4.8 9.6 1.0 CA A:ASP188 4.8 11.5 1.0 CA A:ASP163 4.9 7.4 1.0 N A:ASP163 5.0 7.7 1.0

T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, S.Ito. Ancestral Sequence Evolutionary Trace and Crystal Structure Analyses of Alkaline Alpha-Amylase From Bacillus Sp. Ksm-1378 to Clarify the Alkaline Adaptation Process of Proteins Proteins V. 66 600 2007.
ISSN: ISSN 0887-3585
PubMed: 17154418
DOI: 10.1002/PROT.21255