Sodium in PDB 3bh4: High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase

All present enzymatic activity of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase:
3.2.1.1;

The structure of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase, PDB code: 3bh4 was solved by J.Alikhajeh, K.Khajeh, B.Ranjbar, H.Naderi-Manesh, Y.H.Lin, M.Y.Liu, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.760, 148.676, 76.197, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 21.9

The structure of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Sodium atom in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase (pdb code 3bh4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase, PDB code: 3bh4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na489 b:12.6 occ:1.00 OD2 A:ASP160 2.4 15.3 1.0 OD2 A:ASP201 2.4 15.6 1.0 OD2 A:ASP195 2.5 13.9 1.0 O A:VAL202 2.5 13.0 1.0 OD2 A:ASP184 2.5 12.8 1.0 OD1 A:ASP195 2.9 14.4 1.0 CG A:ASP195 3.0 14.7 1.0 CG A:ASP184 3.2 14.9 1.0 CG A:ASP160 3.4 14.6 1.0 C A:VAL202 3.5 12.7 1.0 CG A:ASP201 3.6 13.9 1.0 O A:HOH506 3.6 16.5 1.0 O A:HOH495 3.7 13.0 1.0 CB A:ASP160 3.7 13.7 1.0 CA A:ASP203 3.9 13.8 1.0 OD1 A:ASP184 3.9 15.5 1.0 CA A:CA486 4.0 11.3 1.0 CB A:ASP184 4.0 14.0 1.0 N A:ASP203 4.1 13.3 1.0 OD1 A:ASP201 4.2 13.8 1.0 N A:ASP184 4.3 14.2 1.0 N A:TYR204 4.3 13.5 1.0 CB A:ASP195 4.5 14.7 1.0 CA A:CA488 4.6 13.6 1.0 O A:ASP201 4.6 13.1 1.0 OD1 A:ASP160 4.6 16.3 1.0 C A:ASP201 4.6 13.1 1.0 CB A:ASP201 4.6 13.3 1.0 N A:VAL202 4.6 12.4 1.0 C A:ASP203 4.7 13.3 1.0 CA A:VAL202 4.7 12.2 1.0 CA A:ASP184 4.8 14.9 1.0 CE3 A:TRP183 4.9 15.0 1.0 CB A:ASP203 4.9 13.3 1.0 N A:ASP160 4.9 13.9 1.0 CA A:ASP160 5.0 13.4 1.0

Sodium binding site 2 out of 2 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na488 b:10.9 occ:1.00 OD2 B:ASP160 2.4 12.0 1.0 OD2 B:ASP201 2.5 12.5 1.0 OD2 B:ASP195 2.5 11.5 1.0 O B:VAL202 2.5 11.8 1.0 OD2 B:ASP184 2.5 11.5 1.0 OD1 B:ASP195 2.8 11.4 1.0 CG B:ASP195 3.0 12.2 1.0 CG B:ASP184 3.2 11.5 1.0 CG B:ASP160 3.4 12.3 1.0 C B:VAL202 3.6 10.7 1.0 CG B:ASP201 3.6 11.8 1.0 O B:HOH492 3.6 14.9 1.0 O B:HOH493 3.6 11.2 1.0 CB B:ASP160 3.7 12.2 1.0 OD1 B:ASP184 3.8 13.1 1.0 CA B:ASP203 3.9 11.4 1.0 CA B:CA1 4.0 10.4 1.0 CB B:ASP184 4.0 11.5 1.0 N B:ASP203 4.1 10.5 1.0 OD1 B:ASP201 4.2 12.1 1.0 N B:TYR204 4.2 10.2 1.0 N B:ASP184 4.3 12.0 1.0 CB B:ASP195 4.5 10.9 1.0 OD1 B:ASP160 4.5 12.9 1.0 CA B:CA486 4.5 11.2 1.0 O B:ASP201 4.6 11.1 1.0 C B:ASP201 4.6 10.8 1.0 C B:ASP203 4.6 11.4 1.0 CB B:ASP201 4.6 12.2 1.0 N B:VAL202 4.7 10.9 1.0 CA B:VAL202 4.7 10.7 1.0 CA B:ASP184 4.8 11.9 1.0 CA B:ASP160 4.9 11.7 1.0 CB B:ASP203 4.9 12.5 1.0 N B:ASP160 4.9 11.5 1.0 OD1 B:ASP203 5.0 12.3 1.0

J.Alikhajeh, K.Khajeh, B.Ranjbar, H.Naderi-Manesh, Y.H.Lin, E.Liu, H.H.Guan, Y.C.Hsieh, P.Chuankhayan, Y.C.Huang, J.Jeyaraman, M.Y.Liu, C.J.Chen. Structure of Bacillus Amyloliquefaciens Alpha-Amylase at High Resolution: Implications For Thermal Stability. Acta Crystallogr.,Sect.F V. 66 121 2010.
ISSN: ESSN 1744-3091
PubMed: 20124706
DOI: 10.1107/S1744309109051938