Sodium in PDB 8jjm: X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63

The structure of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63, PDB code: 8jjm was solved by Y.F.Sun, W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.79 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.785, 55.495, 106.755, 90, 91.29, 90
R / Rfree (%)	16.1 / 19.2

The structure of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 (pdb code 8jjm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63, PDB code: 8jjm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:12.4 occ:1.00 OD2 A:ASP199 2.3 14.2 1.0 OD2 A:ASP205 2.3 15.6 1.0 OD2 A:ASP164 2.3 11.7 1.0 O A:LEU206 2.4 14.0 1.0 OD2 A:ASP188 2.4 16.0 1.0 OD1 A:ASP199 2.8 12.8 1.0 CG A:ASP199 2.9 14.0 1.0 CG A:ASP188 3.2 14.9 1.0 CG A:ASP164 3.3 14.5 1.0 CG A:ASP205 3.5 11.3 1.0 C A:LEU206 3.5 13.8 1.0 O A:HOH747 3.6 16.4 1.0 O A:HOH814 3.6 13.8 1.0 CB A:ASP164 3.6 13.0 1.0 OD1 A:ASP188 3.8 15.5 1.0 CA A:ASP207 4.0 13.6 1.0 CB A:ASP188 4.0 14.2 1.0 CA A:CA503 4.0 13.5 1.0 OD1 A:ASP205 4.1 12.4 1.0 N A:ASP207 4.2 13.9 1.0 N A:ASP188 4.2 13.8 1.0 N A:MET208 4.3 12.6 1.0 CB A:ASP199 4.4 12.2 1.0 CA A:CA502 4.4 14.5 1.0 OD1 A:ASP164 4.5 15.4 1.0 CB A:ASP205 4.6 12.4 1.0 O A:ASP205 4.6 13.7 1.0 N A:LEU206 4.6 11.4 1.0 C A:ASP205 4.7 11.3 1.0 CA A:LEU206 4.7 11.7 1.0 C A:ASP207 4.7 15.4 1.0 CA A:ASP188 4.8 15.6 1.0 CA A:ASP164 4.9 11.8 1.0 CE3 A:TRP187 5.0 13.7 1.0 N A:ASP164 5.0 13.4 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:13.7 occ:1.00 OD2 B:ASP199 2.3 16.2 1.0 OD2 B:ASP164 2.4 14.5 1.0 O B:LEU206 2.4 11.4 1.0 OD2 B:ASP205 2.4 17.2 1.0 OD2 B:ASP188 2.4 14.4 1.0 OD1 B:ASP199 2.9 14.1 1.0 CG B:ASP199 3.0 15.8 1.0 CG B:ASP188 3.1 17.4 1.0 CG B:ASP164 3.3 17.5 1.0 C B:LEU206 3.5 12.7 1.0 O B:HOH848 3.5 14.2 1.0 CG B:ASP205 3.6 16.8 1.0 O B:HOH690 3.6 15.7 1.0 CB B:ASP164 3.6 13.6 1.0 OD1 B:ASP188 3.7 14.3 1.0 CA B:ASP207 3.8 13.8 1.0 CB B:ASP188 4.0 14.0 1.0 N B:ASP207 4.1 15.2 1.0 CA B:CA502 4.1 13.0 1.0 N B:MET208 4.2 15.4 1.0 OD1 B:ASP205 4.2 15.6 1.0 N B:ASP188 4.3 14.4 1.0 CA B:CA503 4.4 14.7 1.0 OD1 B:ASP164 4.4 16.1 1.0 CB B:ASP199 4.5 13.8 1.0 C B:ASP207 4.6 15.8 1.0 O B:ASP205 4.6 13.6 1.0 N B:LEU206 4.6 12.7 1.0 C B:ASP205 4.6 15.6 1.0 CB B:ASP205 4.7 12.9 1.0 CA B:LEU206 4.7 14.9 1.0 CA B:ASP188 4.8 13.8 1.0 CA B:ASP164 4.9 11.9 1.0 CB B:ASP207 4.9 14.6 1.0 OD1 B:ASP207 4.9 14.3 1.0 N B:ASP164 4.9 12.8 1.0

Y.Sun, G.Liu, G.Liu, H.Tang, C.Sun, W.Zhang, L.Chen. The Novel Amylase Function of the Carboxyl Terminal Domain of AMY63. Biochem.Biophys.Res.Commun. V. 671 10 2023.
ISSN: ESSN 1090-2104
PubMed: 37290279
DOI: 10.1016/J.BBRC.2023.05.071