Sodium in PDB 7d2a: CBM32 of Alyq in Complex with 4,5-Unsaturated Mannuronic Acid

The structure of CBM32 of Alyq in Complex with 4,5-Unsaturated Mannuronic Acid, PDB code: 7d2a was solved by A.H.Teh, P.F.Sim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.34 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.608, 55.773, 58.427, 90, 90, 90
R / Rfree (%)	16.8 / 19.5

The structure of CBM32 of Alyq in Complex with 4,5-Unsaturated Mannuronic Acid also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the CBM32 of Alyq in Complex with 4,5-Unsaturated Mannuronic Acid (pdb code 7d2a). 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 CBM32 of Alyq in Complex with 4,5-Unsaturated Mannuronic Acid, PDB code: 7d2a:

Sodium binding site 1 out of 1 in the CBM32 of Alyq in Complex with 4,5-Unsaturated Mannuronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CBM32 of Alyq in Complex with 4,5-Unsaturated Mannuronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:17.1 occ:1.00 O A:HOH604 3.0 26.7 1.0 O A:HOH660 3.1 28.0 1.0 N A:ASN219 3.2 14.6 1.0 CA A:ALA218 3.6 12.4 1.0 C A:ALA218 3.9 13.5 1.0 CZ3 A:TRP303 4.0 15.4 1.0 C A:HIS199 4.0 13.8 1.0 CB A:ASN219 4.1 15.7 1.0 CH2 A:TRP303 4.1 15.5 1.0 CB A:ASP200 4.1 13.9 1.0 N A:ASP200 4.1 13.8 1.0 O A:HIS199 4.2 16.1 1.0 CA A:ASN219 4.2 14.9 1.0 CB A:ALA218 4.2 13.9 1.0 CA A:ASP200 4.4 14.3 1.0 CA A:HIS199 4.4 12.4 1.0 O A:SER217 4.4 11.8 1.0 CB A:ALA198 4.5 16.4 1.0 N A:HIS199 4.5 13.1 1.0 NE2 A:GLN223 4.5 14.0 0.5 O A:ASN219 4.6 16.8 1.0 N A:ALA218 4.7 12.1 1.0 C A:ASN219 4.9 15.3 1.0 CE3 A:TRP303 5.0 14.8 1.0 C A:SER217 5.0 12.0 1.0 C A:ALA198 5.0 12.2 1.0

A.H.Teh, P.F.Sim, T.Hisano. Structural Basis For Binding Uronic Acids By Family 32 Carbohydrate-Binding Modules. Biochem.Biophys.Res.Commun. V. 533 257 2020.
ISSN: ESSN 1090-2104
PubMed: 33010888
DOI: 10.1016/J.BBRC.2020.09.064