Sodium in PDB 6k96: Crystal Structure of ARI2

The structure of Crystal Structure of ARI2, PDB code: 6k96 was solved by A.Miyanaga, T.Tsunoda, F.Kudo, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.18 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.180, 101.180, 389.662, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 28

The binding sites of Sodium atom in the Crystal Structure of ARI2 (pdb code 6k96). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of ARI2, PDB code: 6k96:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of ARI2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of ARI2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.9 occ:1.00 O2N A:NAD400 2.3 25.5 1.0 O7N A:NAD400 2.4 26.2 1.0 OD1 A:ASN15 2.4 24.0 1.0 OG A:SER293 2.6 26.8 1.0 PN A:NAD400 3.4 25.5 1.0 CG A:ASN15 3.5 23.4 1.0 O5D A:NAD400 3.6 25.6 1.0 C7N A:NAD400 3.6 26.8 1.0 CB A:SER293 3.7 27.0 1.0 OD2 A:ASP221 3.8 34.6 1.0 CA A:SER293 4.0 26.9 1.0 ND2 A:ASN15 4.1 23.4 1.0 O1N A:NAD400 4.2 25.8 1.0 C2N A:NAD400 4.2 27.2 1.0 OD1 A:ASP264 4.2 27.1 1.0 N A:ASN15 4.3 23.2 1.0 CB A:ASN14 4.3 22.6 1.0 O A:HOH515 4.3 22.2 1.0 ND2 A:ASN219 4.4 27.8 1.0 N A:SER293 4.4 26.7 1.0 CB A:ASP221 4.4 32.8 1.0 N7N A:NAD400 4.4 27.6 1.0 CG A:ASP221 4.4 33.4 1.0 OD2 A:ASP292 4.5 30.9 1.0 C3N A:NAD400 4.5 27.0 1.0 O3 A:NAD400 4.7 25.4 1.0 CB A:ASN15 4.7 23.6 1.0 CB A:ALA296 4.7 25.8 1.0 CA A:ASN15 4.7 23.5 1.0 C5D A:NAD400 4.8 26.1 1.0 C A:ASP292 4.8 26.9 1.0 O4D A:NAD400 4.9 26.5 1.0 O A:ASP292 4.9 26.2 1.0 C A:ASN14 5.0 23.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of ARI2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of ARI2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:27.1 occ:1.00 O2N B:NAD400 2.3 27.2 1.0 O7N B:NAD400 2.3 26.1 1.0 OD1 B:ASN15 2.4 27.2 1.0 OG B:SER293 2.5 30.1 1.0 PN B:NAD400 3.3 27.1 1.0 C7N B:NAD400 3.5 26.4 1.0 CG B:ASN15 3.6 27.9 1.0 O5D B:NAD400 3.6 27.4 1.0 CB B:SER293 3.7 31.4 1.0 CA B:SER293 3.9 31.9 1.0 O1N B:NAD400 4.0 27.1 1.0 O B:HOH507 4.0 19.9 1.0 OD1 B:ASP264 4.0 27.1 1.0 C2N B:NAD400 4.1 27.0 1.0 ND2 B:ASN15 4.2 26.9 1.0 OD2 B:ASP292 4.2 36.8 1.0 CB B:ASN14 4.2 32.0 1.0 N B:SER293 4.3 31.3 1.0 ND2 B:ASN219 4.3 26.9 1.0 C3N B:NAD400 4.3 26.3 1.0 CB B:ASP221 4.4 32.5 1.0 N B:ASN15 4.4 30.7 1.0 N7N B:NAD400 4.5 26.1 1.0 OD2 B:ASP221 4.6 32.7 1.0 O3 B:NAD400 4.6 28.7 1.0 C B:ASP292 4.6 31.5 1.0 CB B:ASN15 4.7 28.7 1.0 CG B:ASP221 4.8 33.0 1.0 CB B:ALA296 4.8 30.9 1.0 O B:ASP292 4.8 31.8 1.0 CG B:ASP292 4.8 34.7 1.0 CA B:ASN15 4.9 29.7 1.0 C B:ASN14 4.9 31.8 1.0

F.Kudo, T.Tsunoda, K.Yamaguchi, A.Miyanaga, T.Eguchi. Stereochemistry in the Reaction of Themyo-Inositol Phosphate Synthase Ortholog ARI2 During Aristeromycin Biosynthesis. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31825604
DOI: 10.1021/ACS.BIOCHEM.9B00981