Sodium in PDB 6ils: Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp

All present enzymatic activity of Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp:
2.7.1.15;

The structure of Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp, PDB code: 6ils was solved by P.Kang, J.Oh, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.83 / 1.80
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.460, 99.460, 165.740, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.1

The binding sites of Sodium atom in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp (pdb code 6ils). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp, PDB code: 6ils:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:25.2 occ:1.00 O A:CYS355 2.6 32.0 1.0 O A:GLY360 2.6 36.0 1.0 O A:VAL358 2.7 35.2 1.0 O A:ASP319 2.7 34.6 1.0 OG A:SER364 2.9 33.5 1.0 O A:THR321 3.0 30.5 1.0 CB A:SER364 3.2 35.4 1.0 C A:CYS355 3.6 31.8 1.0 SG A:CYS355 3.6 33.3 1.0 C A:ASP319 3.8 37.4 1.0 C A:GLY360 3.9 36.5 1.0 C A:VAL358 3.9 40.0 1.0 CB A:ASP319 4.1 37.6 1.0 C A:THR321 4.2 31.7 1.0 CG A:ASP319 4.2 37.1 1.0 OD2 A:ASP319 4.2 39.6 1.0 CA A:VAL356 4.2 31.9 1.0 N A:THR321 4.3 34.7 1.0 N A:GLY360 4.3 37.3 1.0 N A:VAL356 4.4 31.4 1.0 C A:LYS359 4.5 39.4 1.0 CA A:CYS355 4.5 29.4 1.0 CA A:ASP319 4.5 37.2 1.0 C A:THR320 4.6 36.2 1.0 CA A:THR321 4.7 34.2 1.0 N A:VAL358 4.7 37.0 1.0 CA A:GLY360 4.7 36.7 1.0 C A:VAL356 4.7 36.7 1.0 N A:THR320 4.7 33.8 1.0 CA A:SER364 4.7 35.3 1.0 CB A:CYS355 4.7 31.0 1.0 N A:ALA361 4.8 35.5 1.0 CA A:VAL358 4.8 38.8 1.0 OD1 A:ASP319 4.8 37.4 1.0 CA A:ALA361 4.8 34.6 1.0 N A:LYS359 4.8 39.7 1.0 CA A:LYS359 4.8 40.1 1.0 O A:ALA361 4.8 34.8 1.0 CA A:THR320 4.9 34.8 1.0 CB A:THR321 4.9 31.5 1.0 O A:LYS359 4.9 41.2 1.0

Sodium binding site 2 out of 2 in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Arabidopsis Thaliana Ribokinase Complexed with Ribose and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:24.4 occ:1.00 O B:ASP319 2.6 27.8 1.0 O B:CYS355 2.7 25.1 1.0 O B:VAL358 2.7 32.3 1.0 O B:GLY360 2.9 38.0 1.0 O B:THR321 3.0 24.9 1.0 OG B:SER364 3.0 31.9 1.0 CB B:SER364 3.3 30.8 1.0 SG B:CYS355 3.6 31.7 1.0 C B:CYS355 3.7 23.0 1.0 C B:ASP319 3.7 28.8 1.0 C B:VAL358 4.0 36.4 1.0 C B:GLY360 4.0 35.3 1.0 C B:THR321 4.1 25.5 1.0 CB B:ASP319 4.1 32.8 1.0 OD2 B:ASP319 4.1 40.4 1.0 CG B:ASP319 4.2 33.2 1.0 N B:THR321 4.2 27.8 1.0 N B:GLY360 4.3 35.5 1.0 CA B:VAL356 4.3 24.6 1.0 N B:VAL356 4.5 20.3 1.0 C B:THR320 4.5 26.6 1.0 CA B:ASP319 4.5 33.0 1.0 C B:LYS359 4.6 35.2 1.0 CA B:CYS355 4.6 20.0 1.0 N B:THR320 4.6 31.6 1.0 CA B:THR321 4.6 27.6 1.0 CA B:LYS359 4.7 35.1 1.0 CA B:THR320 4.7 27.5 1.0 N B:VAL358 4.8 31.8 1.0 OD1 B:ASP319 4.8 35.5 1.0 C B:VAL356 4.8 29.3 1.0 CA B:GLY360 4.8 34.1 1.0 CB B:CYS355 4.8 25.5 1.0 N B:LYS359 4.8 38.3 1.0 N B:ALA361 4.8 36.0 1.0 CA B:ALA361 4.8 32.2 1.0 CA B:SER364 4.9 31.1 1.0 CA B:VAL358 4.9 33.9 1.0 CB B:THR321 5.0 30.7 1.0 O B:ALA361 5.0 31.4 1.0

P.A.Kang, J.Oh, H.Lee, C.P.Witte, S.Rhee. Crystal Structure and Mutational Analyses of Ribokinase From Arabidopsis Thaliana. J. Struct. Biol. V. 206 110 2019.
ISSN: ESSN 1095-8657
PubMed: 30822455
DOI: 10.1016/J.JSB.2019.02.007