Sodium in PDB 6ilr: Structure of Arabidopsis Thaliana Ribokinase in Unligand Form

All present enzymatic activity of Structure of Arabidopsis Thaliana Ribokinase in Unligand Form:
2.7.1.15;

The structure of Structure of Arabidopsis Thaliana Ribokinase in Unligand Form, PDB code: 6ilr 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)	27.47 / 1.97
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.040, 99.040, 165.458, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.1

The binding sites of Sodium atom in the Structure of Arabidopsis Thaliana Ribokinase in Unligand Form (pdb code 6ilr). 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 in Unligand Form, PDB code: 6ilr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Arabidopsis Thaliana Ribokinase in Unligand Form


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 in Unligand Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:43.5 occ:1.00 O A:VAL358 2.5 58.6 1.0 O A:CYS355 2.6 51.3 1.0 O A:ASP319 2.6 55.2 1.0 O A:GLY360 2.7 64.6 1.0 OG A:SER364 3.0 57.7 1.0 CB A:SER364 3.3 58.6 1.0 O A:THR321 3.4 52.5 1.0 C A:CYS355 3.6 45.1 1.0 C A:ASP319 3.6 62.9 1.0 C A:VAL358 3.8 62.8 1.0 SG A:CYS355 3.8 59.4 1.0 CB A:ASP319 3.9 61.3 1.0 C A:GLY360 3.9 59.0 1.0 CA A:VAL356 4.1 52.3 1.0 OD2 A:ASP319 4.1 62.5 1.0 CG A:ASP319 4.1 61.3 1.0 N A:GLY360 4.3 55.1 1.0 N A:VAL356 4.3 49.0 1.0 OG1 A:THR321 4.3 60.7 1.0 CA A:ASP319 4.3 58.3 1.0 N A:THR321 4.4 48.7 1.0 C A:THR321 4.5 51.6 1.0 C A:LYS359 4.5 57.8 1.0 N A:VAL358 4.5 62.9 1.0 C A:VAL356 4.6 54.3 1.0 N A:THR320 4.6 54.2 1.0 CA A:LYS359 4.6 56.1 1.0 CA A:VAL358 4.7 52.7 1.0 N A:LYS359 4.7 65.4 1.0 CA A:CYS355 4.7 43.3 1.0 CA A:GLY360 4.7 60.6 1.0 C A:THR320 4.7 53.1 1.0 CA A:THR320 4.8 59.1 1.0 OD1 A:ASP319 4.8 62.5 1.0 CA A:SER364 4.9 57.4 1.0 N A:ALA361 4.9 54.5 1.0 CA A:ALA361 4.9 56.0 1.0 N A:ASP319 4.9 64.6 1.0 CB A:CYS355 4.9 45.6 1.0 CA A:THR321 4.9 62.4 1.0

Sodium binding site 2 out of 2 in the Structure of Arabidopsis Thaliana Ribokinase in Unligand Form


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 in Unligand Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:38.7 occ:1.00 O B:ASP319 2.6 40.8 1.0 O B:CYS355 2.7 37.0 1.0 O B:VAL358 2.8 42.3 1.0 OG B:SER364 2.9 46.3 1.0 O B:THR321 3.1 38.8 1.0 O B:GLY360 3.1 52.1 1.0 CB B:SER364 3.4 43.9 1.0 SG B:CYS355 3.5 52.2 1.0 C B:CYS355 3.7 29.9 1.0 C B:ASP319 3.7 42.7 1.0 C B:VAL358 4.0 49.2 1.0 C B:GLY360 4.0 46.8 1.0 CB B:ASP319 4.1 43.4 1.0 OD2 B:ASP319 4.1 56.2 1.0 CA B:VAL356 4.2 34.7 1.0 CG B:ASP319 4.2 39.3 1.0 C B:THR321 4.2 37.5 1.0 N B:THR321 4.3 35.6 1.0 N B:VAL356 4.3 32.3 1.0 N B:GLY360 4.4 42.2 1.0 CA B:ASP319 4.5 43.8 1.0 C B:THR320 4.6 39.4 1.0 CA B:CYS355 4.6 31.1 1.0 C B:VAL356 4.6 45.7 1.0 C B:LYS359 4.7 37.3 1.0 N B:THR320 4.7 40.2 1.0 CA B:ALA361 4.7 42.4 1.0 N B:VAL358 4.7 39.6 1.0 CA B:THR321 4.7 38.5 1.0 N B:ALA361 4.7 40.3 1.0 CB B:CYS355 4.8 29.8 1.0 CA B:THR320 4.8 42.6 1.0 OD1 B:ASP319 4.9 51.3 1.0 CA B:GLY360 4.9 40.2 1.0 CA B:LYS359 4.9 44.4 1.0 N B:LYS359 4.9 48.6 1.0 CA B:VAL358 4.9 44.0 1.0 O B:ALA361 4.9 40.1 1.0 CA B:SER364 5.0 41.0 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