Sodium in PDB 6ilt: Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion

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

The structure of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion, PDB code: 6ilt 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)	32.34 / 2.20
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.445, 99.445, 164.952, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.8

The structure of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion (pdb code 6ilt). 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 Atp and Magnesium Ion, PDB code: 6ilt:
Jump to Sodium binding site number: 1; 2;

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


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 Atp and Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:35.2 occ:1.00 O A:CYS355 2.6 54.7 1.0 O A:GLY360 2.6 62.1 1.0 OG A:SER364 2.7 55.6 1.0 O A:VAL358 2.8 65.6 1.0 O A:ASP319 2.9 60.4 1.0 O A:THR321 2.9 52.6 1.0 CB A:SER364 3.0 67.0 1.0 SG A:CYS355 3.4 58.5 1.0 C A:CYS355 3.6 56.6 1.0 C A:GLY360 3.8 62.7 1.0 C A:ASP319 3.9 65.9 1.0 C A:VAL358 4.0 67.7 1.0 CB A:ASP319 4.1 59.5 1.0 C A:THR321 4.1 53.8 1.0 CG2 A:THR321 4.1 55.8 1.0 CA A:VAL356 4.3 65.6 1.0 N A:GLY360 4.3 57.3 1.0 CG A:ASP319 4.3 69.4 1.0 N A:VAL356 4.4 48.3 1.0 C A:LYS359 4.5 58.6 1.0 N A:THR321 4.5 54.4 1.0 CA A:CYS355 4.5 47.6 1.0 CA A:SER364 4.5 56.5 1.0 OD2 A:ASP319 4.6 65.6 1.0 CA A:ALA361 4.6 56.8 1.0 CA A:ASP319 4.6 70.7 1.0 N A:ALA361 4.7 61.8 1.0 CB A:CYS355 4.7 50.1 1.0 CA A:GLY360 4.7 53.1 1.0 CA A:LYS359 4.7 65.4 1.0 N A:VAL358 4.7 69.5 1.0 C A:THR320 4.7 57.4 1.0 CA A:THR321 4.8 51.5 1.0 N A:LYS359 4.8 60.3 1.0 OD1 A:ASP319 4.8 66.5 1.0 C A:VAL356 4.8 65.1 1.0 CA A:VAL358 4.8 59.1 1.0 O A:ALA361 4.9 53.7 1.0 N A:THR320 4.9 56.9 1.0 O A:LYS359 4.9 70.5 1.0

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


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 Atp and Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:33.5 occ:1.00 O B:ASP319 2.5 46.4 1.0 O B:GLY360 2.6 53.0 1.0 O B:CYS355 2.7 41.7 1.0 O B:VAL358 2.8 40.7 1.0 OG B:SER364 2.9 55.5 1.0 O B:THR321 2.9 46.1 1.0 CB B:SER364 3.4 60.0 1.0 C B:CYS355 3.6 34.0 1.0 SG B:CYS355 3.6 43.6 1.0 C B:ASP319 3.7 42.5 1.0 C B:GLY360 3.8 56.3 1.0 C B:THR321 4.0 44.5 1.0 C B:VAL358 4.0 50.9 1.0 OD2 B:ASP319 4.1 57.5 1.0 CG B:ASP319 4.1 53.1 1.0 CB B:ASP319 4.2 44.0 1.0 N B:THR321 4.2 35.9 1.0 CA B:VAL356 4.2 39.8 1.0 N B:VAL356 4.3 33.6 1.0 N B:GLY360 4.3 49.1 1.0 CA B:CYS355 4.5 36.0 1.0 C B:THR320 4.5 48.9 1.0 CA B:ASP319 4.5 55.3 1.0 CA B:THR321 4.5 41.9 1.0 N B:THR320 4.6 44.6 1.0 CA B:ALA361 4.6 40.6 1.0 C B:LYS359 4.6 45.1 1.0 N B:ALA361 4.6 52.6 1.0 CB B:CYS355 4.6 32.8 1.0 C B:VAL356 4.7 46.4 1.0 CA B:THR320 4.7 53.4 1.0 CA B:GLY360 4.7 43.0 1.0 OD1 B:ASP319 4.8 55.1 1.0 N B:VAL358 4.8 45.9 1.0 CB B:THR321 4.8 51.5 1.0 CA B:LYS359 4.8 55.3 1.0 N B:LYS359 4.9 56.4 1.0 CA B:SER364 4.9 54.9 1.0 O B:ALA361 5.0 54.5 1.0 CA B:VAL358 5.0 39.4 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