Sodium in PDB 6fdm: Human RIO2 Kinase Structure

All present enzymatic activity of Human RIO2 Kinase Structure:
2.7.11.1;

The structure of Human RIO2 Kinase Structure, PDB code: 6fdm was solved by S.Fribourg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.64 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.920, 98.327, 117.069, 90.00, 95.22, 90.00
R / Rfree (%)	20.2 / 23.7

The binding sites of Sodium atom in the Human RIO2 Kinase Structure (pdb code 6fdm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human RIO2 Kinase Structure, PDB code: 6fdm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human RIO2 Kinase Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human RIO2 Kinase Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:73.3 occ:1.00 OE1 A:GLU170 2.3 64.3 1.0 OH A:TYR305 3.0 65.7 1.0 NH1 A:ARG171 3.1 51.8 1.0 OG A:SER301 3.2 58.3 1.0 CB A:SER301 3.2 52.0 1.0 CD A:GLU170 3.6 78.4 1.0 CZ A:TYR305 3.7 62.2 1.0 CE2 A:TYR305 3.7 50.2 1.0 CZ A:ARG171 4.0 64.6 1.0 NH2 A:ARG171 4.1 58.4 1.0 CA A:ALA167 4.1 41.5 1.0 CB A:GLU170 4.1 51.3 1.0 O A:HOH645 4.3 74.8 1.0 OE2 A:GLU170 4.4 72.9 1.0 CG A:GLU170 4.4 58.6 1.0 O A:ALA167 4.5 45.4 1.0 CA A:SER301 4.6 48.4 1.0 CB A:ALA167 4.6 41.8 1.0 C A:ALA167 4.9 45.4 1.0 CE1 A:TYR305 5.0 54.9 1.0 N A:ALA167 5.0 41.9 1.0 CD2 A:TYR305 5.0 47.7 1.0

Sodium binding site 2 out of 2 in the Human RIO2 Kinase Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human RIO2 Kinase Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:82.1 occ:1.00 OE1 C:GLU170 2.2 64.4 1.0 OH C:TYR305 2.8 63.4 1.0 NH1 C:ARG171 3.0 41.4 1.0 CB C:SER301 3.2 46.4 1.0 OG C:SER301 3.3 51.2 1.0 CD C:GLU170 3.5 80.0 1.0 CZ C:TYR305 3.6 58.7 1.0 CE2 C:TYR305 3.6 46.4 1.0 O C:HOH621 3.7 66.5 1.0 CZ C:ARG171 4.0 62.5 1.0 CA C:ALA167 4.1 40.1 1.0 NH2 C:ARG171 4.1 55.0 1.0 CB C:GLU170 4.1 46.7 1.0 OE2 C:GLU170 4.3 79.3 1.0 CG C:GLU170 4.4 57.0 1.0 O C:ALA167 4.5 45.2 1.0 CB C:ALA167 4.6 40.2 1.0 CA C:SER301 4.6 44.3 1.0 O C:HOH640 4.6 81.5 1.0 CE1 C:TYR305 4.8 51.0 1.0 C C:ALA167 4.8 43.7 1.0 CD2 C:TYR305 4.9 44.1 1.0 N C:ALA167 4.9 40.0 1.0 O C:LYS166 4.9 43.1 1.0 O C:HOH550 5.0 64.9 1.0

F.Maurice, N.Perebaskine, S.Thore, S.Fribourg. In Vitro Dimerization of Human RIO2 Kinase. Rna Biol. V. 16 1633 2019.
ISSN: ESSN 1555-8584
PubMed: 31390939
DOI: 10.1080/15476286.2019.1653679