Sodium in PDB 5h9w: Crystal Structure of Regnase Pin Domain, Form II

The structure of Crystal Structure of Regnase Pin Domain, Form II, PDB code: 5h9w was solved by M.Yokogawa, T.Tsushima, W.Adachi, N.N.Noda, F.Inagaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.94 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.333, 113.333, 78.373, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 23.1

The binding sites of Sodium atom in the Crystal Structure of Regnase Pin Domain, Form II (pdb code 5h9w). 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 Regnase Pin Domain, Form II, PDB code: 5h9w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Regnase Pin Domain, Form II


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 Regnase Pin Domain, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:61.5 occ:1.00 O A:HIS149 2.0 54.1 1.0 O A:ASN151 2.2 45.8 1.0 O A:VAL154 2.3 58.0 1.0 O A:MET147 2.5 52.5 1.0 O A:ALA146 2.6 58.2 1.0 C A:MET147 3.0 48.8 1.0 C A:HIS149 3.2 51.7 1.0 C A:ASN151 3.4 54.0 1.0 CA A:MET147 3.4 47.7 1.0 C A:VAL154 3.4 57.3 1.0 C A:ALA146 3.7 51.9 1.0 N A:HIS149 3.8 50.9 1.0 CB A:SER156 3.8 54.1 1.0 N A:SER148 3.9 49.9 1.0 C A:SER148 3.9 51.6 1.0 N A:SER156 4.0 49.1 1.0 CA A:LYS152 4.0 54.6 1.0 N A:MET147 4.0 47.2 1.0 N A:VAL154 4.0 52.5 1.0 C A:GLY150 4.1 56.3 1.0 CA A:HIS149 4.1 51.2 1.0 N A:LYS152 4.1 54.0 1.0 N A:GLY150 4.2 55.7 1.0 O A:GLY150 4.2 54.7 1.0 CA A:VAL154 4.2 55.1 1.0 N A:ASN151 4.2 59.1 1.0 O A:SER148 4.3 50.3 1.0 C A:LYS152 4.3 50.8 1.0 CA A:GLY150 4.4 56.2 1.0 CA A:ASN151 4.4 57.4 1.0 CA A:SER148 4.4 51.6 1.0 CB A:VAL154 4.4 56.0 1.0 N A:PHE155 4.5 58.7 1.0 CA A:SER156 4.6 53.1 1.0 CB A:MET147 4.7 43.7 1.0 CA A:PHE155 4.7 55.7 1.0 O A:LYS152 4.7 46.3 1.0 N A:GLU153 4.7 52.9 1.0 C A:PHE155 4.7 54.1 1.0 CB A:HIS149 4.8 53.1 1.0 OG A:SER156 5.0 58.4 1.0 CA A:ALA146 5.0 51.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Regnase Pin Domain, Form II


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 Regnase Pin Domain, Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:61.7 occ:1.00 O B:HIS149 2.1 54.6 1.0 O B:VAL154 2.2 49.3 1.0 O B:ASN151 2.2 55.9 1.0 O B:MET147 2.4 50.0 1.0 O B:ALA146 2.6 51.9 1.0 C B:MET147 2.9 49.2 1.0 C B:HIS149 3.3 51.4 1.0 CA B:MET147 3.3 46.5 1.0 C B:ASN151 3.4 64.9 1.0 C B:VAL154 3.4 49.4 1.0 C B:ALA146 3.6 46.1 1.0 N B:HIS149 3.8 53.5 1.0 N B:SER148 3.9 55.3 1.0 CB B:SER156 3.9 52.3 1.0 C B:SER148 3.9 54.5 1.0 N B:SER156 4.0 49.5 1.0 N B:MET147 4.0 46.5 1.0 C B:GLY150 4.0 55.6 1.0 CA B:LYS152 4.1 61.3 1.0 N B:VAL154 4.1 51.7 1.0 N B:LYS152 4.1 62.5 1.0 CA B:HIS149 4.2 52.5 1.0 N B:ASN151 4.2 57.7 1.0 CA B:VAL154 4.2 49.6 1.0 O B:GLY150 4.2 67.3 1.0 N B:GLY150 4.2 53.3 1.0 O B:SER148 4.3 60.2 1.0 C B:LYS152 4.3 57.1 1.0 CA B:ASN151 4.4 63.1 1.0 CA B:GLY150 4.4 55.7 1.0 CA B:SER148 4.4 54.4 1.0 CB B:VAL154 4.5 49.3 1.0 N B:PHE155 4.5 46.9 1.0 CB B:MET147 4.6 46.1 1.0 CA B:SER156 4.6 49.8 1.0 CA B:PHE155 4.6 48.6 1.0 C B:PHE155 4.7 48.7 1.0 O B:LYS152 4.7 53.0 1.0 N B:GLU153 4.8 59.6 1.0 CB B:HIS149 4.9 52.0 1.0 CA B:ALA146 5.0 47.1 1.0 CE B:MET147 5.0 48.4 1.0

M.Yokogawa, T.Tsushima, N.N.Noda, H.Kumeta, Y.Enokizono, K.Yamashita, D.M.Standley, O.Takeuchi, S.Akira, F.Inagaki. Structural Basis For the Regulation of Enzymatic Activity of Regnase-1 By Domain-Domain Interactions Sci Rep V. 6 22324 2016.
ISSN: ESSN 2045-2322
PubMed: 26927947
DOI: 10.1038/SREP22324