Sodium in PDB 2ek3: Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M)

All present enzymatic activity of Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M):
2.1.1.98;

The structure of Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M), PDB code: 2ek3 was solved by Y.Asada, H.Shimada, M.Taketa, Y.Matsuura, N.Kunishima, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.68 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.714, 104.714, 138.892, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 24.7

The binding sites of Sodium atom in the Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M) (pdb code 2ek3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M), PDB code: 2ek3:

Sodium binding site 1 out of 1 in the Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:43.1 occ:1.00 OH A:TYR117 2.3 29.7 1.0 CZ A:TYR117 3.2 26.3 1.0 CE2 A:TYR117 3.7 26.8 1.0 O A:HOH405 3.9 33.8 1.0 O B:GLY131 3.9 27.3 1.0 CB A:PHE130 4.1 22.2 1.0 O A:ILE127 4.1 29.3 1.0 O A:PHE130 4.2 24.2 1.0 CD1 B:TYR117 4.2 25.7 1.0 CE1 A:TYR117 4.2 25.8 1.0 CE1 B:TYR117 4.3 25.0 1.0 OG B:SER133 4.3 33.9 1.0 O B:HOH348 4.4 22.9 1.0 CB B:PHE130 4.5 22.3 1.0 C A:PHE130 4.7 23.3 1.0 O B:HOH278 4.7 26.6 1.0 O A:GLY131 4.8 24.4 1.0 O B:PHE130 4.8 27.7 1.0 CA A:PHE130 4.9 22.1 1.0 O B:HOH295 5.0 24.9 1.0 CD2 A:TYR117 5.0 27.3 1.0

Y.Asada, H.Shimada, M.Taketa, Y.Matsuura, N.Kunishima. Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L3M) To Be Published.