Sodium in PDB 5dqb: Green/Cyan Wascfp at pH 8.0

The structure of Green/Cyan Wascfp at pH 8.0, PDB code: 5dqb was solved by V.Pletnev, N.Pletneva, S.Pletnev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.401, 51.370, 50.033, 90.00, 103.98, 90.00
R / Rfree (%)	17.9 / 23.1

The binding sites of Sodium atom in the Green/Cyan Wascfp at pH 8.0 (pdb code 5dqb). 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 Green/Cyan Wascfp at pH 8.0, PDB code: 5dqb:

Sodium binding site 1 out of 1 in the Green/Cyan Wascfp at pH 8.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Green/Cyan Wascfp at pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:20.1 occ:1.00 OD1 A:ASP36 2.4 17.3 1.0 OG1 A:THR38 2.7 13.7 1.0 N A:THR38 2.9 7.7 1.0 O A:PHE8 2.9 13.2 1.0 O A:GLY10 3.1 12.7 1.0 N A:ALA37 3.2 8.4 1.0 CB A:THR38 3.3 11.1 1.0 O A:THR9 3.3 14.8 1.0 C A:THR9 3.4 14.3 1.0 O A:HOH552 3.5 26.4 1.0 C A:ASP36 3.5 7.9 1.0 O A:HOH501 3.5 10.5 1.0 CG A:ASP36 3.6 15.1 1.0 C A:GLY10 3.6 11.2 1.0 CA A:ASP36 3.7 8.2 1.0 CA A:THR38 3.7 9.3 1.0 N A:GLY10 3.7 12.2 1.0 CA A:GLY10 3.8 12.3 1.0 C A:ALA37 3.9 7.4 1.0 CA A:ALA37 4.0 8.3 1.0 CA A:THR9 4.0 15.0 1.0 C A:PHE8 4.0 11.5 1.0 O A:HOH612 4.2 31.4 1.0 CB A:ASP36 4.2 11.1 1.0 O A:ASP36 4.3 8.6 1.0 CB A:ALA37 4.5 8.9 1.0 N A:THR9 4.5 13.3 1.0 OD2 A:ASP36 4.5 18.3 1.0 N A:VAL11 4.6 12.0 1.0 CG2 A:THR38 4.7 11.9 1.0 C A:THR38 4.9 8.3 1.0 N A:TYR39 5.0 8.4 1.0

V.Z.Pletnev, N.Pletneva, R.G.Efremov, E.A.Goryacheva, I.V.Artemyev, S.F.Arkhipova, K.S.Sarkisyan, A.S.Mishin, K.A.Lukyanov, S.V.Pletnev. Crystal Structure of pH and T Dependent Green Fluorescent Protein Wascfp with Trp Based Chromophore Russ.J.Bioorganic Chem. V. (6) 2016.
ISSN: ISSN 1068-1620