Sodium in PDB 5hbq: C63D Mutant of the Rhodanese Domain of Ygap

The structure of C63D Mutant of the Rhodanese Domain of Ygap, PDB code: 5hbq was solved by C.Eichmann, C.Tzitzilonis, T.Nakamura, W.Kwiatkowski, I.Maslennikov, S.Choe, S.A.Lipton, R.Riek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 1.66
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	43.896, 43.896, 52.667, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.3

The structure of C63D Mutant of the Rhodanese Domain of Ygap also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the C63D Mutant of the Rhodanese Domain of Ygap (pdb code 5hbq). 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 C63D Mutant of the Rhodanese Domain of Ygap, PDB code: 5hbq:

Sodium binding site 1 out of 1 in the C63D Mutant of the Rhodanese Domain of Ygap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C63D Mutant of the Rhodanese Domain of Ygap within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:23.5 occ:1.00 O A:LEU88 2.8 16.5 1.0 OG1 A:THR69 2.8 21.3 1.0 OD1 A:ASP63 2.9 14.0 1.0 CG A:ASP63 3.5 14.6 1.0 CG2 A:THR69 3.5 21.0 1.0 CA A:HIS62 3.6 12.8 1.0 N A:ASP63 3.6 13.8 1.0 CB A:THR69 3.7 21.1 1.0 C A:LEU88 3.7 17.0 1.0 N A:LEU88 3.7 16.1 1.0 O A:HOH308 3.7 22.0 1.0 N A:GLY91 3.8 19.6 1.0 CA A:GLY91 3.8 18.3 1.0 OD2 A:ASP63 3.8 15.2 1.0 O A:PHE61 3.9 12.0 1.0 CA A:GLY66 3.9 22.2 1.0 CA A:LEU88 4.0 16.3 1.0 CB A:LEU88 4.0 16.6 1.0 C A:HIS62 4.1 13.6 1.0 CB A:HIS62 4.3 12.3 1.0 N A:GLY66 4.3 20.3 1.0 CB A:ASP63 4.4 14.7 1.0 C A:LEU87 4.5 16.2 1.0 C A:PHE61 4.6 12.2 1.0 N A:HIS62 4.6 13.0 1.0 CA A:ASP63 4.6 14.6 1.0 CB A:LEU87 4.7 16.6 1.0 C A:GLY66 4.8 21.6 1.0 CA A:LEU87 4.9 16.3 1.0 N A:GLU89 4.9 19.8 1.0 C A:ASP90 5.0 21.0 1.0 O A:GLY66 5.0 20.4 1.0 CA A:THR69 5.0 20.7 1.0

C.Eichmann, C.Tzitzilonis, T.Nakamura, W.Kwiatkowski, I.Maslennikov, S.Choe, S.A.Lipton, R.Riek. S-Nitrosylation Induces Structural and Dynamical Changes in A Rhodanese Family Protein. J.Mol.Biol. V. 428 3737 2016.
ISSN: ESSN 1089-8638
PubMed: 27473602
DOI: 10.1016/J.JMB.2016.07.010