Sodium in PDB 6xyd: Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi

The structure of Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi, PDB code: 6xyd was solved by Y.Roske, U.Heinemann, E.D.Andrea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.07 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.213, 44.771, 68.654, 90.00, 93.40, 90.00
R / Rfree (%)	18.3 / 21.6

The structure of Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi (pdb code 6xyd). 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 Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi, PDB code: 6xyd:

Sodium binding site 1 out of 1 in the Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi


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 Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:19.6 occ:1.00 O C:ARG93 2.3 16.6 1.0 O B:HOH372 2.3 32.7 1.0 O B:ARG93 2.4 16.1 1.0 O A:ARG93 2.4 15.9 1.0 O D:ARG93 2.5 21.0 1.0 C C:ARG93 3.4 16.5 1.0 C A:ARG93 3.5 17.2 1.0 C B:ARG93 3.5 19.3 1.0 C D:ARG93 3.5 20.8 1.0 CA C:ARG93 4.2 15.1 1.0 CA B:ARG93 4.3 18.9 1.0 CA A:ARG93 4.3 17.4 1.0 N C:ALA94 4.3 13.3 1.0 CA D:ARG93 4.3 21.3 1.0 N A:ALA94 4.4 13.8 1.0 N B:ALA94 4.4 16.6 1.0 N D:ALA94 4.4 16.8 1.0 CA C:ALA94 4.5 12.7 1.0 CA A:ALA94 4.5 13.3 1.0 CA B:ALA94 4.5 15.4 1.0 CA D:ALA94 4.6 15.6 1.0 CL A:CL203 4.7 17.2 1.0 CB B:ALA94 4.9 15.9 1.0 CB A:ALA94 4.9 14.2 1.0 CB C:ALA94 5.0 12.8 1.0

E.Dias D'andrea, Y.Roske, G.A.P.De Oliveira, N.Cremer, A.Diehl, P.Schmieder, U.Heinemann, H.Oschkinat, J.Ricardo Pires. Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi. J.Struct.Biol. 07536 2020.
ISSN: ESSN 1095-8657
PubMed: 32473201
DOI: 10.1016/J.JSB.2020.107536