Sodium in PDB 5xdz: Crystal Structure of Zebrafish SNX25 Px Domain

The structure of Crystal Structure of Zebrafish SNX25 Px Domain, PDB code: 5xdz was solved by K.Su, Y.Zhang, J.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.63 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.150, 82.830, 36.500, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.7

The structure of Crystal Structure of Zebrafish SNX25 Px Domain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Zebrafish SNX25 Px Domain (pdb code 5xdz). 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 Zebrafish SNX25 Px Domain, PDB code: 5xdz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Zebrafish SNX25 Px Domain


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 Zebrafish SNX25 Px Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na801 b:21.2 occ:1.00 H B:ALA655 2.6 23.5 1.0 HB3 B:LEU680 2.8 19.8 1.0 H B:ILE681 2.8 22.6 1.0 HG23 B:ILE681 2.8 42.8 1.0 HB2 B:MET654 2.8 34.1 1.0 HB3 B:LYS679 2.9 26.6 1.0 H B:LEU680 3.0 17.7 1.0 HA B:MET654 3.1 25.1 1.0 HG12 B:ILE681 3.2 22.4 1.0 HD11 B:LEU705 3.4 50.4 1.0 N B:ALA655 3.4 19.6 1.0 N B:LEU680 3.5 14.8 1.0 O B:ALA655 3.5 20.2 1.0 N B:ILE681 3.6 18.8 1.0 CB B:MET654 3.6 28.5 1.0 CA B:MET654 3.7 20.9 1.0 CB B:LEU680 3.7 16.5 1.0 CG2 B:ILE681 3.7 35.7 1.0 HB3 B:MET654 3.9 34.1 1.0 CB B:LYS679 3.9 22.1 1.0 CA B:LEU680 4.0 12.4 1.0 HD12 B:LEU705 4.0 50.4 1.0 HG21 B:ILE681 4.0 42.8 1.0 C B:MET654 4.0 30.0 1.0 HB2 B:LEU680 4.0 19.8 1.0 CG1 B:ILE681 4.1 18.7 1.0 CD1 B:LEU705 4.1 42.0 1.0 C B:LEU680 4.3 13.5 1.0 HB3 B:ALA655 4.3 23.4 1.0 C B:LYS679 4.3 14.9 1.0 CB B:ILE681 4.3 15.9 1.0 HB2 B:LYS679 4.3 26.6 1.0 C B:ALA655 4.3 19.4 1.0 HA B:LYS679 4.4 18.5 1.0 CA B:ALA655 4.4 16.0 1.0 HG22 B:ILE681 4.4 42.8 1.0 HD3 B:LYS679 4.4 42.7 1.0 HD23 B:LEU680 4.4 24.9 1.0 HD13 B:ILE681 4.5 43.7 1.0 CA B:LYS679 4.5 15.4 1.0 CA B:ILE681 4.5 17.3 1.0 HG2 B:LYS679 4.6 32.3 1.0 HD13 B:LEU705 4.7 50.4 1.0 HG13 B:ILE681 4.7 22.4 1.0 CG B:LYS679 4.7 26.9 1.0 HG B:LEU680 4.8 20.3 1.0 CG B:LEU680 4.8 16.9 1.0 CD1 B:ILE681 4.8 36.4 1.0 CG B:MET654 4.8 43.5 1.0 SD B:MET654 4.8 61.7 1.0 CB B:ALA655 4.8 19.5 1.0 HA B:LEU680 4.9 14.9 1.0 HD11 B:ILE681 5.0 43.7 1.0 CD B:LYS679 5.0 35.6 1.0 HG B:LEU705 5.0 40.1 1.0 HA B:ILE681 5.0 20.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Zebrafish SNX25 Px Domain


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 Zebrafish SNX25 Px Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:35.8 occ:1.00 H A:ILE681 2.5 26.6 1.0 HB3 A:LYS679 2.7 24.5 1.0 O A:HOH926 2.7 25.9 1.0 HG23 A:ILE681 2.7 61.6 1.0 HG12 A:ILE681 2.8 42.7 1.0 HB3 A:LEU680 2.8 26.6 1.0 HB3 A:MET654 2.9 53.8 1.0 H A:LEU680 3.1 21.8 1.0 H A:ALA655 3.2 35.9 1.0 N A:ILE681 3.3 22.2 1.0 N A:LEU680 3.4 18.1 1.0 O A:ALA655 3.5 26.8 1.0 CG2 A:ILE681 3.6 51.3 1.0 CB A:LYS679 3.6 20.4 1.0 CG1 A:ILE681 3.7 35.6 1.0 CB A:LEU680 3.7 22.2 1.0 N A:ALA655 3.8 29.9 1.0 CB A:MET654 3.8 44.9 1.0 HA A:MET654 3.8 40.1 1.0 HG21 A:ILE681 3.9 61.6 1.0 CA A:LEU680 3.9 18.9 1.0 CB A:ILE681 4.0 25.4 1.0 HB2 A:LYS679 4.0 24.5 1.0 C A:LEU680 4.1 21.2 1.0 SD A:MET654 4.1 66.2 1.0 C A:LYS679 4.1 17.1 1.0 HB3 A:ALA655 4.1 33.3 1.0 HB2 A:LEU680 4.1 26.6 1.0 HD13 A:ILE681 4.2 53.5 1.0 HD2 A:LYS679 4.2 58.9 1.0 CA A:MET654 4.2 33.4 1.0 CA A:ILE681 4.2 23.4 1.0 HA A:LYS679 4.2 21.9 1.0 CA A:LYS679 4.3 18.2 1.0 HG2 A:MET654 4.3 75.8 1.0 CG A:MET654 4.3 63.2 1.0 HG13 A:ILE681 4.3 42.7 1.0 HG22 A:ILE681 4.3 61.6 1.0 C A:ALA655 4.4 31.1 1.0 C A:MET654 4.4 32.0 1.0 CD1 A:ILE681 4.4 44.6 1.0 HB2 A:MET654 4.5 53.8 1.0 HG2 A:LYS679 4.5 39.5 1.0 HD23 A:LEU680 4.5 25.3 1.0 CA A:ALA655 4.5 32.1 1.0 CG A:LYS679 4.5 32.9 1.0 HD11 A:ILE681 4.6 53.5 1.0 HA A:ILE681 4.7 28.1 1.0 HE2 A:MET654 4.8 71.4 1.0 HG A:LEU680 4.8 23.0 1.0 CB A:ALA655 4.8 27.8 1.0 CG A:LEU680 4.8 19.2 1.0 HA A:LEU680 4.9 22.7 1.0 CD A:LYS679 4.9 49.0 1.0 H A:GLU682 4.9 23.1 1.0 HB A:ILE681 4.9 30.4 1.0 O A:LYS679 5.0 20.7 1.0

K.Su, T.Xu, Z.Yu, J.Zhu, Y.Zhang, M.Wu, Y.Xiong, J.Liu, J.Xu. Structure of the Px Domain of SNX25 Reveals A Novel Phospholipid Recognition Model By Dimerization in the Px Domain Febs Lett. V. 591 2011 2017.
ISSN: ISSN 1873-3468
PubMed: 28542875
DOI: 10.1002/1873-3468.12688