Sodium in PDB 4ikd: Crystal Structure of SNX11 Px Domain

The structure of Crystal Structure of SNX11 Px Domain, PDB code: 4ikd was solved by J.Xu, T.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.29 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.120, 62.400, 66.060, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.7

The structure of Crystal Structure of SNX11 Px Domain also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of SNX11 Px Domain (pdb code 4ikd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of SNX11 Px Domain, PDB code: 4ikd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of SNX11 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 SNX11 Px Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:37.6 occ:1.00 O A:HOH325 2.5 27.0 1.0 O A:HOH434 3.2 37.5 1.0 SD A:MET156 3.4 47.1 0.5 CG A:ARG153 3.9 18.5 1.0 CB A:MET156 3.9 35.9 0.5 CB A:MET156 4.0 29.1 0.5 CA A:ARG153 4.0 16.5 1.0 CG A:MET156 4.2 29.4 0.5 CG A:MET156 4.3 40.4 0.5 CB A:ARG153 4.4 16.9 1.0 O A:HOH429 4.6 36.2 1.0 O A:LEU152 4.6 15.2 1.0 N A:ARG153 4.7 15.2 1.0 O A:ARG153 4.8 19.3 1.0 C A:ARG153 4.9 16.9 1.0 C A:LEU152 5.0 14.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of SNX11 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 SNX11 Px Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:38.7 occ:1.00 O A:HOH357 2.6 31.2 1.0 CB A:MLY47 4.0 25.0 1.0 CA A:MLY47 4.8 20.0 1.0 O A:MLY47 4.9 21.5 1.0 O A:HOH335 4.9 27.3 1.0 CD A:MLY47 4.9 36.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of SNX11 Px Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of SNX11 Px Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:41.4 occ:1.00 O A:HOH316 2.6 21.3 1.0 SD A:MET145 2.8 35.0 0.5 CE A:MET145 3.3 24.1 0.5 CE A:MET145 3.4 31.4 0.5 CA A:ALA150 4.1 14.0 1.0 CD2 A:LEU130 4.1 13.9 0.5 CD1 A:LEU130 4.1 12.9 0.5 CB A:ALA150 4.2 14.2 1.0 O A:HOH384 4.2 47.8 1.0 O A:HOH347 4.3 31.0 1.0 SD A:MET145 4.3 22.3 0.5 CG A:MET145 4.3 22.5 0.5 O A:ALA150 4.5 12.6 1.0 CG A:MET145 4.5 29.5 0.5 CD A:ARG153 4.5 19.2 1.0 CB A:ARG153 4.7 16.9 1.0 O A:HOH307 4.8 18.3 1.0 C A:ALA150 4.8 12.8 1.0 NH1 A:ARG153 5.0 24.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of SNX11 Px Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of SNX11 Px Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:34.7 occ:1.00 O A:HOH331 3.0 26.9 1.0 CD1 A:ILE96 3.5 27.3 1.0 CG2 A:VAL36 3.9 18.6 1.0 NH1 A:ARG99 4.0 17.6 1.0 CB A:VAL36 4.0 16.9 1.0 CE2 A:PHE95 4.3 26.1 1.0 O A:HOH304 4.4 16.9 1.0 CG1 A:ILE96 4.7 22.8 1.0 N A:VAL36 4.8 16.5 1.0 CD2 A:PHE95 4.8 25.8 1.0 OH A:TYR38 4.9 18.5 1.0 CG1 A:VAL36 5.0 18.6 1.0

J.Xu, T.Xu, J.Liu. Structure of Sorting Nexin 11 (SNX11) Reveals A Novel Extended Px Domain (Pxe Domain) Critical For the Inhibition of Sorting Nexin 10 (SNX10) Induced Vacuolation To Be Published.