Sodium in PDB 5znn: Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin

The structure of Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin, PDB code: 5znn was solved by T.Yabe-Wada, M.Unno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.61 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.264, 138.496, 146.680, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.7

The binding sites of Sodium atom in the Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin (pdb code 5znn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin, PDB code: 5znn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin


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 Ligand-Free Form of the VPS10 Ectodomain of Sortilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na808 b:74.9 occ:1.00 OE1 A:GLU185 2.4 70.9 1.0 OG A:SER190 2.7 51.9 1.0 O A:HOH1078 2.9 55.6 1.0 N A:VAL186 3.0 45.8 1.0 O A:GLY192 3.1 48.2 1.0 CB A:VAL186 3.5 38.4 1.0 N A:SER190 3.5 46.8 1.0 CE1 A:HIS213 3.6 44.0 1.0 CD A:GLU185 3.6 67.4 1.0 CA A:VAL186 3.7 44.1 1.0 CB A:SER190 3.7 52.1 1.0 CG2 A:VAL186 3.8 42.3 1.0 C A:GLU185 3.9 45.0 1.0 C A:GLY192 3.9 48.1 1.0 CA A:GLU185 4.0 44.0 1.0 O A:VAL186 4.0 46.0 1.0 CB A:GLU185 4.0 54.1 1.0 ND1 A:HIS213 4.1 42.6 1.0 CA A:SER190 4.1 40.6 1.0 C A:GLY189 4.1 46.9 1.0 O A:SER190 4.2 42.1 1.0 CA A:GLY189 4.3 41.0 1.0 C A:VAL186 4.3 45.0 1.0 C A:SER190 4.4 40.4 1.0 CG A:GLU185 4.4 64.8 1.0 CA A:GLY193 4.5 35.9 1.0 N A:GLY193 4.5 43.4 1.0 OE2 A:GLU185 4.6 65.9 1.0 NE2 A:HIS213 4.8 43.4 1.0 O A:HOH1036 4.8 46.9 1.0 CG1 A:VAL186 4.8 39.9 1.0 N A:GLY192 4.8 42.0 1.0 O A:GLY189 4.9 44.9 1.0 CA A:GLY192 4.9 46.4 1.0 N A:GLY189 5.0 41.5 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin


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 Ligand-Free Form of the VPS10 Ectodomain of Sortilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na809 b:88.4 occ:1.00 N A:ASN262 2.4 60.4 1.0 N A:PRO261 2.6 62.1 1.0 N A:ILE264 2.6 52.5 1.0 CB A:ILE264 2.7 43.7 1.0 C A:GLY260 2.8 55.6 1.0 CD A:PRO261 2.9 64.0 1.0 CG1 A:ILE264 3.1 48.3 1.0 CA A:GLY260 3.1 50.9 1.0 CA A:ILE264 3.2 49.6 1.0 C A:PRO261 3.2 72.0 1.0 C A:ASN262 3.2 51.9 1.0 N A:ASN263 3.2 47.4 1.0 CA A:ASN262 3.3 55.6 1.0 CA A:PRO261 3.3 66.6 1.0 CD1 A:ILE264 3.5 52.6 1.0 O A:GLY260 3.5 52.2 1.0 C A:ASN263 3.7 52.6 1.0 O A:ILE264 3.8 41.6 1.0 O A:ASN262 3.8 49.5 1.0 N A:GLY260 3.9 54.9 1.0 C A:ILE264 3.9 44.6 1.0 CB A:ASN262 4.0 60.7 1.0 CA A:ASN263 4.0 46.2 1.0 CG2 A:ILE264 4.0 43.8 1.0 CG A:PRO261 4.1 62.7 1.0 CB A:PRO261 4.1 63.0 1.0 O A:PRO261 4.3 81.1 1.0 O A:HOH938 4.5 44.4 1.0 ND2 A:ASN262 4.8 64.9 1.0 O A:ASN263 4.8 58.9 1.0 CG A:ASN262 4.9 66.7 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin


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 Ligand-Free Form of the VPS10 Ectodomain of Sortilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na810 b:88.8 occ:1.00 N2 A:NAG801 2.5 52.9 1.0 OE2 A:GLU573 2.7 56.6 1.0 O A:HOH1024 3.1 57.3 1.0 OG A:SER118 3.1 67.9 1.0 C8 A:NAG801 3.1 47.1 1.0 C7 A:NAG801 3.2 55.9 1.0 CD A:GLU573 3.3 56.4 1.0 OE1 A:GLU573 3.4 54.8 1.0 C2 A:NAG801 3.5 49.8 1.0 O3 A:NAG801 3.6 48.9 1.0 CA A:SER118 3.6 67.1 1.0 CB A:SER118 3.7 67.0 1.0 N A:SER118 4.1 65.0 1.0 C3 A:NAG801 4.1 48.2 1.0 CE1 A:TYR148 4.2 52.4 1.0 O7 A:NAG801 4.4 68.1 1.0 OD1 A:ASP117 4.5 60.2 0.5 CG A:GLU573 4.5 54.5 1.0 OH A:TYR148 4.7 63.1 1.0 C1 A:NAG801 4.8 40.4 1.0 CZ A:TYR148 4.9 56.8 1.0 C A:SER118 4.9 61.4 1.0 ND2 A:ASN580 4.9 58.4 1.0 CD1 A:TYR148 4.9 52.0 1.0 O A:HOH945 4.9 42.6 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin


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 Ligand-Free Form of the VPS10 Ectodomain of Sortilin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na811 b:73.9 occ:1.00 O B:HOH1010 2.5 58.2 1.0 O B:HOH1048 3.1 39.4 1.0 N B:SER225 3.4 33.9 1.0 CA B:ASN224 3.7 42.5 1.0 OG B:SER225 3.9 44.4 1.0 C B:ASN224 4.0 41.6 1.0 N B:ASN224 4.1 45.2 1.0 CB B:SER225 4.2 30.1 1.0 O B:GLN223 4.2 49.2 1.0 C B:GLN223 4.3 44.5 1.0 CA B:SER225 4.4 31.7 1.0 O B:HOH919 4.7 39.2 1.0 OD1 B:ASN224 4.9 47.7 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Ligand-Free Form of the VPS10 Ectodomain of Sortilin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na812 b:65.7 occ:1.00 OG1 B:THR216 2.4 52.7 1.0 N B:LEU231 2.9 47.5 1.0 O B:GLN217 3.2 43.8 1.0 CA B:ALA230 3.5 41.6 1.0 O B:THR216 3.6 43.1 1.0 CB B:THR216 3.6 49.1 1.0 C B:ALA230 3.6 47.2 1.0 CB B:LEU231 3.7 39.8 1.0 C B:THR216 3.8 45.0 1.0 CA B:LEU231 3.9 43.7 1.0 CA B:THR216 4.1 46.5 1.0 C B:GLN217 4.1 38.4 1.0 N B:THR216 4.2 42.0 1.0 CB B:ALA230 4.2 28.6 1.0 O B:LEU229 4.3 36.0 1.0 O B:LEU231 4.4 41.3 1.0 CE B:MET219 4.4 33.0 0.3 N B:GLN217 4.4 42.4 1.0 N B:ALA230 4.5 42.3 1.0 CG B:MET219 4.6 38.3 0.4 CG B:MET219 4.6 38.4 0.3 C B:LEU231 4.6 41.8 1.0 CD1 B:LEU229 4.7 45.0 1.0 N B:MET218 4.8 42.5 1.0 C B:LEU229 4.8 37.7 1.0 O B:ALA230 4.8 52.9 1.0 CG2 B:THR216 4.8 41.8 1.0 CA B:MET218 4.8 43.2 1.0 CG B:MET219 4.9 38.5 0.3 CA B:GLN217 4.9 31.3 1.0 SD B:MET219 4.9 40.7 0.4

T.Yabe-Wada, S.Matsuba, M.Unno, N.Onai. Crystal Structure of the Ligand-Free Form of the VPS10 Ectodomain of Dimerized Sortilin at Acidic pH Febs Lett. V. 592 2647 2018.
ISSN: ISSN 1873-3468
PubMed: 29972886
DOI: 10.1002/1873-3468.13181