Atomistry » Sodium » PDB 5yt7-5zo8 » 5znn
Atomistry »
  Sodium »
    PDB 5yt7-5zo8 »
      5znn »

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

Protein crystallography data

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

Sodium Binding Sites:

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 5znn

Go back to Sodium Binding Sites List in 5znn
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 5znn

Go back to Sodium Binding Sites List in 5znn
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 5znn

Go back to Sodium Binding Sites List in 5znn
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 5znn

Go back to Sodium Binding Sites List in 5znn
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 5znn

Go back to Sodium Binding Sites List in 5znn
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

Reference:

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
Page generated: Tue Oct 8 01:32:00 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy