Sodium in PDB 4nds: Crystal Structure of L. Decastes Alpha-Galactosyl-Binding Lectin

The structure of Crystal Structure of L. Decastes Alpha-Galactosyl-Binding Lectin, PDB code: 4nds was solved by A.Van Eerde, E.Grahn, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.29 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.840, 56.774, 44.458, 90.00, 107.10, 90.00
R / Rfree (%)	10.9 / 12.4

The binding sites of Sodium atom in the Crystal Structure of L. Decastes Alpha-Galactosyl-Binding Lectin (pdb code 4nds). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of L. Decastes Alpha-Galactosyl-Binding Lectin, PDB code: 4nds:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of L. Decastes Alpha-Galactosyl-Binding Lectin


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 L. Decastes Alpha-Galactosyl-Binding Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:19.1 occ:1.00 O B:HOH234 2.2 23.8 1.0 O B:HOH302 2.4 18.7 1.0 O B:HOH281 2.5 24.7 1.0 O B:THR66 2.5 14.5 1.0 HZ3 B:LYS16 2.7 28.9 1.0 HZ2 B:LYS16 3.3 28.9 1.0 NZ B:LYS16 3.4 24.1 1.0 O B:HOH245 3.6 21.6 1.0 C B:THR66 3.6 11.5 1.0 HA B:THR66 3.8 13.5 0.7 HG23 B:THR66 3.8 15.1 0.3 HG22 B:THR66 3.9 15.1 0.3 HZ1 B:LYS16 4.0 28.9 1.0 HE2 B:LYS16 4.0 26.1 1.0 O B:HIS69 4.2 12.6 1.0 CA B:THR66 4.3 11.3 0.7 CA B:THR66 4.3 11.3 0.3 CE B:LYS16 4.3 21.8 1.0 CG2 B:THR66 4.3 12.6 0.3 HB B:THR66 4.4 15.6 0.7 HA B:SER67 4.5 13.0 1.0 N B:SER67 4.7 10.4 1.0 HE3 B:LYS16 4.7 26.1 1.0 C B:SER67 4.8 10.1 1.0 O B:ILE65 4.8 9.4 1.0 O B:SER67 4.8 13.5 1.0 CA B:SER67 4.9 10.8 1.0 CB B:THR66 4.9 13.0 0.7 CB B:THR66 5.0 12.5 0.3

Sodium binding site 2 out of 3 in the Crystal Structure of L. Decastes Alpha-Galactosyl-Binding Lectin


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 L. Decastes Alpha-Galactosyl-Binding Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:18.0 occ:1.00 O B:HOH349 2.3 30.1 1.0 OE1 B:GLU52 2.5 26.2 1.0 O B:HOH343 2.5 28.3 1.0 CD B:GLU52 3.4 25.5 1.0 OE2 B:GLU52 3.7 28.7 1.0 O B:HOH264 4.2 23.4 1.0 O B:HOH249 4.3 22.3 1.0 HA B:GLU52 4.3 15.7 1.0 HB3 B:GLU52 4.6 18.9 1.0 CG B:GLU52 4.8 20.1 1.0 O B:GLU52 5.0 14.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of L. Decastes Alpha-Galactosyl-Binding Lectin


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 L. Decastes Alpha-Galactosyl-Binding Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:29.4 occ:1.00 O B:GLY41 2.3 9.4 1.0 O B:HOH308 2.4 34.1 1.0 O B:HOH330 2.5 33.8 1.0 O B:HOH213 2.5 13.2 1.0 C B:GLY41 3.5 8.3 1.0 HA B:TYR42 3.6 9.3 1.0 HB1 B:ALA39 4.0 12.5 1.0 O B:HOH216 4.2 14.7 1.0 N B:TYR42 4.3 7.5 1.0 CA B:TYR42 4.3 7.7 1.0 HA2 B:GLY41 4.4 10.7 1.0 CA B:GLY41 4.4 8.9 1.0 O B:HOH279 4.4 41.6 1.0 O B:HOH239 4.6 12.2 1.0 N B:GLY41 4.7 8.5 1.0 C B:TYR42 4.7 6.6 1.0 O B:HOH352 4.7 30.4 1.0 H B:GLY41 4.8 10.2 1.0 CB B:ALA39 4.9 10.4 1.0 HB3 B:ALA39 5.0 12.5 1.0 O B:HOH332 5.0 32.3 1.0 O B:HOH275 5.0 33.2 0.8 O B:HOH275 5.0 33.3 0.2

A.Van Eerde, E.Grahn, H.C.Winter, I.J.Goldstein, U.Krengel. Atomic-Resolution Structure of the Alpha-Galactosyl Binding Lyophyllum Decastes Lectin Reveals A New Protein Family Found in Both Fungi and Plants Glycobiology 2014.
ISSN: ESSN 1460-2423