Sodium in PDB 4uri: Crystal Structure of Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia

The structure of Crystal Structure of Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia, PDB code: 4uri was solved by G.Sulzenbacher, V.Roig-Zamboni, W.J.Peumans, B.Henrissat, E.J.M.Van Damme, Y.Bourne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.48 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.100, 53.221, 71.271, 106.01, 94.12, 107.59
R / Rfree (%)	14.838 / 18.731

The structure of Crystal Structure of Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia (pdb code 4uri). 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 Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia, PDB code: 4uri:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia


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 Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:22.2 occ:1.00 OG1 A:THR255 2.9 24.3 1.0 CB A:THR255 3.4 23.9 1.0 NE2 A:GLN256 3.4 28.3 1.0 NH1 A:ARG241 3.5 27.4 1.0 CD A:ARG241 3.8 25.2 1.0 CG A:GLN256 4.1 25.3 1.0 CD A:GLN256 4.3 27.1 1.0 CG2 A:THR255 4.3 24.0 1.0 C A:THR255 4.4 23.9 1.0 CZ A:ARG241 4.5 27.8 1.0 O A:THR255 4.6 23.3 1.0 CA A:THR255 4.6 22.8 1.0 NE A:ARG241 4.6 25.9 1.0 CG A:ARG241 4.7 23.3 1.0 N A:GLN256 4.8 22.0 1.0 CB A:GLN256 4.8 24.3 1.0 CB A:ARG241 5.0 21.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia


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 Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:53.7 occ:1.00 NZ A:LYS228 3.5 24.8 1.0 O A:ASN175 3.5 27.5 1.0 O A:LEU177 4.0 18.4 1.0 C A:ASN175 4.1 26.3 1.0 OD1 A:ASP178 4.1 21.4 1.0 NH2 A:ARG135 4.3 23.3 1.0 CZ A:ARG135 4.3 22.1 1.0 C A:ASN176 4.3 21.1 1.0 NE A:ARG135 4.4 22.4 1.0 N A:ASN176 4.4 24.1 1.0 O A:ASN176 4.4 21.4 1.0 C A:LEU177 4.4 18.1 1.0 CA A:ASN176 4.5 23.1 1.0 O A:ALA174 4.7 23.7 1.0 N A:LEU177 4.7 19.7 1.0 CE A:LYS228 4.7 24.3 1.0 NH1 A:ARG135 4.8 21.6 1.0 N A:ASP178 4.8 17.2 1.0 CA A:ASP178 4.9 18.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia


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 Chitinase-Like Agglutinin Robpscra From Robinia Pseudoacacia within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:38.4 occ:1.00 NE A:ARG105 3.2 25.3 1.0 ND2 A:ASN106 3.6 28.9 1.0 CD1 A:LEU102 3.8 34.3 1.0 CB A:ARG105 3.9 24.5 1.0 CD A:ARG105 4.0 24.9 1.0 NH2 A:ARG105 4.0 27.1 1.0 CZ A:ARG105 4.1 26.5 1.0 CG A:ASN106 4.5 29.3 1.0 CG A:ARG105 4.6 24.5 1.0 OD1 A:ASN106 4.6 29.5 1.0 CG A:LEU102 5.0 31.7 1.0

G.Sulzenbacher, V.Roig-Zamboni, W.J.Peumans, B.Henrissat, E.J.Van Damme, Y.Bourne. Structural Basis For Carbohydrate Binding Properties of A Plant Chitinase-Like Agglutinin with Conserved Catalytic Machinery. J.Struct.Biol. 2015.
ISSN: ESSN 1095-8657
PubMed: 25727185
DOI: 10.1016/J.JSB.2015.01.013