Sodium in PDB 1jzn: Crystal Structure of A Galactose-Specific C-Type Lectin

The structure of Crystal Structure of A Galactose-Specific C-Type Lectin, PDB code: 1jzn was solved by J.R.Walker, B.Nagar, N.M.Young, T.Hirama, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.46 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	63.309, 178.486, 137.832, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.1

The structure of Crystal Structure of A Galactose-Specific C-Type Lectin also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	5 atoms

The binding sites of Sodium atom in the Crystal Structure of A Galactose-Specific C-Type Lectin (pdb code 1jzn). 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 A Galactose-Specific C-Type Lectin, PDB code: 1jzn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of A Galactose-Specific C-Type 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 A Galactose-Specific C-Type Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1139 b:24.5 occ:1.00 OH A:TYR15 2.4 22.6 1.0 OE1 A:GLN132 2.4 20.0 1.0 O A:SER42 2.4 22.4 1.0 O A:HOH1251 2.5 27.7 1.0 O A:HOH1182 2.5 33.1 1.0 OG A:SER42 3.0 21.3 1.0 C A:SER42 3.3 25.0 1.0 CD A:GLN132 3.4 27.1 1.0 CZ A:TYR15 3.4 24.4 1.0 CE2 A:TYR15 3.6 21.4 1.0 N A:SER42 3.7 19.4 1.0 CA A:SER42 3.9 22.3 1.0 CB A:SER42 4.0 21.5 1.0 CD1 A:LEU13 4.0 24.3 1.0 NE2 A:GLN132 4.1 23.2 1.0 O A:HOH1190 4.2 31.1 1.0 CD2 A:HIS44 4.2 27.8 1.0 O A:HOH1284 4.3 49.4 1.0 CG A:GLN132 4.3 21.2 1.0 NE2 A:HIS44 4.4 29.0 1.0 N A:PHE43 4.4 23.7 1.0 OD2 A:ASP83 4.6 25.2 1.0 CE1 A:TYR15 4.7 21.9 1.0 CA A:PHE43 4.8 22.2 1.0 OE1 A:GLU48 4.8 34.1 1.0 C A:ALA41 4.9 19.2 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of A Galactose-Specific C-Type 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 A Galactose-Specific C-Type Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2139 b:29.5 occ:1.00 O B:HOH2182 2.4 38.7 1.0 O B:SER42 2.4 24.0 1.0 O B:HOH2187 2.4 39.0 1.0 OE1 B:GLN132 2.6 28.8 1.0 OH B:TYR15 2.7 28.0 1.0 OG B:SER42 2.7 24.0 1.0 C B:SER42 3.2 25.9 1.0 CD B:GLN132 3.6 27.6 1.0 N B:SER42 3.7 24.4 1.0 CZ B:TYR15 3.7 24.7 1.0 CB B:SER42 3.8 24.2 1.0 CA B:SER42 3.8 24.7 1.0 CE2 B:TYR15 3.9 25.9 1.0 CD1 B:LEU13 4.0 37.5 1.0 CD2 B:HIS44 4.0 23.4 1.0 O B:HOH2214 4.1 39.1 1.0 N B:PHE43 4.2 24.4 1.0 NE2 B:GLN132 4.2 30.6 1.0 NE2 B:HIS44 4.4 26.3 1.0 OD2 B:ASP83 4.6 26.9 1.0 CG B:GLN132 4.6 26.2 1.0 CA B:PHE43 4.6 24.5 1.0 OE1 B:GLU48 4.6 39.3 1.0 C B:ALA41 4.9 23.3 1.0 OE2 B:GLU48 5.0 42.0 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of A Galactose-Specific C-Type 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 A Galactose-Specific C-Type Lectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3139 b:33.2 occ:1.00 O C:HOH3211 2.2 49.4 1.0 OE1 C:GLN132 2.4 32.7 1.0 O C:SER42 2.4 36.2 1.0 O C:HOH3162 2.4 49.4 1.0 OG C:SER42 2.6 37.1 1.0 OH C:TYR15 2.7 33.4 1.0 C C:SER42 3.3 37.5 1.0 CD C:GLN132 3.3 32.2 1.0 N C:SER42 3.6 35.8 1.0 CB C:SER42 3.7 35.7 1.0 CA C:SER42 3.8 35.8 1.0 CZ C:TYR15 3.8 34.0 1.0 NE2 C:GLN132 3.9 32.1 1.0 CE2 C:TYR15 4.0 34.0 1.0 CD1 C:LEU13 4.2 34.6 1.0 O C:HOH3160 4.2 38.1 1.0 CD2 C:HIS44 4.2 46.5 1.0 OD2 C:ASP83 4.3 43.6 1.0 N C:PHE43 4.3 39.6 1.0 CG C:GLN132 4.4 33.2 1.0 O C:HOH3165 4.4 52.4 1.0 NE2 C:HIS44 4.5 47.3 1.0 OE1 C:GLU48 4.6 43.3 1.0 CA C:PHE43 4.8 40.0 1.0 C C:ALA41 4.8 33.0 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of A Galactose-Specific C-Type Lectin


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 A Galactose-Specific C-Type Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na4139 b:34.9 occ:1.00 OH D:TYR15 2.2 40.6 1.0 OE1 D:GLN132 2.3 31.4 1.0 O D:SER42 2.5 35.3 1.0 OG D:SER42 2.9 33.4 1.0 CD D:GLN132 3.3 33.6 1.0 CZ D:TYR15 3.3 35.4 1.0 C D:SER42 3.5 34.5 1.0 CE2 D:TYR15 3.6 34.8 1.0 N D:SER42 3.8 30.9 1.0 CD1 D:LEU13 3.8 43.4 1.0 O D:HOH4163 3.8 43.4 1.0 CB D:SER42 4.0 33.0 1.0 CA D:SER42 4.0 33.3 1.0 NE2 D:GLN132 4.1 33.4 1.0 CG D:GLN132 4.2 30.8 1.0 CD2 D:HIS44 4.2 50.6 1.0 NE2 D:HIS44 4.4 50.5 1.0 CE1 D:TYR15 4.5 34.7 1.0 N D:PHE43 4.6 37.1 1.0 OD2 D:ASP83 4.6 35.2 1.0 OE1 D:GLU48 4.7 52.1 1.0 C D:ALA41 4.9 28.0 1.0 CD2 D:TYR15 4.9 31.9 1.0 CA D:PHE43 5.0 37.2 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of A Galactose-Specific C-Type Lectin


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 A Galactose-Specific C-Type Lectin within 5.0Å range: probe atom residue distance (Å) B Occ E:Na5139 b:27.9 occ:1.00 OH E:TYR15 2.3 26.9 1.0 O E:SER42 2.4 18.1 1.0 OE1 E:GLN132 2.4 20.8 1.0 O E:HOH5191 2.6 37.4 1.0 O E:HOH5164 2.6 49.4 1.0 OG E:SER42 3.0 16.8 1.0 CZ E:TYR15 3.3 25.6 1.0 C E:SER42 3.3 19.4 1.0 CD E:GLN132 3.4 23.8 1.0 CE2 E:TYR15 3.4 23.6 1.0 N E:SER42 3.6 22.6 1.0 CD1 E:LEU13 3.8 35.9 1.0 CA E:SER42 3.9 20.2 1.0 O E:HOH5242 4.0 37.0 1.0 CB E:SER42 4.0 20.2 1.0 NE2 E:GLN132 4.2 22.7 1.0 CG E:GLN132 4.2 22.8 1.0 CD2 E:HIS44 4.4 20.6 1.0 N E:PHE43 4.4 18.8 1.0 CE1 E:TYR15 4.6 24.3 1.0 NE2 E:HIS44 4.6 22.1 1.0 OD1 E:ASP83 4.7 18.3 1.0 C E:ALA41 4.8 21.9 1.0 CD2 E:TYR15 4.8 21.6 1.0 CA E:PHE43 4.8 17.9 1.0 CB E:GLN132 5.0 20.7 1.0 OE1 E:GLU48 5.0 31.7 1.0

J.R.Walker, B.Nagar, N.M.Young, T.Hirama, J.M.Rini. X-Ray Crystal Structure of A Galactose-Specific C-Type Lectin Possessing A Novel Decameric Quaternary Structure. Biochemistry V. 43 3783 2004.
ISSN: ISSN 0006-2960
PubMed: 15049685
DOI: 10.1021/BI035871A