Calcium 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
Sodium	(Na)	5 atoms

The binding sites of Calcium 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 Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of A Galactose-Specific C-Type Lectin, PDB code: 1jzn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium 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 Calcium with other atoms in the Ca 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:Ca1138 b:23.2 occ:1.00 OD1 A:ASP120 2.2 25.0 1.0 OE1 A:GLN96 2.5 23.3 1.0 OE2 A:GLU104 2.5 21.7 1.0 OD1 A:ASN119 2.5 19.8 1.0 O4 A:GAL137 2.6 30.3 1.0 O A:ASP120 2.6 21.0 1.0 OD1 A:ASP98 2.6 28.1 1.0 O3 A:GAL137 2.7 26.5 1.0 CG A:ASP120 3.3 22.7 1.0 CD A:GLN96 3.3 23.9 1.0 CD A:GLU104 3.4 23.5 1.0 C4 A:GAL137 3.5 30.7 1.0 CG A:ASN119 3.5 20.6 1.0 CG A:ASP98 3.5 28.2 1.0 C3 A:GAL137 3.6 30.2 1.0 C A:ASP120 3.7 21.9 1.0 N A:ASP120 3.8 20.9 1.0 OE1 A:GLU104 3.8 24.7 1.0 NE2 A:GLN96 3.8 21.4 1.0 OD2 A:ASP98 3.9 26.8 1.0 ND2 A:ASN119 4.0 15.3 1.0 OD2 A:ASP120 4.0 22.0 1.0 CA A:ASP120 4.1 21.4 1.0 C2 A:GAL137 4.2 34.0 1.0 CB A:ASP120 4.3 20.9 1.0 N A:ASP98 4.3 27.2 1.0 CG A:GLN96 4.5 22.2 1.0 C A:ASN119 4.7 20.4 1.0 CG A:GLU104 4.7 24.2 1.0 CB A:TYR100 4.7 25.6 1.0 CB A:ASP98 4.7 26.0 1.0 CB A:ASN119 4.8 19.2 1.0 CB A:GLU104 4.8 25.7 1.0 N A:GLN121 4.8 21.9 1.0 N A:TYR100 4.9 26.1 1.0 C5 A:GAL137 4.9 33.8 1.0 N A:HIS99 4.9 26.8 1.0 CA A:ASN119 4.9 19.8 1.0 CA A:ASP98 5.0 26.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca2138 b:25.4 occ:1.00 OD1 B:ASP120 2.4 24.0 1.0 O4 B:GAL137 2.4 31.3 1.0 O B:ASP120 2.5 22.5 1.0 OD1 B:ASN119 2.5 23.2 1.0 OE1 B:GLN96 2.5 27.2 1.0 OE2 B:GLU104 2.5 31.3 1.0 OD1 B:ASP98 2.6 24.9 1.0 O3 B:GAL137 2.6 35.0 1.0 C4 B:GAL137 3.2 36.0 1.0 CG B:ASP120 3.3 20.1 1.0 C3 B:GAL137 3.4 36.4 1.0 CD B:GLN96 3.4 25.6 1.0 CG B:ASN119 3.5 23.9 1.0 CD B:GLU104 3.5 28.1 1.0 CG B:ASP98 3.5 30.5 1.0 C B:ASP120 3.6 22.6 1.0 N B:ASP120 3.8 20.9 1.0 ND2 B:ASN119 3.8 17.5 1.0 NE2 B:GLN96 3.8 23.6 1.0 OE1 B:GLU104 3.8 30.9 1.0 OD2 B:ASP98 3.9 26.1 1.0 OD2 B:ASP120 4.0 22.5 1.0 CA B:ASP120 4.1 21.7 1.0 C2 B:GAL137 4.1 39.5 1.0 N B:ASP98 4.2 31.4 1.0 CB B:ASP120 4.3 23.4 1.0 C B:ASN119 4.6 22.9 1.0 C5 B:GAL137 4.7 36.6 1.0 CG B:GLN96 4.7 22.9 1.0 CB B:ASP98 4.7 30.8 1.0 CG B:GLU104 4.7 27.7 1.0 N B:HIS99 4.7 34.2 1.0 N B:GLN121 4.7 23.6 1.0 N B:TYR100 4.8 33.6 1.0 CB B:TYR100 4.8 33.2 1.0 CB B:ASN119 4.8 19.4 1.0 CB B:GLU104 4.8 28.1 1.0 CA B:ASP98 4.9 32.3 1.0 CA B:ASN119 5.0 23.1 1.0 O2 B:GAL137 5.0 39.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca3138 b:41.1 occ:1.00 O4 C:GAL137 2.3 54.4 1.0 OD1 C:ASP120 2.4 39.2 1.0 OD1 C:ASN119 2.5 44.0 1.0 O C:ASP120 2.5 36.1 1.0 OE1 C:GLN96 2.5 41.6 1.0 O3 C:GAL137 2.6 52.6 1.0 OD1 C:ASP98 2.7 48.0 1.0 OE2 C:GLU104 2.7 48.0 1.0 C4 C:GAL137 3.1 57.1 1.0 CG C:ASP120 3.3 41.1 1.0 C3 C:GAL137 3.3 56.3 1.0 CD C:GLN96 3.4 40.1 1.0 CG C:ASN119 3.5 44.0 1.0 CG C:ASP98 3.5 46.8 1.0 C C:ASP120 3.6 38.2 1.0 CD C:GLU104 3.6 47.0 1.0 OD2 C:ASP98 3.8 44.7 1.0 N C:ASP120 3.8 38.6 1.0 NE2 C:GLN96 3.9 42.1 1.0 ND2 C:ASN119 3.9 44.0 1.0 OD2 C:ASP120 4.0 39.1 1.0 OE1 C:GLU104 4.0 47.0 1.0 CA C:ASP120 4.1 37.3 1.0 C2 C:GAL137 4.1 57.1 1.0 N C:ASP98 4.2 48.9 1.0 CB C:ASP120 4.3 39.4 1.0 C5 C:GAL137 4.5 58.4 1.0 CG C:GLN96 4.5 40.2 1.0 C C:ASN119 4.6 40.5 1.0 CB C:ASN119 4.7 42.0 1.0 N C:GLN121 4.7 38.9 1.0 CB C:TYR100 4.7 59.2 1.0 CB C:ASP98 4.7 47.1 1.0 CG C:GLU104 4.8 48.2 1.0 CA C:ASN119 4.9 41.4 1.0 CB C:GLU104 4.9 49.9 1.0 CA C:ASP98 4.9 50.2 1.0 N C:HIS99 5.0 54.0 1.0 O5 C:GAL137 5.0 60.7 1.0 N C:TYR100 5.0 57.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca4138 b:44.4 occ:1.00 O3 D:GAL137 2.3 60.3 1.0 OD1 D:ASP98 2.3 58.4 1.0 OE2 D:GLU104 2.4 47.3 1.0 O D:ASP120 2.6 42.8 1.0 OE1 D:GLN96 2.6 48.2 1.0 OD1 D:ASP120 2.6 45.7 1.0 O4 D:GAL137 2.7 61.5 1.0 OD1 D:ASN119 2.8 41.6 1.0 CG D:ASP120 3.2 47.4 1.0 C3 D:GAL137 3.3 62.5 1.0 C4 D:GAL137 3.3 61.6 1.0 CG D:ASP98 3.3 58.5 1.0 CD D:GLN96 3.5 49.4 1.0 CD D:GLU104 3.5 49.5 1.0 C D:ASP120 3.6 43.4 1.0 OD2 D:ASP120 3.6 48.9 1.0 CG D:ASN119 3.7 41.3 1.0 N D:ASP120 3.7 44.0 1.0 NE2 D:GLN96 3.8 49.9 1.0 OD2 D:ASP98 3.9 58.7 1.0 OE1 D:GLU104 4.0 49.3 1.0 CA D:ASP120 4.0 43.6 1.0 CB D:ASP120 4.1 46.2 1.0 N D:ASP98 4.1 56.3 1.0 C2 D:GAL137 4.1 62.7 1.0 ND2 D:ASN119 4.2 35.7 1.0 CB D:ASP98 4.5 58.2 1.0 C D:ASN119 4.6 43.8 1.0 CB D:TYR100 4.6 61.7 1.0 N D:TYR100 4.7 61.0 1.0 CG D:GLU104 4.7 50.1 1.0 N D:HIS99 4.7 61.1 1.0 CB D:GLU104 4.7 52.7 1.0 CA D:ASP98 4.7 58.7 1.0 N D:GLN121 4.7 43.4 1.0 CG D:GLN96 4.7 48.6 1.0 C5 D:GAL137 4.8 62.5 1.0 C D:ASP98 4.9 60.1 1.0 O2 D:GAL137 4.9 63.6 1.0 CB D:ASN119 4.9 41.1 1.0 CA D:ASN119 4.9 42.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca5138 b:20.3 occ:1.00 OD1 E:ASN119 2.3 16.5 1.0 OE2 E:GLU104 2.4 27.2 1.0 OD1 E:ASP120 2.5 18.9 1.0 O E:ASP120 2.5 20.5 1.0 OE1 E:GLN96 2.5 17.9 1.0 O4 E:GAL137 2.7 22.9 1.0 OD1 E:ASP98 2.7 24.5 1.0 O3 E:GAL137 2.7 26.3 1.0 CG E:ASN119 3.3 22.4 1.0 CD E:GLN96 3.4 19.2 1.0 CG E:ASP120 3.4 20.4 1.0 CD E:GLU104 3.4 25.8 1.0 C4 E:GAL137 3.5 24.5 1.0 CG E:ASP98 3.6 26.2 1.0 C3 E:GAL137 3.6 26.9 1.0 C E:ASP120 3.6 20.6 1.0 N E:ASP120 3.6 18.4 1.0 OE1 E:GLU104 3.7 27.5 1.0 ND2 E:ASN119 3.8 17.9 1.0 NE2 E:GLN96 3.8 17.6 1.0 OD2 E:ASP98 3.9 23.2 1.0 CA E:ASP120 4.0 20.7 1.0 OD2 E:ASP120 4.0 22.2 1.0 C2 E:GAL137 4.2 26.2 1.0 CB E:ASP120 4.3 20.3 1.0 N E:ASP98 4.3 24.2 1.0 C E:ASN119 4.5 19.7 1.0 CG E:GLN96 4.5 18.1 1.0 CB E:ASN119 4.6 20.2 1.0 CG E:GLU104 4.7 24.0 1.0 N E:GLN121 4.7 21.3 1.0 CB E:TYR100 4.8 25.9 1.0 CB E:ASP98 4.8 25.8 1.0 CA E:ASN119 4.8 20.8 1.0 CB E:GLU104 4.8 20.7 1.0 N E:TYR100 4.8 25.2 1.0 C5 E:GAL137 4.9 23.0 1.0 CB E:GLN96 4.9 18.4 1.0 N E:HIS99 4.9 23.1 1.0 CA E:ASP98 5.0 24.5 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