Calcium in PDB 2zez: Family 16 Carbohydrate Binding Module-2

The structure of Family 16 Carbohydrate Binding Module-2, PDB code: 2zez was solved by B.Bae, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.425, 99.525, 139.390, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 27.2

The binding sites of Calcium atom in the Family 16 Carbohydrate Binding Module-2 (pdb code 2zez). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Family 16 Carbohydrate Binding Module-2, PDB code: 2zez:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Family 16 Carbohydrate Binding Module-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Family 16 Carbohydrate Binding Module-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:19.1 occ:1.00 O A:LYS36 2.3 28.9 1.0 O A:THR9 2.4 29.2 1.0 O A:HOH212 2.4 18.6 1.0 O A:GLY33 2.4 28.1 1.0 OD1 A:ASP137 2.5 29.6 1.0 OE2 A:GLU11 2.5 27.1 1.0 OD2 A:ASP137 2.6 28.4 1.0 CG A:ASP137 2.9 29.4 1.0 C A:THR9 3.5 29.8 1.0 C A:GLY33 3.5 28.8 1.0 C A:LYS36 3.6 27.4 1.0 CD A:GLU11 3.7 31.5 1.0 CA A:THR9 4.1 29.4 1.0 CB A:THR9 4.1 29.3 1.0 N A:LYS36 4.2 27.9 1.0 OD1 A:ASN138 4.3 37.7 1.0 CG A:GLU11 4.3 31.6 1.0 N A:GLY33 4.3 29.4 1.0 N A:GLY34 4.3 28.9 1.0 CA A:GLY34 4.4 28.7 1.0 CB A:ASP137 4.4 28.5 1.0 CA A:GLY33 4.4 29.1 1.0 N A:GLY37 4.5 26.6 1.0 CA A:GLY37 4.5 26.3 1.0 CA A:LYS36 4.5 27.8 1.0 N A:ALA10 4.6 29.6 1.0 O A:HOH219 4.6 29.0 1.0 N A:THR35 4.6 28.1 1.0 CB A:ALA10 4.7 29.8 1.0 OE1 A:GLU11 4.7 31.3 1.0 C A:GLY34 4.8 28.9 1.0 CB A:ALA31 4.9 29.2 1.0 CA A:ALA31 4.9 28.6 1.0 N A:TYR32 4.9 29.6 1.0 N A:GLU11 5.0 31.1 1.0 CA A:ALA10 5.0 29.9 1.0 OG1 A:THR9 5.0 28.1 1.0

Calcium binding site 2 out of 4 in the Family 16 Carbohydrate Binding Module-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Family 16 Carbohydrate Binding Module-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:21.0 occ:1.00 O B:LYS36 2.4 29.8 1.0 O B:THR9 2.4 27.9 1.0 O B:HOH231 2.4 19.0 1.0 O B:GLY33 2.4 28.7 1.0 OE2 B:GLU11 2.5 29.1 1.0 OD2 B:ASP137 2.6 28.9 1.0 OD1 B:ASP137 2.6 29.6 1.0 CG B:ASP137 3.0 29.8 1.0 C B:THR9 3.5 29.0 1.0 C B:GLY33 3.5 28.8 1.0 C B:LYS36 3.6 28.4 1.0 CD B:GLU11 3.7 30.9 1.0 CA B:THR9 4.1 29.2 1.0 CB B:THR9 4.1 29.3 1.0 N B:LYS36 4.2 27.5 1.0 OD1 B:ASN138 4.3 36.6 1.0 N B:GLY33 4.3 30.0 1.0 N B:GLY34 4.3 29.1 1.0 CA B:GLY34 4.4 27.8 1.0 CG B:GLU11 4.4 30.4 1.0 CA B:GLY33 4.4 29.4 1.0 CB B:ASP137 4.5 27.9 1.0 N B:GLY37 4.5 28.8 1.0 CA B:GLY37 4.5 28.1 1.0 CA B:LYS36 4.5 28.7 1.0 N B:THR35 4.6 27.3 1.0 N B:ALA10 4.6 28.8 1.0 OE1 B:GLU11 4.7 29.1 1.0 CB B:ALA31 4.8 28.1 1.0 CB B:ALA10 4.8 30.0 1.0 C B:GLY34 4.8 28.0 1.0 N B:TYR32 4.9 29.2 1.0 CA B:ALA31 4.9 28.3 1.0 N B:GLU11 5.0 29.7 1.0 OG1 B:THR9 5.0 28.5 1.0

Calcium binding site 3 out of 4 in the Family 16 Carbohydrate Binding Module-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Family 16 Carbohydrate Binding Module-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:21.4 occ:1.00 O C:LYS36 2.4 27.6 1.0 O C:GLY33 2.4 28.2 1.0 O C:HOH213 2.4 20.4 1.0 O C:THR9 2.5 30.3 1.0 OE2 C:GLU11 2.5 27.9 1.0 OD2 C:ASP137 2.6 32.3 1.0 OD1 C:ASP137 2.6 31.3 1.0 CG C:ASP137 2.9 30.2 1.0 C C:GLY33 3.5 28.7 1.0 C C:THR9 3.6 30.2 1.0 C C:LYS36 3.6 28.3 1.0 CD C:GLU11 3.7 31.8 1.0 CA C:THR9 4.2 29.9 1.0 CB C:THR9 4.2 29.7 1.0 N C:LYS36 4.2 28.6 1.0 N C:GLY33 4.2 28.3 1.0 CG C:GLU11 4.3 33.1 1.0 N C:GLY34 4.3 28.9 1.0 CA C:GLY34 4.3 29.4 1.0 OD1 C:ASN138 4.4 35.8 1.0 CA C:GLY33 4.4 29.0 1.0 CB C:ASP137 4.4 28.5 1.0 N C:GLY37 4.5 27.4 1.0 CA C:LYS36 4.5 28.8 1.0 CA C:GLY37 4.5 26.5 1.0 O C:HOH216 4.5 27.9 1.0 N C:THR35 4.6 29.4 1.0 CB C:ALA31 4.7 28.0 1.0 OE1 C:GLU11 4.7 33.7 1.0 N C:ALA10 4.7 29.9 1.0 C C:GLY34 4.7 30.3 1.0 CB C:ALA10 4.8 30.0 1.0 CA C:ALA31 4.8 28.6 1.0 N C:TYR32 4.9 28.5 1.0 OG1 C:THR9 5.0 28.9 1.0

Calcium binding site 4 out of 4 in the Family 16 Carbohydrate Binding Module-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Family 16 Carbohydrate Binding Module-2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca200 b:23.4 occ:1.00 O D:HOH206 2.3 21.0 1.0 O D:LYS36 2.4 27.3 1.0 OE2 D:GLU11 2.4 31.7 1.0 O D:GLY33 2.4 27.5 1.0 O D:THR9 2.4 29.4 1.0 OD2 D:ASP137 2.6 29.4 1.0 OD1 D:ASP137 2.7 30.6 1.0 CG D:ASP137 3.0 29.6 1.0 C D:GLY33 3.5 28.7 1.0 C D:THR9 3.6 30.2 1.0 CD D:GLU11 3.6 33.5 1.0 C D:LYS36 3.6 28.7 1.0 CB D:THR9 4.1 29.4 1.0 CA D:THR9 4.1 29.6 1.0 CG D:GLU11 4.2 33.0 1.0 N D:LYS36 4.2 28.1 1.0 N D:GLY33 4.3 27.9 1.0 CA D:GLY34 4.3 29.4 1.0 N D:GLY34 4.3 29.4 1.0 CA D:GLY33 4.4 28.6 1.0 OD1 D:ASN138 4.4 37.9 1.0 N D:GLY37 4.5 28.0 1.0 CA D:LYS36 4.5 29.1 1.0 CA D:GLY37 4.5 28.0 1.0 CB D:ASP137 4.5 28.8 1.0 OE1 D:GLU11 4.6 36.9 1.0 N D:THR35 4.7 29.2 1.0 N D:ALA10 4.7 30.4 1.0 CB D:ALA10 4.7 31.0 1.0 CB D:ALA31 4.7 27.8 1.0 C D:GLY34 4.8 29.8 1.0 O D:HOH237 4.8 41.3 1.0 N D:TYR32 4.8 26.7 1.0 CA D:ALA31 4.9 27.4 1.0 OG1 D:THR9 5.0 27.0 1.0

B.Bae, S.Ohene-Adjei, S.Kocherginskaya, R.I.Mackie, M.A.Spies, I.K.Cann, S.K.Nair. Molecular Basis For the Selectivity and Specificity of Ligand Recognition By the Family 16 Carbohydrate-Binding Modules From Thermoanaerobacterium Polysaccharolyticum Mana J.Biol.Chem. V. 283 12415 2008.
ISSN: ISSN 0021-9258
PubMed: 18025086
DOI: 10.1074/JBC.M706513200