Calcium in PDB 6ahg: Trimeric Structure of Concanavalin A From Canavalia Ensiformis

The structure of Trimeric Structure of Concanavalin A From Canavalia Ensiformis, PDB code: 6ahg was solved by J.H.Park, D.S.Kim, Y.R.Park, S.J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.29 / 2.83
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	136.461, 136.461, 193.146, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 27.9

The structure of Trimeric Structure of Concanavalin A From Canavalia Ensiformis also contains other interesting chemical elements:

Cadmium

(Cd)

6 atoms

The binding sites of Calcium atom in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis (pdb code 6ahg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis, PDB code: 6ahg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:17.1 occ:1.00 O A:HOH406 2.3 39.2 1.0 OD1 A:ASP10 2.4 41.2 1.0 OD1 A:ASN14 2.4 48.6 1.0 O A:TYR12 2.5 46.4 1.0 OD2 A:ASP19 2.6 46.8 1.0 OD2 A:ASP10 3.0 41.9 1.0 CG A:ASP10 3.1 41.9 1.0 CG A:ASN14 3.5 48.0 1.0 C A:TYR12 3.7 47.0 1.0 CG A:ASP19 3.8 48.0 1.0 CB A:ASN14 3.9 48.2 1.0 N A:ASN14 4.1 49.5 1.0 CD A:CD302 4.4 39.6 1.0 OD1 A:ASP208 4.4 59.4 1.0 CA A:TYR12 4.4 46.5 1.0 OD1 A:ASP19 4.4 49.5 1.0 CB A:TYR12 4.5 47.0 1.0 N A:TYR12 4.5 45.2 1.0 CB A:ASP10 4.6 42.0 1.0 O A:HOH404 4.6 31.0 1.0 CA A:ASN14 4.6 48.6 1.0 ND2 A:ASN14 4.7 48.5 1.0 O A:ARG228 4.7 46.8 1.0 N A:PRO13 4.7 48.5 1.0 CE1 A:HIS24 4.7 39.8 1.0 C A:PRO13 4.7 49.6 1.0 CB A:ASP19 4.8 47.7 1.0 CA A:PRO13 4.8 48.8 1.0 CA A:ARG228 4.9 46.3 1.0 CA A:ASP208 4.9 59.5 1.0 CB A:ARG228 4.9 45.8 1.0

Calcium binding site 2 out of 3 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:16.8 occ:1.00 O B:HOH407 2.3 44.7 1.0 OD1 B:ASP10 2.4 41.0 1.0 OD1 B:ASN14 2.4 48.5 1.0 O B:TYR12 2.5 46.1 1.0 OD2 B:ASP19 2.6 47.2 1.0 OD2 B:ASP10 3.1 42.0 1.0 CG B:ASP10 3.1 41.9 1.0 CG B:ASN14 3.5 48.2 1.0 C B:TYR12 3.6 46.6 1.0 CG B:ASP19 3.8 48.8 1.0 CB B:ASN14 3.9 48.1 1.0 N B:ASN14 4.0 48.7 1.0 CA B:TYR12 4.4 46.4 1.0 CB B:TYR12 4.4 47.6 1.0 CD B:CD302 4.5 41.6 1.0 OD1 B:ASP19 4.5 50.6 1.0 N B:TYR12 4.5 45.2 1.0 OD1 B:ASP208 4.5 60.0 1.0 O B:HOH404 4.6 37.8 1.0 CB B:ASP10 4.6 41.8 1.0 CA B:ASN14 4.6 48.3 1.0 ND2 B:ASN14 4.7 48.8 1.0 N B:PRO13 4.7 47.7 1.0 O B:ARG228 4.7 45.7 1.0 C B:PRO13 4.7 48.5 1.0 CE1 B:HIS24 4.7 39.0 1.0 CA B:PRO13 4.8 47.9 1.0 CB B:ASP19 4.8 48.6 1.0 CA B:ARG228 4.9 45.3 1.0 CA B:ASP208 4.9 59.2 1.0 O B:ASP208 4.9 58.0 1.0 CB B:ARG228 4.9 45.1 1.0 CD2 B:TYR12 5.0 49.7 1.0

Calcium binding site 3 out of 3 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:18.5 occ:1.00 O C:HOH405 2.2 35.1 1.0 OD1 C:ASP10 2.3 40.8 1.0 ND2 C:ASN14 2.4 49.4 1.0 O C:TYR12 2.5 47.8 1.0 OD2 C:ASP19 2.5 50.3 1.0 OD2 C:ASP10 3.0 41.4 1.0 CG C:ASP10 3.1 41.4 1.0 CG C:ASN14 3.5 49.0 1.0 C C:TYR12 3.7 47.7 1.0 CG C:ASP19 3.7 51.0 1.0 CB C:ASN14 3.9 48.5 1.0 N C:ASN14 4.0 48.8 1.0 OD1 C:ASP19 4.4 52.8 1.0 CD C:CD302 4.4 42.2 1.0 CA C:TYR12 4.4 47.2 1.0 O C:HOH404 4.5 39.1 1.0 N C:TYR12 4.5 45.6 1.0 CB C:ASP10 4.5 41.0 1.0 OD1 C:ASP208 4.6 58.3 1.0 CA C:ASN14 4.6 48.4 1.0 CB C:TYR12 4.6 48.0 1.0 OD1 C:ASN14 4.6 50.2 1.0 N C:PRO13 4.7 48.6 1.0 C C:PRO13 4.7 48.9 1.0 CE1 C:HIS24 4.7 39.7 1.0 O C:ARG228 4.7 45.4 1.0 CA C:PRO13 4.8 48.6 1.0 CB C:ASP19 4.8 50.3 1.0 CA C:ARG228 4.9 44.8 1.0 CA C:ASP208 5.0 58.3 1.0 CB C:ARG228 5.0 44.7 1.0

Y.R.Park, D.S.Kim, D.H.Lee, H.G.Kang, J.H.Park, S.J.Lee. Cadmium-Substituted Concanavalin A and Its Trimeric Complexation J. Microbiol. Biotechnol. V.(12) 2106 2018.
ISSN: ISSN 1017-7825
PubMed: 30380822
DOI: 10.4014/JMB.1809.09027