Calcium in PDB 5ygm: Monomeric Structure of Concanavalin A at pH 7.5 From Carnivalia Ensiformis

The structure of Monomeric Structure of Concanavalin A at pH 7.5 From Carnivalia Ensiformis, PDB code: 5ygm was solved by J.H.Park, 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)	44.76 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.303, 86.590, 89.511, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.6

The structure of Monomeric Structure of Concanavalin A at pH 7.5 From Carnivalia Ensiformis also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Monomeric Structure of Concanavalin A at pH 7.5 From Carnivalia Ensiformis (pdb code 5ygm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Monomeric Structure of Concanavalin A at pH 7.5 From Carnivalia Ensiformis, PDB code: 5ygm:

Calcium binding site 1 out of 1 in the Monomeric Structure of Concanavalin A at pH 7.5 From Carnivalia Ensiformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Monomeric Structure of Concanavalin A at pH 7.5 From Carnivalia Ensiformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:12.8 occ:1.00 OD1 A:ASN14 2.3 14.5 1.0 OD2 A:ASP19 2.4 14.1 1.0 O A:HOH452 2.4 12.8 1.0 O A:TYR12 2.4 14.6 1.0 O A:HOH496 2.5 14.7 1.0 OD1 A:ASP10 2.5 12.7 1.0 OD2 A:ASP10 2.5 12.1 1.0 CG A:ASP10 2.8 12.8 1.0 CG A:ASN14 3.5 15.6 1.0 CG A:ASP19 3.5 14.6 1.0 C A:TYR12 3.6 12.1 1.0 OD1 A:ASP19 3.9 12.9 1.0 N A:ASN14 3.9 15.4 1.0 CB A:ASN14 4.2 16.4 1.0 MN A:MN301 4.2 13.5 1.0 CB A:ASP10 4.4 11.2 1.0 N A:TYR12 4.4 12.4 1.0 CA A:TYR12 4.4 12.6 1.0 ND2 A:ASN14 4.5 14.8 1.0 CB A:TYR12 4.6 12.1 1.0 O A:HOH441 4.6 14.7 1.0 N A:PRO13 4.6 14.0 1.0 CE1 A:HIS24 4.6 13.2 1.0 CA A:PRO13 4.6 16.4 1.0 C A:PRO13 4.7 18.4 1.0 O A:ASP208 4.7 11.8 1.0 CA A:ASN14 4.7 14.8 1.0 OD1 A:ASP208 4.7 14.2 1.0 CB A:ASP19 4.8 13.4 1.0 CB A:ARG228 4.8 15.0 1.0 O A:ARG228 4.8 15.1 1.0 CA A:ARG228 4.9 13.0 1.0 NE2 A:HIS24 4.9 12.9 1.0

N.J.Chung, Y.R.Park, D.H.Lee, S.Y.Oh, J.H.Park, S.J.Lee. Heterometal-Coordinated Monomeric Concanavalin A at pH 7.5 From Canavalia Ensiformis J. Microbiol. Biotechnol. V. 27 2241 2017.
ISSN: ESSN 1738-8872
PubMed: 29025256
DOI: 10.4014/JMB.1709.09057