Calcium in PDB 7mg9: Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa

The structure of Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa, PDB code: 7mg9 was solved by B.E.Partridge, P.H.Winegar, C.A.Mirkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.18 / 2.55
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	65.979, 70.18, 124.42, 90, 90, 90
R / Rfree (%)	25 / 31.4

The structure of Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa (pdb code 7mg9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa, PDB code: 7mg9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:35.2 occ:1.00 OD2 A:ASP19 2.3 35.6 1.0 OD1 A:ASN14 2.3 32.6 1.0 OD1 A:ASP10 2.3 35.9 1.0 O A:TYR12 2.3 34.5 1.0 OD2 A:ASP10 2.4 32.3 1.0 CG A:ASP10 2.6 33.7 1.0 CG A:ASN14 3.4 36.4 1.0 CG A:ASP19 3.5 34.7 1.0 C A:TYR12 3.5 34.9 1.0 N A:ASN14 4.0 37.3 1.0 CB A:ASN14 4.0 37.8 1.0 OD1 A:ASP208 4.0 39.5 1.0 MN A:MN301 4.1 40.4 1.0 OD1 A:ASP19 4.1 37.3 1.0 CB A:ASP10 4.2 38.0 1.0 CA A:TYR12 4.4 33.8 1.0 N A:PRO13 4.5 40.4 1.0 CB A:TYR12 4.5 34.3 1.0 N A:TYR12 4.5 35.1 1.0 ND2 A:ASN14 4.5 38.8 1.0 CA A:PRO13 4.5 38.7 1.0 C A:PRO13 4.6 36.6 1.0 CE1 A:HIS24 4.6 28.1 1.0 CB A:ASP19 4.6 35.3 1.0 CA A:ARG228 4.6 30.7 1.0 O A:ASP208 4.6 31.2 1.0 CA A:ASN14 4.7 36.5 1.0 O A:ARG228 4.7 33.9 1.0 CB A:ARG228 4.9 33.1 1.0 CD2 A:TYR12 4.9 32.7 1.0

Calcium binding site 2 out of 2 in the Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A Bound to Dna Glycoconjugates, Man-Tttt and Man-Aaaa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:34.5 occ:1.00 OD1 B:ASP10 2.3 34.6 1.0 O B:TYR12 2.3 35.7 1.0 OD1 B:ASN14 2.3 35.9 1.0 OD2 B:ASP19 2.3 37.7 1.0 O B:HOH419 2.4 28.9 1.0 OD2 B:ASP10 2.4 32.1 1.0 CG B:ASP10 2.6 33.5 1.0 CG B:ASN14 3.4 36.0 1.0 C B:TYR12 3.5 37.7 1.0 CG B:ASP19 3.6 39.9 1.0 N B:ASN14 4.0 34.5 1.0 CB B:ASN14 4.0 35.2 1.0 OD1 B:ASP208 4.1 35.1 1.0 MN B:MN301 4.1 39.1 1.0 CB B:ASP10 4.2 35.4 1.0 OD1 B:ASP19 4.2 42.3 1.0 CA B:TYR12 4.4 36.3 1.0 N B:PRO13 4.4 37.4 1.0 N B:TYR12 4.5 33.8 1.0 CB B:TYR12 4.5 37.0 1.0 CA B:PRO13 4.5 38.8 1.0 O B:ASP208 4.5 31.3 1.0 ND2 B:ASN14 4.5 36.8 1.0 C B:PRO13 4.6 36.7 1.0 CE1 B:HIS24 4.6 25.4 1.0 CB B:ASP19 4.6 39.5 1.0 CA B:ASN14 4.7 35.2 1.0 O B:HOH407 4.7 15.4 1.0 CA B:ARG228 4.7 35.4 1.0 O B:ARG228 4.8 33.0 1.0 CD2 B:TYR12 5.0 36.2 1.0 CA B:ASP10 5.0 33.6 1.0

B.E.Partridge, P.H.Winegar, Z.Han, C.A.Mirkin. Redefining Protein Interfaces Within Protein Single Crystals with Dna Journal of the American 2021CHEMICAL Society.
DOI: 10.1021/JACS.1C04191