Calcium in PDB 7mg6: Concanavalin A Bound to A Dna Glycoconjugate, Man-Agct

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Agct, PDB code: 7mg6 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)	70.89 / 1.70
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	65.729, 70.89, 125.839, 90, 90, 90
R / Rfree (%)	17.7 / 20.7

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Agct also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Agct (pdb code 7mg6). 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 A Dna Glycoconjugate, Man-Agct, PDB code: 7mg6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Agct


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 A Dna Glycoconjugate, Man-Agct within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:21.0 occ:1.00 OD1 A:ASN14 2.3 20.5 1.0 O A:TYR12 2.3 21.8 1.0 OD2 A:ASP19 2.3 21.9 1.0 OD1 A:ASP10 2.4 19.8 1.0 OD2 A:ASP10 2.4 18.8 1.0 O A:HOH498 2.4 19.5 1.0 O A:HOH431 2.5 19.4 1.0 CG A:ASP10 2.7 16.4 1.0 CG A:ASP19 3.4 21.6 1.0 CG A:ASN14 3.5 24.1 1.0 C A:TYR12 3.5 20.5 1.0 OD1 A:ASP19 3.9 20.6 1.0 N A:ASN14 4.0 22.6 1.0 CB A:ASN14 4.1 24.4 1.0 MN A:MN301 4.1 20.8 1.0 CB A:ASP10 4.3 18.5 1.0 CA A:TYR12 4.4 20.8 1.0 N A:TYR12 4.5 19.8 1.0 N A:PRO13 4.5 22.7 1.0 O A:HOH428 4.5 22.1 1.0 CB A:TYR12 4.6 19.2 1.0 CE1 A:HIS24 4.6 21.7 1.0 O A:ASP208 4.6 18.7 1.0 ND2 A:ASN14 4.6 22.9 1.0 CA A:PRO13 4.6 24.4 1.0 C A:PRO13 4.6 25.1 1.0 OD1 A:ASP208 4.7 20.3 1.0 CA A:ASN14 4.7 22.6 1.0 CB A:ARG228 4.7 19.9 1.0 CB A:ASP19 4.7 23.3 1.0 CA A:ARG228 4.7 19.6 1.0 CD2 A:TYR12 4.9 21.4 1.0 O A:ARG228 4.9 19.6 1.0 NE2 A:HIS24 4.9 22.4 1.0

Calcium binding site 2 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Agct


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 A Dna Glycoconjugate, Man-Agct within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:22.1 occ:1.00 O B:TYR12 2.3 24.4 1.0 OD2 B:ASP19 2.3 23.7 1.0 OD1 B:ASN14 2.3 23.3 1.0 OD1 B:ASP10 2.4 21.4 1.0 O B:HOH494 2.4 22.2 1.0 OD2 B:ASP10 2.4 20.4 1.0 O B:HOH440 2.5 21.4 1.0 CG B:ASP10 2.7 16.6 1.0 CG B:ASP19 3.4 24.3 1.0 CG B:ASN14 3.5 26.4 1.0 C B:TYR12 3.5 20.3 1.0 OD1 B:ASP19 3.9 20.8 1.0 N B:ASN14 4.0 24.7 1.0 CB B:ASN14 4.1 26.3 1.0 MN B:MN301 4.1 22.8 1.0 CB B:ASP10 4.2 18.6 1.0 CA B:TYR12 4.3 23.2 1.0 N B:TYR12 4.4 22.6 1.0 N B:PRO13 4.5 25.5 1.0 CB B:TYR12 4.5 20.2 1.0 O B:HOH425 4.6 22.6 1.0 CA B:PRO13 4.6 25.8 1.0 O B:ASP208 4.6 21.7 1.0 ND2 B:ASN14 4.6 24.5 1.0 CE1 B:HIS24 4.6 23.7 1.0 C B:PRO13 4.6 26.8 1.0 CA B:ASN14 4.7 24.7 1.0 CB B:ASP19 4.7 24.6 1.0 OD1 B:ASP208 4.7 21.6 1.0 CB B:ARG228 4.8 23.0 1.0 CA B:ARG228 4.8 20.7 1.0 CD2 B:TYR12 4.8 22.8 1.0 O B:ARG228 4.9 19.0 1.0 NE2 B:HIS24 4.9 23.2 1.0

B.E.Partridge, P.H.Winegar, Z.Han, C.A.Mirkin. Redefining Protein Interfaces Within Protein Single Crystals with Dna J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.1C04191