Calcium in PDB 7mgc: Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac

The structure of Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac, PDB code: 7mgc 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)	84.70 / 2.92
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.33, 117.34, 122.4, 90, 90, 90
R / Rfree (%)	22.9 / 27.7

The structure of Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac (pdb code 7mgc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac, PDB code: 7mgc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac


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, G(Man-T)Ac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:47.5 occ:1.00 OD1 A:ASN14 2.0 73.0 1.0 OD1 A:ASP10 2.4 46.4 1.0 OD2 A:ASP19 2.4 59.4 1.0 O A:TYR12 2.5 43.2 1.0 OD2 A:ASP10 2.7 35.6 1.0 CG A:ASP10 2.9 43.5 1.0 CG A:ASN14 3.2 68.0 1.0 CG A:ASP19 3.6 67.1 1.0 C A:TYR12 3.7 51.5 1.0 N A:ASN14 4.1 66.2 1.0 CB A:ASN14 4.1 72.3 1.0 ND2 A:ASN14 4.1 67.5 1.0 OD1 A:ASP19 4.2 66.9 1.0 CB A:ASP10 4.4 44.0 1.0 CB A:TYR12 4.4 64.9 1.0 CA A:TYR12 4.4 55.8 1.0 MN A:MN302 4.4 72.4 1.0 O A:ASP208 4.4 45.8 1.0 N A:TYR12 4.5 54.3 1.0 CB A:ARG228 4.5 62.9 1.0 CA A:ARG228 4.5 55.2 1.0 O A:ARG228 4.6 46.8 1.0 N A:PRO13 4.7 51.8 1.0 CA A:ASN14 4.7 73.9 1.0 CE1 A:HIS24 4.7 47.4 1.0 CB A:ASP19 4.8 65.7 1.0 C A:PRO13 4.8 59.6 1.0 CA A:PRO13 4.8 56.1 1.0 O A:HOH401 4.9 40.5 1.0

Calcium binding site 2 out of 4 in the Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac


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, G(Man-T)Ac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:45.5 occ:1.00 OD1 B:ASN14 2.0 88.3 1.0 OD2 B:ASP19 2.4 43.7 1.0 OD1 B:ASP10 2.4 37.9 1.0 O B:TYR12 2.4 48.8 1.0 OD2 B:ASP10 2.7 35.7 1.0 CG B:ASP10 2.9 39.9 1.0 CG B:ASN14 3.2 78.9 1.0 CG B:ASP19 3.6 52.2 1.0 C B:TYR12 3.6 55.1 1.0 N B:ASN14 4.1 71.0 1.0 CB B:ASN14 4.1 76.0 1.0 ND2 B:ASN14 4.1 79.3 1.0 OD1 B:ASP19 4.2 53.7 1.0 CB B:ASP10 4.4 44.1 1.0 CA B:TYR12 4.4 56.8 1.0 CB B:TYR12 4.4 62.9 1.0 MN B:MN302 4.4 60.0 1.0 N B:TYR12 4.5 61.2 1.0 O B:ASP208 4.5 56.0 1.0 CA B:ARG228 4.6 49.0 1.0 N B:PRO13 4.6 64.5 1.0 O B:ARG228 4.6 46.1 1.0 CE1 B:HIS24 4.7 55.3 1.0 CB B:ASP19 4.7 55.4 1.0 CA B:ASN14 4.7 72.4 1.0 C B:PRO13 4.8 69.0 1.0 CA B:PRO13 4.8 66.0 1.0

Calcium binding site 3 out of 4 in the Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:57.0 occ:1.00 OD1 C:ASN14 2.1 74.4 1.0 OD1 C:ASP10 2.3 51.5 1.0 OD2 C:ASP19 2.4 54.5 1.0 O C:TYR12 2.4 61.7 1.0 OD2 C:ASP10 2.6 50.5 1.0 CG C:ASP10 2.8 48.5 1.0 CG C:ASN14 3.3 64.4 1.0 CG C:ASP19 3.6 62.3 1.0 C C:TYR12 3.6 62.2 1.0 N C:ASN14 4.1 61.5 1.0 CB C:ASN14 4.2 63.9 1.0 OD1 C:ASP19 4.2 65.7 1.0 ND2 C:ASN14 4.2 56.0 1.0 CB C:ASP10 4.2 45.4 1.0 MN C:MN302 4.3 64.3 1.0 CA C:TYR12 4.3 59.7 1.0 O C:ASP208 4.4 58.8 1.0 CB C:TYR12 4.4 66.5 1.0 N C:TYR12 4.4 55.0 1.0 N C:PRO13 4.6 65.3 1.0 CE1 C:HIS24 4.6 58.3 1.0 CA C:ARG228 4.7 69.0 1.0 O C:ARG228 4.7 58.6 1.0 CB C:ARG228 4.7 73.1 1.0 CB C:ASP19 4.7 61.8 1.0 CA C:ASN14 4.8 65.7 1.0 CA C:PRO13 4.8 65.5 1.0 C C:PRO13 4.8 61.2 1.0 CA C:ASP10 4.9 43.9 1.0 NE2 C:HIS24 5.0 52.1 1.0

Calcium binding site 4 out of 4 in the Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Concanavalin A Bound to A Dna Glycoconjugate, G(Man-T)Ac within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:49.1 occ:1.00 OD1 D:ASN14 2.0 66.3 1.0 OD1 D:ASP10 2.4 58.9 1.0 OD2 D:ASP19 2.5 38.8 1.0 O D:TYR12 2.6 43.1 1.0 OD2 D:ASP10 2.7 49.2 1.0 CG D:ASP10 2.9 50.7 1.0 CG D:ASN14 3.2 60.8 1.0 CG D:ASP19 3.7 47.7 1.0 C D:TYR12 3.8 49.1 1.0 ND2 D:ASN14 4.1 55.0 1.0 CB D:ASN14 4.1 60.3 1.0 N D:ASN14 4.2 57.2 1.0 OD1 D:ASP19 4.2 49.5 1.0 MN D:MN302 4.3 47.5 1.0 CB D:ASP10 4.4 47.8 1.0 O D:ASP208 4.4 57.6 1.0 CA D:ARG228 4.4 63.4 1.0 O D:ARG228 4.4 45.6 1.0 CB D:TYR12 4.5 57.5 1.0 CA D:TYR12 4.5 50.6 1.0 CB D:ARG228 4.5 67.5 1.0 N D:TYR12 4.6 47.3 1.0 CA D:ASN14 4.8 60.0 1.0 N D:PRO13 4.8 52.9 1.0 CE1 D:HIS24 4.8 45.4 1.0 CB D:ASP19 4.8 50.9 1.0 C D:PRO13 4.9 55.8 1.0 C D:ARG228 5.0 52.9 1.0 CA D:PRO13 5.0 54.7 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