Calcium in PDB 7mgb: Concanavalin A Bound to A Dna Glycoconjugate, A(Man-T)at

The structure of Concanavalin A Bound to A Dna Glycoconjugate, A(Man-T)at, PDB code: 7mgb 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)	84.79 / 2.45
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.009, 117.48, 122.49, 90, 90, 90
R / Rfree (%)	21.3 / 26.2

The structure of Concanavalin A Bound to A Dna Glycoconjugate, A(Man-T)at 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, A(Man-T)at (pdb code 7mgb). 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, A(Man-T)at, PDB code: 7mgb:
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, A(Man-T)at


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, A(Man-T)at within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:33.8 occ:1.00 O A:HOH403 2.0 22.8 1.0 O A:HOH406 2.2 17.7 1.0 O A:TYR12 2.3 36.3 1.0 OD1 A:ASN14 2.3 41.6 1.0 OD1 A:ASP10 2.4 27.8 1.0 OD2 A:ASP19 2.4 38.6 1.0 OD2 A:ASP10 2.5 24.6 1.0 CG A:ASP10 2.8 29.6 1.0 CG A:ASN14 3.5 41.0 1.0 C A:TYR12 3.5 36.0 1.0 CG A:ASP19 3.6 42.6 1.0 N A:ASN14 3.9 37.0 1.0 CB A:ASN14 4.1 39.9 1.0 MN A:MN302 4.2 37.6 1.0 OD1 A:ASP19 4.2 38.9 1.0 O A:HOH413 4.3 27.1 1.0 CB A:ASP10 4.3 29.2 1.0 CA A:TYR12 4.4 37.9 1.0 N A:PRO13 4.4 38.3 1.0 CA A:PRO13 4.4 37.3 1.0 N A:TYR12 4.5 40.5 1.0 ND2 A:ASN14 4.5 43.4 1.0 C A:PRO13 4.5 36.6 1.0 CE1 A:HIS24 4.5 31.7 1.0 CB A:TYR12 4.6 38.0 1.0 OD1 A:ASP208 4.7 39.9 1.0 CA A:ASN14 4.7 40.6 1.0 CB A:ASP19 4.7 45.9 1.0 O A:ASP208 4.7 33.3 1.0 O A:ARG228 4.8 31.4 1.0 CA A:ARG228 4.8 39.0 1.0 NE2 A:HIS24 4.8 29.4 1.0 CB A:ARG228 4.9 47.0 1.0

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


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, A(Man-T)at within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:37.6 occ:1.00 O B:TYR12 2.2 37.5 1.0 OD1 B:ASP10 2.3 38.4 1.0 OD2 B:ASP19 2.4 34.2 1.0 O B:HOH409 2.4 25.6 1.0 OD1 B:ASN14 2.4 42.9 1.0 OD2 B:ASP10 2.5 27.5 1.0 CG B:ASP10 2.7 31.1 1.0 C B:TYR12 3.4 39.2 1.0 CG B:ASN14 3.6 41.4 1.0 CG B:ASP19 3.6 46.1 1.0 N B:ASN14 4.0 46.3 1.0 MN B:MN302 4.0 39.0 1.0 OD1 B:ASP19 4.1 44.4 1.0 CB B:ASP10 4.2 31.1 1.0 CB B:ASN14 4.3 41.1 1.0 CA B:TYR12 4.3 35.8 1.0 N B:TYR12 4.4 34.3 1.0 N B:PRO13 4.4 38.9 1.0 CB B:TYR12 4.5 35.6 1.0 CA B:PRO13 4.5 38.2 1.0 CE1 B:HIS24 4.5 29.9 1.0 O B:ASP208 4.5 35.6 1.0 ND2 B:ASN14 4.6 47.3 1.0 OD1 B:ASP208 4.6 48.0 1.0 C B:PRO13 4.6 42.0 1.0 O B:ARG228 4.8 31.4 1.0 CB B:ASP19 4.8 48.8 1.0 O B:HOH404 4.8 24.5 1.0 CA B:ASN14 4.8 43.4 1.0 CA B:ARG228 4.9 35.6 1.0 NE2 B:HIS24 4.9 26.4 1.0 CA B:ASP10 5.0 30.1 1.0

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


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, A(Man-T)at within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:35.5 occ:1.00 OD2 C:ASP19 2.3 35.6 1.0 OD1 C:ASN14 2.3 44.7 1.0 O C:TYR12 2.3 35.1 1.0 O C:HOH402 2.3 27.7 1.0 O C:HOH409 2.4 24.5 1.0 OD1 C:ASP10 2.5 30.9 1.0 OD2 C:ASP10 2.5 32.3 1.0 CG C:ASP10 2.8 34.3 1.0 CG C:ASN14 3.4 35.7 1.0 CG C:ASP19 3.5 39.0 1.0 C C:TYR12 3.5 38.1 1.0 N C:ASN14 3.9 38.2 1.0 OD1 C:ASP19 4.0 39.2 1.0 CB C:ASN14 4.1 35.4 1.0 MN C:MN302 4.1 37.5 1.0 CB C:ASP10 4.3 33.8 1.0 CA C:TYR12 4.4 38.9 1.0 N C:PRO13 4.4 38.1 1.0 CA C:PRO13 4.5 39.5 1.0 ND2 C:ASN14 4.5 38.2 1.0 N C:TYR12 4.5 38.6 1.0 C C:PRO13 4.5 38.6 1.0 CE1 C:HIS24 4.5 27.6 1.0 CB C:TYR12 4.6 45.0 1.0 OD1 C:ASP208 4.6 38.5 1.0 CA C:ASN14 4.6 39.9 1.0 CB C:ASP19 4.7 40.9 1.0 O C:ASP208 4.7 31.6 1.0 O C:ARG228 4.7 34.0 1.0 CA C:ARG228 4.8 39.8 1.0 NE2 C:HIS24 4.9 26.8 1.0 CB C:ARG228 4.9 44.4 1.0

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


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, A(Man-T)at within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:30.0 occ:1.00 O D:TYR12 2.2 38.9 1.0 OD1 D:ASN14 2.3 38.1 1.0 O D:HOH403 2.3 19.0 1.0 OD2 D:ASP19 2.3 39.3 1.0 OD1 D:ASP10 2.4 33.7 1.0 O D:HOH404 2.5 22.7 1.0 OD2 D:ASP10 2.6 33.6 1.0 CG D:ASP10 2.8 34.4 1.0 CG D:ASN14 3.4 42.0 1.0 C D:TYR12 3.4 39.3 1.0 CG D:ASP19 3.5 46.2 1.0 N D:ASN14 3.8 43.6 1.0 OD1 D:ASP19 4.1 49.7 1.0 CB D:ASN14 4.1 43.3 1.0 MN D:MN302 4.3 40.8 1.0 CA D:TYR12 4.3 38.9 1.0 CB D:ASP10 4.4 34.6 1.0 N D:PRO13 4.4 43.5 1.0 O D:HOH408 4.4 20.0 1.0 CA D:PRO13 4.4 46.6 1.0 N D:TYR12 4.4 32.3 1.0 C D:PRO13 4.5 45.2 1.0 ND2 D:ASN14 4.5 42.6 1.0 CB D:TYR12 4.5 42.8 1.0 CE1 D:HIS24 4.5 31.2 1.0 OD1 D:ASP208 4.6 39.7 1.0 CA D:ASN14 4.6 44.2 1.0 CB D:ASP19 4.7 46.9 1.0 O D:ASP208 4.7 36.2 1.0 CA D:ARG228 4.8 41.5 1.0 O D:ARG228 4.8 36.1 1.0 NE2 D:HIS24 4.9 26.7 1.0 CB D:ARG228 4.9 46.4 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