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

The structure of Concanavalin A Bound to A Dna Glycoconjugate, T(Man-T)Tt, PDB code: 7mgd 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)	60.53 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.56, 63.97, 126.45, 90, 93.3, 90
R / Rfree (%)	21 / 25.5

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


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, T(Man-T)Tt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:28.6 occ:1.00 O A:HOH441 2.3 21.5 1.0 O A:TYR12 2.3 31.0 1.0 O A:HOH462 2.3 26.1 1.0 OD2 A:ASP19 2.4 28.8 1.0 OD1 A:ASP10 2.4 27.4 1.0 OD1 A:ASN14 2.6 29.5 1.0 OD2 A:ASP10 2.6 23.7 1.0 CG A:ASP10 2.8 26.2 1.0 C A:TYR12 3.5 29.9 1.0 CG A:ASP19 3.5 31.5 1.0 CG A:ASN14 3.7 33.0 1.0 N A:ASN14 3.9 32.0 1.0 OD1 A:ASP19 4.0 27.7 1.0 MN A:MN301 4.1 36.2 1.0 CB A:ASN14 4.2 33.1 1.0 CB A:ASP10 4.3 27.5 1.0 CA A:TYR12 4.4 32.8 1.0 N A:PRO13 4.4 31.9 1.0 O A:HOH466 4.5 27.4 1.0 CA A:PRO13 4.5 31.7 1.0 N A:TYR12 4.5 31.5 1.0 C A:PRO13 4.5 35.9 1.0 CB A:TYR12 4.5 35.9 1.0 CE1 A:HIS24 4.6 27.7 1.0 CB A:ARG228 4.6 34.7 1.0 O A:ASP208 4.6 32.0 1.0 CA A:ARG228 4.7 33.6 1.0 OD2 A:ASP208 4.7 31.2 1.0 O A:ARG228 4.7 30.7 1.0 CA A:ASN14 4.7 34.0 1.0 CB A:ASP19 4.8 33.0 1.0 ND2 A:ASN14 4.8 28.4 1.0 NE2 A:HIS24 4.9 27.1 1.0 CD2 A:TYR12 4.9 39.1 1.0

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


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, T(Man-T)Tt within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:31.6 occ:1.00 O B:HOH483 2.1 27.2 1.0 O B:TYR12 2.2 34.7 1.0 O B:HOH453 2.3 31.1 1.0 OD2 B:ASP19 2.4 33.9 1.0 OD1 B:ASP10 2.4 28.8 1.0 OD1 B:ASN14 2.5 32.7 1.0 OD2 B:ASP10 2.6 27.0 1.0 CG B:ASP10 2.8 31.6 1.0 C B:TYR12 3.4 34.6 1.0 CG B:ASP19 3.5 38.1 1.0 CG B:ASN14 3.6 36.5 1.0 N B:ASN14 3.9 35.9 1.0 OD1 B:ASP19 4.1 35.1 1.0 CB B:ASN14 4.2 35.4 1.0 MN B:MN301 4.2 37.6 1.0 CA B:TYR12 4.3 40.3 1.0 CB B:ASP10 4.4 30.1 1.0 N B:PRO13 4.4 38.6 1.0 CA B:PRO13 4.4 38.2 1.0 N B:TYR12 4.5 36.5 1.0 C B:PRO13 4.5 40.7 1.0 CB B:TYR12 4.5 41.8 1.0 O B:HOH448 4.5 25.9 1.0 CE1 B:HIS24 4.6 31.1 1.0 CB B:ARG228 4.6 34.2 1.0 O B:ASP208 4.6 31.9 1.0 OD2 B:ASP208 4.6 28.1 1.0 CA B:ARG228 4.7 35.3 1.0 CA B:ASN14 4.7 37.2 1.0 ND2 B:ASN14 4.7 32.7 1.0 CB B:ASP19 4.7 38.9 1.0 O B:ARG228 4.8 33.7 1.0 CD2 B:TYR12 4.9 48.9 1.0 NE2 B:HIS24 4.9 30.6 1.0

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


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, T(Man-T)Tt within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:35.2 occ:1.00 O C:TYR12 2.3 36.0 1.0 O C:HOH450 2.3 30.5 1.0 O C:HOH436 2.4 33.8 1.0 OD2 C:ASP19 2.4 34.1 1.0 OD1 C:ASP10 2.4 29.7 1.0 OD1 C:ASN14 2.5 40.2 1.0 OD2 C:ASP10 2.7 29.3 1.0 CG C:ASP10 2.9 32.1 1.0 C C:TYR12 3.5 37.9 1.0 CG C:ASP19 3.6 35.2 1.0 CG C:ASN14 3.6 49.0 1.0 N C:ASN14 3.9 48.2 1.0 OD1 C:ASP19 4.1 30.0 1.0 MN C:MN301 4.1 40.1 1.0 CB C:ASN14 4.2 46.4 1.0 CA C:TYR12 4.3 39.8 1.0 CB C:ASP10 4.4 29.8 1.0 N C:PRO13 4.4 37.7 1.0 CB C:TYR12 4.5 43.5 1.0 N C:TYR12 4.5 37.5 1.0 CA C:PRO13 4.5 41.4 1.0 C C:PRO13 4.5 48.2 1.0 O C:ASP208 4.6 34.6 1.0 CB C:ARG228 4.6 41.8 1.0 OD2 C:ASP208 4.6 36.5 1.0 CE1 C:HIS24 4.6 32.4 1.0 O C:HOH433 4.6 29.7 1.0 CA C:ARG228 4.7 38.3 1.0 CA C:ASN14 4.7 44.5 1.0 ND2 C:ASN14 4.7 47.4 1.0 O C:ARG228 4.7 38.1 1.0 CB C:ASP19 4.8 37.2 1.0 CD2 C:TYR12 4.8 49.3 1.0 NE2 C:HIS24 5.0 33.4 1.0

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


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, T(Man-T)Tt within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:31.6 occ:1.00 O D:HOH442 2.2 29.1 1.0 O D:TYR12 2.3 36.3 1.0 OD2 D:ASP19 2.4 34.0 1.0 OD1 D:ASP10 2.4 31.3 1.0 O D:HOH430 2.5 32.8 1.0 OD1 D:ASN14 2.5 37.9 1.0 OD2 D:ASP10 2.6 23.9 1.0 CG D:ASP10 2.9 31.4 1.0 C D:TYR12 3.5 35.3 1.0 CG D:ASP19 3.6 36.0 1.0 CG D:ASN14 3.6 42.6 1.0 N D:ASN14 3.9 38.8 1.0 OD1 D:ASP19 4.1 32.0 1.0 MN D:MN301 4.2 39.4 1.0 CB D:ASN14 4.2 43.9 1.0 CA D:TYR12 4.4 39.2 1.0 CB D:ASP10 4.4 28.7 1.0 N D:PRO13 4.5 38.2 1.0 CB D:TYR12 4.5 42.2 1.0 N D:TYR12 4.5 34.5 1.0 CA D:PRO13 4.5 38.8 1.0 C D:PRO13 4.5 39.7 1.0 CB D:ARG228 4.6 39.7 1.0 O D:ASP208 4.6 28.5 1.0 CE1 D:HIS24 4.6 33.0 1.0 CA D:ARG228 4.6 37.2 1.0 OD2 D:ASP208 4.7 32.4 1.0 ND2 D:ASN14 4.7 41.1 1.0 CA D:ASN14 4.7 41.5 1.0 O D:ARG228 4.7 40.3 1.0 CB D:ASP19 4.8 37.9 1.0 CD2 D:TYR12 4.9 44.9 1.0 NE2 D:HIS24 5.0 36.1 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