Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Concanavalin A Bound to A Dna Glycoconjugate, T(Man-T)Tt, PDB code: 7mgd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:36.2 occ:1.00 OD2 A:ASP10 2.0 23.7 1.0 O A:HOH466 2.2 27.4 1.0 NE2 A:HIS24 2.2 27.1 1.0 O A:HOH418 2.2 25.6 1.0 OE2 A:GLU8 2.3 28.3 1.0 OD1 A:ASP19 2.3 27.7 1.0 CG A:ASP10 3.0 26.2 1.0 CG A:ASP19 3.1 31.5 1.0 CE1 A:HIS24 3.2 27.7 1.0 CD2 A:HIS24 3.2 28.1 1.0 CD A:GLU8 3.3 29.2 1.0 OD2 A:ASP19 3.4 28.8 1.0 CB A:ASP10 3.5 27.5 1.0 OE1 A:GLU8 3.7 32.0 1.0 O A:HOH441 4.0 21.5 1.0 CA A:CA302 4.1 28.6 1.0 OD1 A:ASP10 4.1 27.4 1.0 OG A:SER34 4.2 29.1 1.0 O A:HOH502 4.2 46.9 1.0 CB A:ASP19 4.3 33.0 1.0 ND1 A:HIS24 4.3 27.1 1.0 CG A:HIS24 4.3 28.0 1.0 CA A:ASP19 4.6 35.5 1.0 CG A:GLU8 4.6 29.0 1.0 O A:VAL32 4.7 26.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:37.6 occ:1.00 OD2 B:ASP10 2.0 27.0 1.0 O B:HOH448 2.2 25.9 1.0 O B:HOH419 2.3 30.6 1.0 OE2 B:GLU8 2.3 29.9 1.0 NE2 B:HIS24 2.3 30.6 1.0 OD1 B:ASP19 2.4 35.1 1.0 CG B:ASP19 3.1 38.1 1.0 CG B:ASP10 3.1 31.6 1.0 CD B:GLU8 3.3 32.3 1.0 CE1 B:HIS24 3.3 31.1 1.0 CD2 B:HIS24 3.3 32.6 1.0 OD2 B:ASP19 3.4 33.9 1.0 OE1 B:GLU8 3.6 29.6 1.0 CB B:ASP10 3.6 30.1 1.0 O B:HOH483 3.9 27.2 1.0 OG B:SER34 4.1 37.0 1.0 CA B:CA302 4.2 31.6 1.0 OD1 B:ASP10 4.2 28.8 1.0 CB B:ASP19 4.3 38.9 1.0 ND1 B:HIS24 4.4 33.1 1.0 CG B:HIS24 4.4 32.7 1.0 O B:VAL32 4.5 29.3 1.0 CA B:ASP19 4.6 41.1 1.0 CG B:GLU8 4.6 32.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:40.1 occ:1.00 OD2 C:ASP10 1.9 29.3 1.0 O C:HOH442 1.9 25.8 1.0 NE2 C:HIS24 2.2 33.4 1.0 OE2 C:GLU8 2.3 30.2 1.0 O C:HOH433 2.3 29.7 1.0 OD1 C:ASP19 2.3 30.0 1.0 CG C:ASP10 2.9 32.1 1.0 CG C:ASP19 3.0 35.2 1.0 CE1 C:HIS24 3.1 32.4 1.0 CD2 C:HIS24 3.2 36.6 1.0 OD2 C:ASP19 3.3 34.1 1.0 CD C:GLU8 3.4 30.6 1.0 CB C:ASP10 3.4 29.8 1.0 OE1 C:GLU8 3.7 29.6 1.0 O C:HOH450 3.9 30.5 1.0 OD1 C:ASP10 4.0 29.7 1.0 CA C:CA302 4.1 35.2 1.0 ND1 C:HIS24 4.2 30.3 1.0 CB C:ASP19 4.2 37.2 1.0 CG C:HIS24 4.3 37.7 1.0 OG C:SER34 4.3 37.3 1.0 CA C:ASP19 4.6 44.5 1.0 O C:VAL32 4.7 31.0 1.0 CG C:GLU8 4.7 28.9 1.0 CA C:ASP10 5.0 30.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:39.4 occ:1.00 OD2 D:ASP10 1.9 23.9 1.0 O D:HOH437 2.0 21.9 1.0 NE2 D:HIS24 2.2 36.1 1.0 OE2 D:GLU8 2.3 27.4 1.0 OD1 D:ASP19 2.4 32.0 1.0 CG D:ASP10 3.0 31.4 1.0 CG D:ASP19 3.1 36.0 1.0 CE1 D:HIS24 3.1 33.0 1.0 CD2 D:HIS24 3.2 38.7 1.0 CD D:GLU8 3.4 33.7 1.0 OD2 D:ASP19 3.4 34.0 1.0 CB D:ASP10 3.5 28.7 1.0 OE1 D:GLU8 3.7 29.4 1.0 O D:HOH442 3.9 29.1 1.0 OD1 D:ASP10 4.1 31.3 1.0 CA D:CA302 4.2 31.6 1.0 ND1 D:HIS24 4.2 35.5 1.0 OG D:SER34 4.2 39.7 1.0 CB D:ASP19 4.2 37.9 1.0 CG D:HIS24 4.3 38.8 1.0 CA D:ASP19 4.6 42.8 1.0 O D:VAL32 4.6 26.9 1.0 CG D:GLU8 4.7 29.8 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