Manganese in PDB 3d4k: Concanavalin A Complexed to A Synthetic Analog of the Trimannoside

The structure of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside, PDB code: 3d4k was solved by R.Kadirvelraj, B.L.Foley, J.D.Dyekjaer, R.J.Woods, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.015, 63.547, 126.215, 90.00, 86.91, 90.00
R / Rfree (%)	20.5 / 23.8

The structure of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside (pdb code 3d4k). 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 Complexed to A Synthetic Analog of the Trimannoside, PDB code: 3d4k:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:18.6 occ:1.00 OD2 A:ASP10 2.1 14.0 1.0 O A:HOH365 2.2 21.5 1.0 OE2 A:GLU8 2.2 17.6 1.0 O A:HOH307 2.3 20.6 1.0 NE2 A:HIS24 2.4 21.3 1.0 OD2 A:ASP19 2.5 26.9 1.0 OD1 A:ASP19 2.9 26.2 1.0 CG A:ASP19 3.0 26.0 1.0 CG A:ASP10 3.1 14.4 1.0 CD A:GLU8 3.2 18.3 1.0 CE1 A:HIS24 3.3 20.9 1.0 CD2 A:HIS24 3.4 19.7 1.0 OE1 A:GLU8 3.5 17.9 1.0 CB A:ASP10 3.5 14.8 1.0 O A:HOH250 3.9 18.4 1.0 O A:HOH753 4.1 38.8 1.0 OG A:SER34 4.2 19.0 1.0 CA A:CA239 4.2 20.1 1.0 OD1 A:ASP10 4.3 15.9 1.0 CB A:ASP19 4.3 27.8 1.0 ND1 A:HIS24 4.5 21.3 1.0 CG A:HIS24 4.5 21.2 1.0 CG A:GLU8 4.5 16.8 1.0 O A:VAL32 4.6 19.3 1.0 CA A:ASP19 4.9 28.7 1.0

Manganese binding site 2 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:18.8 occ:1.00 OD2 B:ASP10 2.1 14.1 1.0 OE2 B:GLU8 2.2 16.0 1.0 O B:HOH264 2.2 17.0 1.0 O B:HOH306 2.3 20.7 1.0 OD1 B:ASP19 2.3 16.5 1.0 NE2 B:HIS24 2.4 21.4 1.0 CG B:ASP10 3.2 16.3 1.0 CG B:ASP19 3.2 21.4 1.0 CD B:GLU8 3.2 15.4 1.0 CE1 B:HIS24 3.2 20.5 1.0 CD2 B:HIS24 3.5 19.1 1.0 OE1 B:GLU8 3.6 15.5 1.0 CB B:ASP10 3.6 17.0 1.0 OD2 B:ASP19 3.6 19.9 1.0 O B:HOH257 4.0 18.8 1.0 OG B:SER34 4.2 19.7 1.0 CA B:CA239 4.2 18.3 1.0 OD1 B:ASP10 4.3 16.3 1.0 CB B:ASP19 4.4 21.7 1.0 ND1 B:HIS24 4.4 19.6 1.0 CG B:HIS24 4.5 21.7 1.0 CG B:GLU8 4.6 13.0 1.0 O B:VAL32 4.6 17.4 1.0 CA B:ASP19 4.7 24.2 1.0

Manganese binding site 3 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:17.3 occ:1.00 OD2 C:ASP10 2.1 13.6 1.0 O C:HOH386 2.1 23.4 1.0 OD1 C:ASP19 2.2 19.3 1.0 OE2 C:GLU8 2.3 16.3 1.0 O C:HOH256 2.3 17.2 1.0 NE2 C:HIS24 2.4 21.7 1.0 CG C:ASP19 3.1 24.3 1.0 CG C:ASP10 3.1 16.8 1.0 CE1 C:HIS24 3.2 22.1 1.0 CD C:GLU8 3.3 16.4 1.0 CD2 C:HIS24 3.5 19.2 1.0 OD2 C:ASP19 3.6 27.7 1.0 CB C:ASP10 3.6 15.5 1.0 OE1 C:GLU8 3.6 17.1 1.0 O C:HOH281 4.0 18.9 1.0 OG C:SER34 4.1 19.5 1.0 CA C:CA239 4.2 20.0 1.0 CB C:ASP19 4.2 23.1 1.0 OD1 C:ASP10 4.2 16.0 1.0 O C:HOH710 4.3 35.5 1.0 ND1 C:HIS24 4.4 22.3 1.0 CG C:HIS24 4.5 21.4 1.0 O C:VAL32 4.6 18.3 1.0 CG C:GLU8 4.6 15.2 1.0 CA C:ASP19 4.7 25.7 1.0

Manganese binding site 4 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:16.6 occ:1.00 O D:HOH271 2.2 19.8 1.0 OD2 D:ASP10 2.2 14.8 1.0 OE2 D:GLU8 2.2 15.6 1.0 OD1 D:ASP19 2.3 20.8 1.0 NE2 D:HIS24 2.3 20.7 1.0 O D:HOH270 2.3 20.4 1.0 CG D:ASP19 3.1 22.4 1.0 CE1 D:HIS24 3.1 20.3 1.0 CG D:ASP10 3.2 17.5 1.0 CD D:GLU8 3.3 17.9 1.0 CD2 D:HIS24 3.5 17.8 1.0 OD2 D:ASP19 3.5 21.6 1.0 CB D:ASP10 3.6 16.6 1.0 OE1 D:GLU8 3.6 14.8 1.0 O D:HOH253 4.0 16.1 1.0 OG D:SER34 4.1 19.8 1.0 CA D:CA239 4.2 17.2 1.0 CB D:ASP19 4.2 22.2 1.0 O D:HOH755 4.3 41.2 1.0 ND1 D:HIS24 4.3 20.2 1.0 OD1 D:ASP10 4.3 18.4 1.0 CG D:HIS24 4.5 18.7 1.0 O D:VAL32 4.6 18.9 1.0 CG D:GLU8 4.6 16.2 1.0 CA D:ASP19 4.7 23.7 1.0

R.Kadirvelraj, B.L.Foley, J.D.Dyekjaer, R.J.Woods. Involvement of Water in Carbohydrate-Protein Binding: Concanavalin A Revisited. J.Am.Chem.Soc. V. 130 16933 2008.
ISSN: ISSN 0002-7863
PubMed: 19053475
DOI: 10.1021/JA8039663