Manganese in PDB 1ona: Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside

The structure of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside, PDB code: 1ona was solved by J.Bouckaert, D.Maes, F.Poortmans, L.Wyns, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.830, 64.840, 125.920, 90.00, 93.87, 90.00
R / Rfree (%)	22.1 / 28.2

The structure of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside (pdb code 1ona). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside, PDB code: 1ona:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:20.3 occ:1.00 OD2 A:ASP10 2.2 19.0 1.0 NE2 A:HIS24 2.4 6.2 1.0 O A:HOH243 2.5 4.8 1.0 OE2 A:GLU8 2.5 16.2 1.0 OD1 A:ASP19 2.6 12.6 1.0 CG A:ASP19 3.0 12.7 1.0 OD2 A:ASP19 3.0 15.8 1.0 CE1 A:HIS24 3.2 7.0 1.0 CG A:ASP10 3.3 18.1 1.0 CD2 A:HIS24 3.5 3.6 1.0 CD A:GLU8 3.5 8.3 1.0 CB A:ASP10 3.7 8.2 1.0 OE1 A:GLU8 3.7 11.1 1.0 OG A:SER34 4.2 5.4 1.0 CB A:ASP19 4.3 15.5 1.0 CA A:CA239 4.3 10.3 1.0 OD1 A:ASP10 4.3 19.7 1.0 O A:VAL32 4.4 7.8 1.0 ND1 A:HIS24 4.4 4.7 1.0 O A:HOH258 4.5 13.9 1.0 CG A:HIS24 4.6 4.0 1.0 CA A:ASP19 4.8 18.5 1.0 CG A:GLU8 4.8 7.4 1.0

Manganese binding site 2 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:14.4 occ:1.00 OD2 C:ASP10 2.2 11.6 1.0 NE2 C:HIS24 2.3 11.9 1.0 O C:HOH257 2.3 10.6 1.0 OD1 C:ASP19 2.4 16.4 1.0 OE2 C:GLU8 2.5 18.6 1.0 CG C:ASP19 2.9 15.3 1.0 CE1 C:HIS24 3.1 7.0 1.0 OD2 C:ASP19 3.1 11.8 1.0 CG C:ASP10 3.2 9.8 1.0 CD2 C:HIS24 3.4 4.6 1.0 CD C:GLU8 3.5 16.1 1.0 CB C:ASP10 3.6 9.4 1.0 OE1 C:GLU8 3.9 14.3 1.0 CB C:ASP19 4.2 20.5 1.0 CA B:CA239 4.2 12.7 1.0 OG C:SER34 4.2 2.0 1.0 ND1 C:HIS24 4.3 8.2 1.0 OD1 C:ASP10 4.3 4.5 1.0 O C:HOH246 4.4 6.5 1.0 CG C:HIS24 4.5 5.8 1.0 O C:VAL32 4.6 10.2 1.0 CA C:ASP19 4.7 20.9 1.0 CG C:GLU8 4.8 13.4 1.0

Manganese binding site 3 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:21.4 occ:1.00 NE2 D:HIS24 2.3 13.4 1.0 OD2 D:ASP10 2.3 4.5 1.0 OE2 D:GLU8 2.4 15.4 1.0 O D:HOH257 2.4 12.6 1.0 OD1 D:ASP19 2.6 24.1 1.0 CG D:ASP19 3.2 24.9 1.0 CE1 D:HIS24 3.2 11.8 1.0 OD2 D:ASP19 3.3 29.2 1.0 CD D:GLU8 3.3 13.4 1.0 CD2 D:HIS24 3.4 8.3 1.0 CG D:ASP10 3.4 8.2 1.0 OE1 D:GLU8 3.6 7.9 1.0 CB D:ASP10 3.8 11.9 1.0 O D:HOH268 3.8 18.7 1.0 OG D:SER34 3.9 8.5 1.0 O D:VAL32 4.3 17.9 1.0 CA C:CA239 4.4 18.0 1.0 ND1 D:HIS24 4.4 10.3 1.0 CB D:ASP19 4.4 23.6 1.0 CG D:HIS24 4.5 10.5 1.0 OD1 D:ASP10 4.5 10.2 1.0 CG D:GLU8 4.6 12.5 1.0 CA D:ASP19 4.9 22.7 1.0

Manganese binding site 4 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:15.9 occ:1.00 O B:HOH252 1.9 14.0 1.0 O B:HOH248 2.1 10.4 1.0 OE2 B:GLU8 2.1 10.6 1.0 OD2 B:ASP10 2.2 6.7 1.0 NE2 B:HIS24 2.3 11.2 1.0 OD1 B:ASP19 2.7 22.4 1.0 CE1 B:HIS24 3.2 9.9 1.0 CD B:GLU8 3.2 14.6 1.0 CG B:ASP10 3.2 6.5 1.0 CG B:ASP19 3.2 22.6 1.0 OD2 B:ASP19 3.3 25.9 1.0 CD2 B:HIS24 3.4 5.1 1.0 CB B:ASP10 3.5 9.9 1.0 OE1 B:GLU8 3.6 10.0 1.0 OG B:SER34 4.0 4.1 1.0 O B:HOH261 4.1 17.7 1.0 CA D:CA239 4.3 14.3 1.0 OD1 B:ASP10 4.3 6.6 1.0 ND1 B:HIS24 4.4 15.4 1.0 CB B:ASP19 4.5 20.3 1.0 CG B:HIS24 4.5 12.5 1.0 O B:VAL32 4.5 11.2 1.0 CG B:GLU8 4.5 13.4 1.0 CA B:ASP19 5.0 20.1 1.0

R.Loris, D.Maes, F.Poortmans, L.Wyns, J.Bouckaert. A Structure of the Complex Between Concanavalin A and Methyl-3,6-Di-O-(Alpha-D-Mannopyranosyl) -Alpha-D-Mannopyranoside Reveals Two Binding Modes. J.Biol.Chem. V. 271 30614 1996.
ISSN: ISSN 0021-9258
PubMed: 8940035
DOI: 10.1074/JBC.271.48.30614