Calcium 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:

Manganese

(Mn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca239 b:10.3 occ:1.00 OD1 A:ASN14 2.1 24.2 1.0 O A:TYR12 2.1 15.7 1.0 OD1 A:ASP10 2.4 19.7 1.0 O A:HOH247 2.5 6.8 1.0 OD2 A:ASP19 2.6 15.8 1.0 OD2 A:ASP10 2.7 19.0 1.0 CG A:ASP10 2.9 18.1 1.0 CG A:ASN14 3.3 20.2 1.0 C A:TYR12 3.4 15.7 1.0 CG A:ASP19 3.8 12.7 1.0 N A:ASN14 3.8 9.6 1.0 CB A:ASN14 4.1 11.9 1.0 N A:PRO13 4.3 14.6 1.0 ND2 A:ASN14 4.3 17.6 1.0 CA A:PRO13 4.3 12.4 1.0 C A:PRO13 4.3 10.0 1.0 MN A:MN238 4.3 20.3 1.0 CA A:TYR12 4.4 11.9 1.0 CB A:ASP10 4.4 8.2 1.0 OD1 A:ASP19 4.5 12.6 1.0 CB A:TYR12 4.5 7.8 1.0 OD2 A:ASP208 4.5 8.6 1.0 N A:TYR12 4.6 12.0 1.0 CA A:ASN14 4.6 10.0 1.0 O A:ASP208 4.7 3.6 1.0 CB A:ARG228 4.7 9.6 1.0 CD2 A:TYR12 4.7 15.3 1.0 CB A:ASP19 4.8 15.5 1.0 CE1 A:HIS24 4.8 7.0 1.0 CA A:ARG228 4.9 5.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca239 b:12.7 occ:1.00 O C:TYR12 2.1 8.5 1.0 OD1 C:ASP10 2.2 4.5 1.0 OD1 C:ASN14 2.2 20.2 1.0 O C:HOH248 2.3 7.6 1.0 OD2 C:ASP10 2.5 11.6 1.0 OD2 C:ASP19 2.5 11.8 1.0 CG C:ASP10 2.7 9.8 1.0 O C:HOH246 2.7 6.5 1.0 C C:TYR12 3.4 7.6 1.0 CG C:ASN14 3.4 12.6 1.0 CG C:ASP19 3.8 15.3 1.0 N C:ASN14 4.0 12.3 1.0 CB C:ASP10 4.2 9.4 1.0 CB C:ASN14 4.2 5.6 1.0 MN B:MN238 4.2 14.4 1.0 N C:PRO13 4.3 6.2 1.0 CA C:PRO13 4.3 6.6 1.0 CA C:TYR12 4.3 9.8 1.0 ND2 C:ASN14 4.4 7.7 1.0 OD1 C:ASP19 4.4 16.4 1.0 C C:PRO13 4.4 9.6 1.0 N C:TYR12 4.5 15.4 1.0 CB C:TYR12 4.6 12.2 1.0 O C:ASP208 4.6 2.0 1.0 OD2 C:ASP208 4.7 12.1 1.0 CA C:ASN14 4.7 9.4 1.0 CE1 C:HIS24 4.7 7.0 1.0 O C:HOH257 4.8 10.6 1.0 CB C:ASP19 4.8 20.5 1.0 CB C:ARG228 4.8 6.3 1.0 CD2 C:TYR12 4.9 16.0 1.0 CA C:ASP10 4.9 8.2 1.0 CA C:ARG228 5.0 6.3 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca239 b:18.0 occ:1.00 O D:TYR12 2.1 19.8 1.0 OD1 D:ASP10 2.3 10.2 1.0 OD1 D:ASN14 2.3 31.0 1.0 O D:HOH268 2.5 18.7 1.0 OD2 D:ASP10 2.5 4.5 1.0 OD2 D:ASP19 2.5 29.2 1.0 O D:HOH247 2.5 8.2 1.0 CG D:ASP10 2.7 8.2 1.0 C D:TYR12 3.3 14.3 1.0 CG D:ASN14 3.5 23.2 1.0 CG D:ASP19 3.8 24.9 1.0 N D:ASN14 3.9 19.0 1.0 CA D:PRO13 4.2 18.1 1.0 N D:PRO13 4.2 18.1 1.0 CB D:ASP10 4.2 11.9 1.0 CB D:ASN14 4.2 21.5 1.0 C D:PRO13 4.3 19.1 1.0 CA D:TYR12 4.3 10.7 1.0 MN C:MN238 4.4 21.4 1.0 ND2 D:ASN14 4.5 16.2 1.0 CE1 D:HIS24 4.5 11.8 1.0 OD1 D:ASP19 4.5 24.1 1.0 N D:TYR12 4.5 13.8 1.0 O D:ASP208 4.6 4.3 1.0 CB D:TYR12 4.6 11.8 1.0 CA D:ASN14 4.7 20.9 1.0 CB D:ASP19 4.7 23.6 1.0 OD2 D:ASP208 4.7 14.8 1.0 O D:HOH257 4.8 12.6 1.0 CD2 D:TYR12 4.9 18.8 1.0 CB D:ARG228 4.9 12.2 1.0 NE2 D:HIS24 5.0 13.4 1.0 CA D:ASP10 5.0 6.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca239 b:14.3 occ:1.00 OD1 B:ASP10 2.2 6.6 1.0 O B:HOH261 2.3 17.7 1.0 OD1 B:ASN14 2.3 21.9 1.0 O B:TYR12 2.3 14.7 1.0 OD2 B:ASP10 2.5 6.7 1.0 OD2 B:ASP19 2.6 25.9 1.0 CG B:ASP10 2.7 6.5 1.0 CG B:ASN14 3.5 19.6 1.0 C B:TYR12 3.6 14.3 1.0 CG B:ASP19 3.8 22.6 1.0 N B:ASN14 4.1 17.3 1.0 CB B:ASP10 4.1 9.9 1.0 CB B:ASN14 4.3 14.7 1.0 MN D:MN238 4.3 15.9 1.0 ND2 B:ASN14 4.4 17.9 1.0 N B:PRO13 4.5 14.8 1.0 OD1 B:ASP19 4.5 22.4 1.0 CA B:TYR12 4.5 12.2 1.0 CA B:PRO13 4.5 14.7 1.0 O B:HOH248 4.6 10.4 1.0 O B:ASP208 4.6 8.2 1.0 N B:TYR12 4.6 16.6 1.0 C B:PRO13 4.6 15.6 1.0 OD2 B:ASP208 4.7 17.2 1.0 CB B:TYR12 4.7 14.0 1.0 CB B:ARG228 4.7 6.1 1.0 CE1 B:HIS24 4.8 9.9 1.0 CA B:ARG228 4.8 6.5 1.0 CA B:ASN14 4.8 16.3 1.0 CB B:ASP19 4.9 20.3 1.0 CA B:ASP10 4.9 13.0 1.0 O B:ARG228 4.9 5.6 1.0 CD2 B:TYR12 5.0 14.1 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