Calcium in PDB 1qdo: Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex

The structure of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdo was solved by J.Bouckaert, R.Loris, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.410, 64.530, 126.960, 90.00, 93.21, 90.00
R / Rfree (%)	16.4 / 25.7

The structure of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex (pdb code 1qdo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca241 b:49.9 occ:1.00 O A:TYR12 2.2 45.0 1.0 OD1 A:ASP10 2.5 43.7 1.0 OD2 A:ASP19 2.7 44.7 1.0 OD1 A:ASN14 3.0 39.5 1.0 CG A:ASP10 3.3 27.9 1.0 OD2 A:ASP10 3.4 15.8 1.0 C A:TYR12 3.4 41.5 1.0 OD2 A:ASP208 3.9 26.1 1.0 CG A:ASP19 3.9 38.0 1.0 CG A:ASN14 3.9 44.9 1.0 CB A:ASN14 4.1 30.1 1.0 CA A:TYR12 4.2 39.5 1.0 N A:ASN14 4.2 24.6 1.0 CB A:TYR12 4.3 28.6 1.0 O A:ASP208 4.3 43.7 1.0 N A:TYR12 4.3 38.7 1.0 CA A:ARG228 4.3 16.9 1.0 N A:PRO13 4.4 45.1 1.0 CB A:ARG228 4.5 35.5 1.0 OD1 A:ASP19 4.5 41.6 1.0 CD1 A:TYR12 4.6 42.6 1.0 CA A:PRO13 4.7 39.9 1.0 C A:PRO13 4.7 41.3 1.0 CB A:ASP10 4.8 22.8 1.0 O4 A:MAN238 4.8 40.2 1.0 CA A:ASN14 4.8 20.9 1.0 O A:ARG228 4.8 34.7 1.0 CG A:ASP208 4.8 42.9 1.0 CB A:ASP19 4.9 16.6 1.0 CG A:TYR12 5.0 31.9 1.0

Calcium binding site 2 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca243 b:39.4 occ:1.00 O B:TYR12 2.3 25.9 1.0 O B:HOH1240 2.4 16.4 1.0 OD1 B:ASP10 2.4 46.8 1.0 OD2 B:ASP19 2.6 32.4 1.0 OD2 B:ASP10 2.8 25.0 1.0 CG B:ASP10 3.0 36.8 1.0 OD1 B:ASN14 3.4 37.0 1.0 C B:TYR12 3.5 33.6 1.0 CG B:ASP19 3.7 33.0 1.0 OD2 B:ASP208 4.0 41.9 1.0 CB B:ASN14 4.1 35.0 1.0 N B:ASN14 4.1 25.5 1.0 CG B:ASN14 4.2 39.5 1.0 OD1 B:ASP19 4.2 45.5 1.0 CA B:TYR12 4.3 34.5 1.0 O B:ASP208 4.4 42.6 1.0 CA B:ARG228 4.4 23.1 1.0 CB B:TYR12 4.4 25.9 1.0 CB B:ASP10 4.4 20.8 1.0 N B:TYR12 4.4 34.6 1.0 MN B:MN242 4.5 42.3 1.0 N B:PRO13 4.5 41.5 1.0 O B:ARG228 4.6 41.4 1.0 CB B:ARG228 4.7 38.6 1.0 CA B:PRO13 4.7 40.2 1.0 CA B:ASN14 4.8 19.5 1.0 C B:PRO13 4.8 44.0 1.0 CD1 B:TYR12 4.9 17.4 1.0 CG B:ASP208 4.9 33.4 1.0 CB B:ASP19 5.0 21.4 1.0

Calcium binding site 3 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca245 b:47.0 occ:1.00 OD1 C:ASP10 2.2 36.0 1.0 O C:TYR12 2.2 31.8 1.0 OD2 C:ASP19 2.4 41.1 1.0 OD1 C:ASN14 2.9 42.5 1.0 CG C:ASP10 3.0 23.0 1.0 OD2 C:ASP10 3.3 10.3 1.0 C C:TYR12 3.4 36.1 1.0 CG C:ASP19 3.6 42.0 1.0 CG C:ASN14 3.7 50.7 1.0 CB C:ASN14 3.9 44.4 1.0 N C:ASN14 4.0 32.1 1.0 OD1 C:ASP19 4.2 44.5 1.0 OD2 C:ASP208 4.2 39.3 1.0 CA C:TYR12 4.3 33.5 1.0 CB C:TYR12 4.4 34.5 1.0 N C:TYR12 4.4 38.6 1.0 CB C:ASP10 4.4 10.3 1.0 N C:PRO13 4.4 44.7 1.0 O C:ASP208 4.4 36.1 1.0 CA C:ASN14 4.6 24.6 1.0 CA C:PRO13 4.7 33.4 1.0 C C:PRO13 4.7 36.5 1.0 CB C:ASP19 4.7 32.1 1.0 CD2 C:TYR12 4.7 39.8 1.0 CA C:ARG228 4.8 16.6 1.0 O C:ARG228 4.9 35.1 1.0 MN C:MN244 4.9 42.8 1.0 CB C:ARG228 4.9 33.5 1.0 ND2 C:ASN14 4.9 59.3 1.0 CA C:ASP10 4.9 11.1 1.0 CE1 C:HIS24 5.0 14.3 1.0

Calcium binding site 4 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca247 b:42.8 occ:1.00 OD1 D:ASP10 2.1 53.8 1.0 O D:TYR12 2.4 33.2 1.0 OD2 D:ASP19 2.7 42.0 1.0 CG D:ASP10 2.8 37.2 1.0 OD2 D:ASP10 2.9 20.2 1.0 OD1 D:ASN14 3.4 47.9 1.0 C D:TYR12 3.6 45.4 1.0 CG D:ASP19 3.9 37.5 1.0 OD2 D:ASP208 4.0 32.5 1.0 CB D:ASN14 4.1 37.1 1.0 CG D:ASN14 4.1 39.1 1.0 N D:ASN14 4.1 25.8 1.0 CB D:ASP10 4.3 30.3 1.0 OD1 D:ASP19 4.4 33.1 1.0 CA D:TYR12 4.4 47.1 1.0 MN D:MN246 4.4 48.0 1.0 O D:ASP208 4.5 33.7 1.0 CA D:ARG228 4.5 21.8 1.0 N D:TYR12 4.5 44.1 1.0 CB D:ARG228 4.5 25.3 1.0 CB D:TYR12 4.6 22.8 1.0 N D:PRO13 4.6 50.7 1.0 O D:ARG228 4.7 27.9 1.0 CA D:ASN14 4.8 24.2 1.0 CA D:PRO13 4.8 43.9 1.0 CD1 D:TYR12 4.8 17.3 1.0 C D:PRO13 4.8 48.1 1.0 CA D:ASP10 4.9 15.0 1.0 O4 D:MAN3238 5.0 38.4 1.0 CB D:ASP19 5.0 28.9 1.0

J.Bouckaert, T.W.Hamelryck, L.Wyns, R.Loris. The Crystal Structures of Man(ALPHA1-3)Man(ALPHA1-O)Me and Man(ALPHA1-6)Man(ALPHA1-O)Me in Complex with Concanavalin A. J.Biol.Chem. V. 274 29188 1999.
ISSN: ISSN 0021-9258
PubMed: 10506175
DOI: 10.1074/JBC.274.41.29188