Calcium in PDB 1qdc: Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex

The structure of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdc 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)	15.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.510, 117.030, 120.920, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.1

The structure of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex (pdb code 1qdc). 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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca241 b:12.5 occ:1.00 O A:TYR12 2.3 14.6 1.0 OD1 A:ASN14 2.4 15.1 1.0 OD2 A:ASP19 2.4 13.0 1.0 OD1 A:ASP10 2.5 17.6 1.0 OD2 A:ASP10 2.5 11.9 1.0 O A:HOH246 2.5 13.4 1.0 O A:HOH244 2.5 11.9 1.0 CG A:ASP10 2.8 13.7 1.0 CG A:ASP19 3.5 13.5 1.0 CG A:ASN14 3.5 15.8 1.0 C A:TYR12 3.6 16.3 1.0 OD1 A:ASP19 3.9 14.3 1.0 N A:ASN14 3.9 18.9 1.0 CB A:ASN14 4.1 17.1 1.0 CB A:ASP10 4.3 12.5 1.0 MN A:MN240 4.3 33.8 1.0 CA A:TYR12 4.4 15.0 1.0 N A:TYR12 4.5 14.7 1.0 CB A:TYR12 4.5 12.8 1.0 N A:PRO13 4.5 19.7 1.0 CA A:PRO13 4.5 19.4 1.0 O A:HOH251 4.6 16.4 1.0 ND2 A:ASN14 4.6 16.5 1.0 C A:PRO13 4.6 18.7 1.0 OD1 A:ASP208 4.7 8.7 1.0 CA A:ASN14 4.7 17.6 1.0 CB A:ASP19 4.7 14.2 1.0 O A:ASP208 4.7 11.3 1.0 CE1 A:HIS24 4.8 13.0 1.0 CA A:ARG228 4.9 14.1 1.0 CB A:ARG228 4.9 18.6 1.0 O A:ARG228 4.9 11.9 1.0 CD2 A:TYR12 5.0 13.0 1.0

Calcium binding site 2 out of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca244 b:17.3 occ:1.00 O B:TYR12 2.4 19.3 1.0 OD2 B:ASP19 2.5 15.4 1.0 OD2 B:ASP10 2.5 16.4 1.0 OD1 B:ASN14 2.5 19.0 1.0 OD1 B:ASP10 2.5 17.0 1.0 O B:HOH1250 2.6 18.2 1.0 O B:HOH1241 2.6 14.2 1.0 CG B:ASP10 2.8 17.8 1.0 C B:TYR12 3.6 21.3 1.0 CG B:ASP19 3.6 16.5 1.0 CG B:ASN14 3.6 18.6 1.0 N B:ASN14 4.0 21.7 1.0 OD1 B:ASP19 4.1 15.4 1.0 CB B:ASN14 4.2 17.9 1.0 CB B:ASP10 4.3 13.3 1.0 MN B:MN243 4.3 37.0 1.0 CA B:TYR12 4.4 20.9 1.0 CB B:TYR12 4.5 20.0 1.0 N B:PRO13 4.5 23.5 1.0 N B:TYR12 4.5 21.8 1.0 CA B:PRO13 4.6 22.6 1.0 O B:ASP208 4.6 16.1 1.0 C B:PRO13 4.7 23.6 1.0 O B:HOH1248 4.7 17.2 1.0 OD1 B:ASP208 4.7 16.9 1.0 ND2 B:ASN14 4.7 14.1 1.0 CA B:ASN14 4.7 20.8 1.0 CB B:ASP19 4.8 16.6 1.0 CA B:ARG228 4.8 16.4 1.0 O B:ARG228 4.8 15.6 1.0 CE1 B:HIS24 4.9 13.2 1.0 CB B:ARG228 4.9 17.4 1.0 CD2 B:TYR12 5.0 23.8 1.0

Calcium binding site 3 out of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca246 b:21.6 occ:1.00 O C:TYR12 2.3 22.9 1.0 OD2 C:ASP10 2.4 20.4 1.0 OD1 C:ASN14 2.4 30.2 1.0 OD2 C:ASP19 2.5 22.6 1.0 OD1 C:ASP10 2.6 24.9 1.0 O C:HOH2244 2.6 18.9 1.0 O C:HOH2243 2.6 18.2 1.0 CG C:ASP10 2.8 23.1 1.0 C C:TYR12 3.6 26.9 1.0 CG C:ASN14 3.6 32.4 1.0 CG C:ASP19 3.7 25.9 1.0 N C:ASN14 4.0 28.7 1.0 CB C:ASN14 4.1 28.5 1.0 OD1 C:ASP19 4.1 21.0 1.0 CB C:ASP10 4.3 24.1 1.0 CA C:TYR12 4.4 25.5 1.0 MN C:MN245 4.4 41.5 1.0 O C:HOH2254 4.4 23.9 1.0 N C:TYR12 4.5 23.2 1.0 CB C:TYR12 4.5 27.6 1.0 N C:PRO13 4.5 27.7 1.0 CA C:PRO13 4.6 28.5 1.0 O C:ASP208 4.6 16.7 1.0 C C:PRO13 4.6 27.9 1.0 CA C:ASN14 4.7 29.6 1.0 ND2 C:ASN14 4.7 25.0 1.0 OD1 C:ASP208 4.7 26.4 1.0 CE1 C:HIS24 4.8 17.3 1.0 O C:ARG228 4.8 20.6 1.0 CB C:ASP19 4.9 25.1 1.0 CA C:ARG228 4.9 22.3 1.0 CD2 C:TYR12 5.0 28.3 1.0

Calcium binding site 4 out of 4 in the Man(APLHA1-6)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(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca248 b:17.6 occ:1.00 O D:TYR12 2.4 21.3 1.0 OD2 D:ASP10 2.4 14.4 1.0 O D:HOH3245 2.5 18.2 1.0 OD1 D:ASN14 2.5 21.1 1.0 OD2 D:ASP19 2.5 18.9 1.0 O D:HOH3242 2.5 15.9 1.0 OD1 D:ASP10 2.6 19.1 1.0 CG D:ASP10 2.9 18.9 1.0 CG D:ASN14 3.6 22.6 1.0 C D:TYR12 3.6 20.0 1.0 CG D:ASP19 3.6 20.7 1.0 N D:ASN14 4.0 20.7 1.0 OD1 D:ASP19 4.1 17.6 1.0 CB D:ASN14 4.1 19.6 1.0 MN D:MN247 4.3 38.4 1.0 CB D:ASP10 4.3 14.4 1.0 CA D:TYR12 4.5 19.1 1.0 CB D:TYR12 4.6 16.5 1.0 N D:PRO13 4.6 22.4 1.0 CA D:PRO13 4.6 22.4 1.0 N D:TYR12 4.6 19.4 1.0 O D:ASP208 4.6 11.7 1.0 OD1 D:ASP208 4.7 12.0 1.0 C D:PRO13 4.7 23.5 1.0 CA D:ARG228 4.7 17.3 1.0 O D:HOH3252 4.7 23.6 1.0 CA D:ASN14 4.7 22.2 1.0 ND2 D:ASN14 4.7 18.9 1.0 O D:ARG228 4.8 16.1 1.0 CB D:ARG228 4.8 22.0 1.0 CB D:ASP19 4.8 21.2 1.0 CE1 D:HIS24 4.9 10.9 1.0 CD2 D:TYR12 5.0 19.5 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