Manganese 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:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	4 atoms

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

Manganese 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 Manganese with other atoms in the Mn 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:Mn240 b:33.8 occ:1.00 O A:HOH260 2.4 21.0 1.0 OE2 A:GLU8 2.4 13.8 1.0 OD1 A:ASP19 2.4 14.3 1.0 OD2 A:ASP10 2.4 11.9 1.0 NE2 A:HIS24 2.5 11.6 1.0 O A:HOH251 2.5 16.4 1.0 CG A:ASP19 3.3 13.5 1.0 CD A:GLU8 3.3 17.2 1.0 CE1 A:HIS24 3.4 13.0 1.0 CG A:ASP10 3.4 13.7 1.0 OE1 A:GLU8 3.4 13.3 1.0 CD2 A:HIS24 3.5 14.9 1.0 OD2 A:ASP19 3.7 13.0 1.0 CB A:ASP10 3.7 12.5 1.0 O A:HOH244 4.1 11.9 1.0 OG A:SER34 4.2 15.2 1.0 CA A:CA241 4.3 12.5 1.0 O A:HOH288 4.3 33.2 1.0 CB A:ASP19 4.4 14.2 1.0 O A:HOH352 4.4 81.4 1.0 OD1 A:ASP10 4.5 17.6 1.0 O A:VAL32 4.5 14.0 1.0 ND1 A:HIS24 4.6 16.3 1.0 CA A:ASP19 4.6 19.8 1.0 CG A:HIS24 4.7 14.2 1.0 CG A:GLU8 4.7 13.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn243 b:37.0 occ:1.00 O B:HOH1242 2.0 14.6 1.0 OD1 B:ASP19 2.4 15.4 1.0 O B:HOH1248 2.4 17.2 1.0 NE2 B:HIS24 2.5 14.1 1.0 OE2 B:GLU8 2.5 20.6 1.0 OD2 B:ASP10 2.5 16.4 1.0 CG B:ASP19 3.2 16.5 1.0 CD B:GLU8 3.3 20.2 1.0 CE1 B:HIS24 3.4 13.2 1.0 OE1 B:GLU8 3.4 18.6 1.0 OD2 B:ASP19 3.4 15.4 1.0 CG B:ASP10 3.5 17.8 1.0 CD2 B:HIS24 3.5 14.3 1.0 CB B:ASP10 3.7 13.3 1.0 O B:HOH1241 4.1 14.2 1.0 OG B:SER34 4.2 18.7 1.0 O B:HOH1333 4.2 59.8 1.0 CA B:CA244 4.3 17.3 1.0 CB B:ASP19 4.4 16.6 1.0 O B:VAL32 4.5 17.1 1.0 OD1 B:ASP10 4.6 17.0 1.0 ND1 B:HIS24 4.6 17.2 1.0 CG B:HIS24 4.6 16.9 1.0 CA B:ASP19 4.7 22.1 1.0 CG B:GLU8 4.8 14.7 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn245 b:41.5 occ:1.00 O C:HOH2248 2.0 20.9 1.0 O C:HOH2254 2.1 23.9 1.0 OE2 C:GLU8 2.4 16.6 1.0 NE2 C:HIS24 2.5 20.0 1.0 OD1 C:ASP19 2.6 21.0 1.0 OD2 C:ASP10 2.6 20.4 1.0 CD C:GLU8 3.3 19.3 1.0 CG C:ASP19 3.3 25.9 1.0 OE1 C:GLU8 3.4 16.8 1.0 CE1 C:HIS24 3.5 17.3 1.0 CD2 C:HIS24 3.6 18.7 1.0 OD2 C:ASP19 3.6 22.6 1.0 CG C:ASP10 3.7 23.1 1.0 CB C:ASP10 3.9 24.1 1.0 OG C:SER34 4.0 19.6 1.0 O C:HOH2244 4.1 18.9 1.0 O C:HOH2301 4.4 46.1 1.0 CA C:CA246 4.4 21.6 1.0 O C:VAL32 4.5 21.3 1.0 CB C:ASP19 4.5 25.1 1.0 ND1 C:HIS24 4.6 18.4 1.0 CG C:GLU8 4.7 19.7 1.0 CA C:ASP19 4.7 26.1 1.0 CG C:HIS24 4.7 17.4 1.0 OD1 C:ASP10 4.8 24.9 1.0 CB C:SER34 4.9 17.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn247 b:38.4 occ:1.00 O D:HOH3256 1.9 25.7 1.0 OD1 D:ASP19 2.4 17.6 1.0 OE2 D:GLU8 2.4 20.8 1.0 OD2 D:ASP10 2.5 14.4 1.0 NE2 D:HIS24 2.5 12.5 1.0 O D:HOH3252 2.6 23.6 1.0 CG D:ASP19 3.3 20.7 1.0 CD D:GLU8 3.3 20.4 1.0 OE1 D:GLU8 3.4 17.3 1.0 CE1 D:HIS24 3.4 10.9 1.0 CG D:ASP10 3.5 18.9 1.0 CD2 D:HIS24 3.6 13.2 1.0 OD2 D:ASP19 3.6 18.9 1.0 CB D:ASP10 3.7 14.4 1.0 O D:HOH3242 4.0 15.9 1.0 OG D:SER34 4.2 19.8 1.0 CA D:CA248 4.3 17.6 1.0 CB D:ASP19 4.5 21.2 1.0 O D:VAL32 4.5 15.7 1.0 OD1 D:ASP10 4.6 19.1 1.0 ND1 D:HIS24 4.6 13.3 1.0 CG D:GLU8 4.7 15.4 1.0 O D:HOH3274 4.7 36.1 1.0 CG D:HIS24 4.7 12.1 1.0 CA D:ASP19 4.8 25.5 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