Manganese 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:

Calcium

(Ca)

4 atoms

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

Manganese 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 Manganese with other atoms in the Mn 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:Mn240 b:43.9 occ:1.00 OE2 A:GLU8 1.9 38.3 1.0 OD2 A:ASP10 2.2 15.8 1.0 OD1 A:ASP19 2.2 41.6 1.0 NE2 A:HIS24 2.6 17.3 1.0 CD A:GLU8 3.0 45.8 1.0 CG A:ASP19 3.2 38.0 1.0 CG A:ASP10 3.3 27.9 1.0 OG A:SER34 3.4 15.3 1.0 OE1 A:GLU8 3.5 27.0 1.0 CD2 A:HIS24 3.5 17.4 1.0 OD2 A:ASP19 3.7 44.7 1.0 CE1 A:HIS24 3.7 15.2 1.0 CB A:ASP10 3.7 22.8 1.0 O A:VAL32 4.2 24.1 1.0 CG A:GLU8 4.3 38.1 1.0 OD1 A:ASP10 4.3 43.7 1.0 CB A:ASP19 4.4 16.6 1.0 CA A:ASP19 4.5 51.2 1.0 CG A:HIS24 4.7 31.3 1.0 ND1 A:HIS24 4.8 20.9 1.0 CB A:SER34 4.8 16.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn242 b:42.3 occ:1.00 OE2 B:GLU8 2.0 37.9 1.0 OD2 B:ASP10 2.0 25.0 1.0 O B:HOH1242 2.1 23.4 1.0 OD1 B:ASP19 2.2 45.5 1.0 NE2 B:HIS24 2.5 15.7 1.0 CG B:ASP10 3.1 36.8 1.0 CG B:ASP19 3.1 33.0 1.0 CD B:GLU8 3.2 34.9 1.0 CD2 B:HIS24 3.4 28.9 1.0 OD2 B:ASP19 3.5 32.4 1.0 CE1 B:HIS24 3.5 27.6 1.0 CB B:ASP10 3.5 20.8 1.0 O B:HOH1240 3.6 16.4 1.0 OE1 B:GLU8 3.9 18.2 1.0 OG B:SER34 4.2 32.0 1.0 OD1 B:ASP10 4.2 46.8 1.0 CG B:GLU8 4.3 29.7 1.0 CB B:ASP19 4.4 21.4 1.0 CA B:CA243 4.5 39.4 1.0 CG B:HIS24 4.6 31.6 1.0 CA B:ASP19 4.6 46.0 1.0 ND1 B:HIS24 4.6 16.2 1.0 O B:VAL32 4.7 28.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn244 b:42.8 occ:1.00 OE2 C:GLU8 1.8 30.5 1.0 OD2 C:ASP10 2.0 10.3 1.0 OD1 C:ASP19 2.0 44.5 1.0 NE2 C:HIS24 2.5 23.1 1.0 CD C:GLU8 3.0 39.6 1.0 CG C:ASP19 3.2 42.0 1.0 CG C:ASP10 3.3 23.0 1.0 CE1 C:HIS24 3.4 14.3 1.0 OG C:SER34 3.4 30.8 1.0 OE1 C:GLU8 3.6 29.4 1.0 CD2 C:HIS24 3.6 21.4 1.0 OD2 C:ASP19 3.7 41.1 1.0 CB C:ASP10 3.9 10.3 1.0 O C:VAL32 4.0 26.6 1.0 CG C:GLU8 4.3 37.0 1.0 OD1 C:ASP10 4.3 36.0 1.0 CB C:ASP19 4.4 32.1 1.0 CA C:ASP19 4.6 48.5 1.0 ND1 C:HIS24 4.6 28.4 1.0 CG C:HIS24 4.7 32.8 1.0 CB C:SER34 4.8 12.3 1.0 CA C:CA245 4.9 47.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn246 b:48.0 occ:1.00 O D:HOH3243 1.8 29.3 1.0 OD2 D:ASP10 1.9 20.2 1.0 OD1 D:ASP19 2.1 33.1 1.0 OE2 D:GLU8 2.1 31.7 1.0 NE2 D:HIS24 2.6 13.1 1.0 CG D:ASP10 3.0 37.2 1.0 CG D:ASP19 3.0 37.5 1.0 CD D:GLU8 3.3 28.8 1.0 OD2 D:ASP19 3.4 42.0 1.0 CB D:ASP10 3.5 30.3 1.0 CE1 D:HIS24 3.5 13.1 1.0 CD2 D:HIS24 3.7 27.0 1.0 OE1 D:GLU8 4.0 14.7 1.0 OD1 D:ASP10 4.0 53.8 1.0 OG D:SER34 4.1 23.2 1.0 CB D:ASP19 4.4 28.9 1.0 CG D:GLU8 4.4 29.4 1.0 CA D:CA247 4.4 42.8 1.0 O D:VAL32 4.6 23.2 1.0 ND1 D:HIS24 4.7 18.9 1.0 CA D:ASP19 4.7 40.3 1.0 CG D:HIS24 4.8 32.8 1.0 CA D:ASP10 4.9 15.0 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