Calcium in PDB 1dbn: Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose

The structure of Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose, PDB code: 1dbn was solved by A.Imberty, C.Gautier, J.Lescar, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.742, 88.450, 84.496, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.3

The structure of Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose (pdb code 1dbn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose, PDB code: 1dbn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:43.9 occ:1.00 O A:HOH827 2.3 26.8 1.0 OD1 A:ASP137 2.3 57.8 1.0 O A:HOH828 2.3 30.4 1.0 O A:TYR131 2.3 53.5 1.0 OD1 A:ASP140 2.4 50.6 1.0 OD1 A:ASP129 2.4 40.4 1.0 OD2 A:ASP129 2.5 34.9 1.0 CG A:ASP129 2.8 39.9 1.0 CG A:ASP137 3.4 52.8 1.0 C A:TYR131 3.5 50.6 1.0 CG A:ASP140 3.6 51.2 1.0 CB A:ASP137 3.8 53.8 1.0 OD2 A:ASP140 4.2 49.2 1.0 MN A:MN302 4.2 49.5 1.0 O A:HOH825 4.2 41.5 1.0 CA A:TYR131 4.3 47.8 1.0 CB A:TYR131 4.3 44.2 1.0 CB A:ASP129 4.3 43.2 1.0 N A:TYR131 4.4 43.7 1.0 OD2 A:ASP137 4.4 51.7 1.0 O A:LYS107 4.5 41.6 1.0 NE1 A:TRP139 4.5 47.0 1.0 N A:PHE132 4.5 54.1 1.0 CD1 A:TYR131 4.6 52.7 1.0 OD1 A:ASP87 4.6 43.3 1.0 CA A:PHE132 4.7 60.9 1.0 CB A:ASP140 4.7 50.8 1.0 O A:ASP87 4.7 43.0 1.0 CE1 A:HIS145 4.8 37.5 1.0 CG A:TYR131 5.0 50.7 1.0

Calcium binding site 2 out of 2 in the Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Maackia Amurensis Leukoagglutinin (Lectin) with Sialyllactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:53.5 occ:1.00 OD1 B:ASP140 2.3 54.7 1.0 OD1 B:ASP129 2.3 59.1 1.0 OD2 B:ASP129 2.3 51.5 1.0 O B:TYR131 2.4 58.9 1.0 O B:HOH928 2.5 58.0 1.0 O B:HOH927 2.5 58.0 1.0 OD1 B:ASP137 2.5 66.0 1.0 CG B:ASP129 2.6 57.5 1.0 CG B:ASP140 3.4 55.0 1.0 CG B:ASP137 3.5 62.1 1.0 C B:TYR131 3.6 57.6 1.0 CB B:ASP137 3.9 62.9 1.0 OD2 B:ASP140 4.0 54.5 1.0 MN B:MN304 4.1 44.0 1.0 CB B:ASP129 4.2 51.7 1.0 CA B:TYR131 4.4 54.6 1.0 NE1 B:TRP139 4.4 62.2 1.0 N B:TYR131 4.5 53.1 1.0 O B:HOH925 4.5 34.6 1.0 CB B:TYR131 4.5 53.4 1.0 O B:LYS107 4.5 56.0 1.0 CB B:ASP140 4.6 53.6 1.0 N B:PHE132 4.6 61.0 1.0 OD2 B:ASP137 4.6 60.2 1.0 CE1 B:HIS145 4.7 35.2 1.0 CA B:PHE132 4.7 63.7 1.0 O B:ASP87 4.8 52.4 1.0 CD1 B:TYR131 4.8 56.2 1.0 OD1 B:ASP87 4.8 49.4 1.0

A.Imberty, C.Gautier, J.Lescar, S.Perez, L.Wyns, R.Loris. An Unusual Carbohydrate Binding Site Revealed By the Structures of Two Maackia Amurensis Lectins Complexed with Sialic Acid-Containing Oligosaccharides. J.Biol.Chem. V. 275 17541 2000.
ISSN: ISSN 0021-9258
PubMed: 10747930
DOI: 10.1074/JBC.M000560200