Calcium in PDB 1lgc: Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety

The structure of Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety, PDB code: 1lgc was solved by Y.Bourne, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.000, 117.000, 120.100, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / n/a

The structure of Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Calcium atom in the Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety (pdb code 1lgc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety, PDB code: 1lgc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:36.3 occ:1.00 OD1 A:ASN125 2.0 32.7 1.0 O A:PHE123 2.0 28.6 1.0 O A:HOH374 2.1 12.9 1.0 OD1 A:ASP121 2.3 25.0 1.0 OD2 A:ASP121 2.5 33.6 1.0 CG A:ASP121 2.8 27.9 1.0 OD1 A:ASP81 2.9 47.1 1.0 OD2 A:ASP129 3.1 38.2 1.0 C A:PHE123 3.1 30.1 1.0 CG A:ASN125 3.2 29.8 1.0 OD2 A:ASP81 3.3 60.4 1.0 CG A:ASP81 3.5 50.2 1.0 CB A:PHE123 3.7 24.4 1.0 CA A:PHE123 3.7 28.7 1.0 N A:PHE123 3.9 30.1 1.0 ND2 A:ASN125 3.9 23.5 1.0 CG A:ASP129 4.2 38.8 1.0 CD1 A:PHE123 4.2 21.2 1.0 N A:TYR124 4.2 32.6 1.0 N A:ASN125 4.3 36.6 1.0 CB A:ASN125 4.3 30.9 1.0 CB A:ASP121 4.3 21.1 1.0 O A:ASP81 4.4 43.1 1.0 O A:GLY99 4.4 29.5 1.0 CG A:PHE123 4.5 25.3 1.0 C A:TYR124 4.6 35.9 1.0 CA A:TYR124 4.6 35.1 1.0 OD1 A:ASP129 4.6 35.2 1.0 CA A:GLY99 4.8 27.3 1.0 CA A:ASN125 4.9 30.4 1.0 CB A:ASP81 4.9 36.9 1.0 NE1 A:TRP128 5.0 27.1 1.0

Calcium binding site 2 out of 3 in the Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:34.5 occ:1.00 OD1 C:ASN125 1.9 41.0 1.0 OD1 C:ASP121 2.3 45.0 1.0 O C:PHE123 2.5 33.0 1.0 OD2 C:ASP121 2.6 38.2 1.0 CG C:ASP121 2.8 40.6 1.0 CG C:ASN125 3.1 42.3 1.0 OD1 C:ASP81 3.4 44.5 1.0 C C:PHE123 3.5 26.4 1.0 OD2 C:ASP129 3.5 59.0 1.0 ND2 C:ASN125 3.7 34.1 1.0 O C:ASP81 3.8 38.4 1.0 CB C:PHE123 3.9 24.6 1.0 CA C:PHE123 4.0 20.8 1.0 N C:PHE123 4.1 21.6 1.0 CD2 C:PHE123 4.2 25.7 1.0 O C:GLY99 4.2 39.9 1.0 CA C:GLY99 4.3 39.4 1.0 CB C:ASN125 4.3 41.8 1.0 CB C:ASP121 4.3 31.5 1.0 CG C:PHE123 4.5 26.3 1.0 N C:ASN125 4.6 38.8 1.0 N C:TYR124 4.6 30.3 1.0 CG C:ASP129 4.6 51.8 1.0 CG C:ASP81 4.6 42.5 1.0 C C:GLY99 4.7 36.2 1.0 O4 I:MAN501 4.8 29.2 1.0 NE1 C:TRP128 4.8 41.0 1.0 C C:TYR124 4.9 30.7 1.0 C C:ASP81 4.9 39.7 1.0 OD1 C:ASP129 4.9 48.2 1.0

Calcium binding site 3 out of 3 in the Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Interaction of A Legume Lectin with the N2 Fragment of Human Lactotransferrin or with the Isolated Biantennary Glycopeptide: Role of the Fucose Moiety within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:34.0 occ:1.00 OD1 E:ASN125 2.0 39.4 1.0 O E:PHE123 2.1 44.4 1.0 OD1 E:ASP121 2.5 38.4 1.0 OD2 E:ASP121 2.5 29.2 1.0 OD1 E:ASP81 2.8 69.7 1.0 CG E:ASP121 2.9 35.5 1.0 C E:PHE123 3.1 41.1 1.0 CG E:ASN125 3.1 33.3 1.0 CB E:PHE123 3.4 27.9 1.0 OD2 E:ASP129 3.4 45.7 1.0 CG E:ASP81 3.5 66.0 1.0 CA E:PHE123 3.6 35.3 1.0 OD2 E:ASP81 3.7 70.5 1.0 ND2 E:ASN125 3.7 20.8 1.0 CD2 E:PHE123 3.8 23.8 1.0 O E:ASP81 3.8 42.0 1.0 N E:PHE123 3.8 29.2 1.0 CG E:PHE123 4.0 23.4 1.0 CA E:GLY99 4.1 29.9 1.0 N E:TYR124 4.2 42.5 1.0 N E:ASN125 4.3 45.9 1.0 CB E:ASN125 4.3 38.2 1.0 CB E:ASP121 4.4 31.7 1.0 O E:GLY99 4.5 28.0 1.0 CG E:ASP129 4.6 42.5 1.0 CA E:TYR124 4.6 45.3 1.0 C E:TYR124 4.7 46.5 1.0 O4 J:MAN501 4.7 44.1 1.0 C E:ASP81 4.8 46.6 1.0 CB E:ASP81 4.8 55.4 1.0 C E:GLY99 4.9 28.5 1.0 CA E:ASN125 4.9 41.9 1.0 OD1 E:ASP129 5.0 38.7 1.0 CE2 E:PHE123 5.0 21.4 1.0

Y.Bourne, J.Mazurier, D.Legrand, P.Rouge, J.Montreuil, G.Spik, C.Cambillau. Structures of A Legume Lectin Complexed with the Human Lactotransferrin N2 Fragment, and with An Isolated Biantennary Glycopeptide: Role of the Fucose Moiety. Structure V. 2 209 1994.
ISSN: ISSN 0969-2126
PubMed: 8069634
DOI: 10.1016/S0969-2126(00)00022-8