Calcium in PDB 3zyr: Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide

The structure of Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide, PDB code: 3zyr was solved by R.G.Benevides, G.Ganne, B.S.Cavazza, A.Varrot, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.400, 76.980, 125.590, 90.00, 90.00, 90.00
R / Rfree (%)	15.56 / 18.816

The structure of Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide (pdb code 3zyr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide, PDB code: 3zyr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:5.9 occ:1.00 O A:PHE141 2.3 5.8 1.0 OD1 A:ASN147 2.3 5.2 1.0 OD2 A:ASP150 2.3 4.8 1.0 O A:HOH2137 2.4 6.2 1.0 O A:HOH2152 2.4 5.2 1.0 OD2 A:ASP139 2.5 6.1 1.0 OD1 A:ASP139 2.5 5.6 1.0 CG A:ASP139 2.8 4.7 1.0 CG A:ASN147 3.4 6.4 1.0 CG A:ASP150 3.4 6.1 1.0 C A:PHE141 3.5 6.8 1.0 OD1 A:ASP150 3.8 5.5 1.0 CB A:ASN147 4.0 7.4 1.0 MN A:MN400 4.2 6.0 1.0 CB A:ASP139 4.4 4.6 1.0 NE1 A:TRP149 4.4 10.1 1.0 CA A:PHE141 4.4 7.1 1.0 N A:PHE141 4.4 6.7 1.0 ND2 A:ASN147 4.5 8.2 1.0 N A:PHE142 4.5 6.7 1.0 CA A:PHE142 4.6 6.5 1.0 CA A:GLY115 4.6 6.5 1.0 OD1 A:ASP95 4.6 6.5 1.0 O A:GLY115 4.6 7.6 1.0 O A:HOH2175 4.7 6.1 1.0 CB A:ASP150 4.7 7.2 1.0 O A:ASP95 4.7 5.4 1.0 CE1 A:HIS155 4.7 7.6 1.0 CB A:PHE141 4.7 5.3 1.0 NE2 A:HIS155 5.0 5.7 1.0

Calcium binding site 2 out of 2 in the Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Lectin From Platypodium Elegans in Complex with Heptasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:7.3 occ:1.00 OD2 B:ASP150 2.3 6.8 1.0 OD1 B:ASN147 2.3 8.2 1.0 O B:PHE141 2.3 6.7 1.0 O B:HOH2084 2.4 7.4 1.0 O B:HOH2098 2.4 9.7 1.0 OD2 B:ASP139 2.5 5.8 1.0 OD1 B:ASP139 2.5 6.1 1.0 CG B:ASP139 2.8 5.8 1.0 CG B:ASN147 3.4 8.3 1.0 CG B:ASP150 3.4 6.1 1.0 C B:PHE141 3.6 7.3 1.0 OD1 B:ASP150 3.8 5.4 1.0 CB B:ASN147 4.0 7.9 1.0 MN B:MN400 4.2 6.7 1.0 CB B:ASP139 4.3 5.5 1.0 ND2 B:ASN147 4.4 8.6 1.0 NE1 B:TRP149 4.4 8.4 1.0 N B:PHE141 4.5 6.0 1.0 CA B:PHE141 4.5 7.2 1.0 N B:PHE142 4.5 8.4 1.0 CA B:PHE142 4.6 8.6 1.0 O B:GLY115 4.6 7.6 1.0 CA B:GLY115 4.6 7.4 1.0 O B:HOH2113 4.6 8.0 1.0 OD1 B:ASP95 4.7 7.4 1.0 CB B:ASP150 4.7 8.0 1.0 O B:ASP95 4.7 6.7 1.0 CE1 B:HIS155 4.7 7.8 1.0 CB B:PHE141 4.8 6.6 1.0 NE2 B:HIS155 4.9 6.7 1.0

R.G.Benevides, G.Ganne, R.D.C.Simoes, V.Schubert, M.Niemietz, C.Unverzagt, V.Chazalet, C.Breton, A.Varrot, B.S.Cavada, A.Imberty. A Lectin From Platypodium Elegans with Unusual Specificity and Affinity For Asymmetric Complex N-Glycans. J.Biol.Chem. V. 287 26352 2012.
ISSN: ISSN 0021-9258
PubMed: 22692206
DOI: 10.1074/JBC.M112.375816