Calcium in PDB 3zvx: Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside

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

Resolution Low / High (Å)	42.25 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.620, 80.680, 148.760, 90.00, 90.00, 90.00
R / Rfree (%)	19.497 / 25.18

The structure of Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside 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 A Trimannoside (pdb code 3zvx). 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 A Trimannoside, PDB code: 3zvx:
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 A Trimannoside


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 A Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:19.7 occ:1.00 OD2 A:ASP150 2.3 17.0 1.0 O A:HOH2090 2.3 19.0 1.0 O A:PHE141 2.4 20.7 1.0 OD1 A:ASN147 2.4 20.2 1.0 OD2 A:ASP139 2.5 16.1 1.0 O A:HOH2101 2.5 16.0 1.0 OD1 A:ASP139 2.5 16.6 1.0 CG A:ASP139 2.9 19.1 1.0 CG A:ASN147 3.4 23.7 1.0 CG A:ASP150 3.4 19.7 1.0 C A:PHE141 3.6 20.7 1.0 OD1 A:ASP150 3.9 17.6 1.0 CB A:ASN147 4.0 25.2 1.0 MN A:MN300 4.2 20.9 1.0 CB A:ASP139 4.4 19.0 1.0 CA A:PHE142 4.4 21.8 1.0 N A:PHE142 4.5 21.6 1.0 NE1 A:TRP149 4.5 22.5 1.0 ND2 A:ASN147 4.5 21.4 1.0 O A:GLY115 4.5 17.0 1.0 CA A:PHE141 4.6 20.8 1.0 N A:PHE141 4.6 20.0 1.0 OD1 A:ASP95 4.6 15.5 1.0 O A:HOH2114 4.7 15.1 1.0 CA A:GLY115 4.7 18.9 1.0 CB A:ASP150 4.7 20.9 1.0 O A:ASP95 4.8 15.3 1.0 CE1 A:HIS155 4.8 20.4 1.0 CB A:PHE141 4.9 20.7 1.0

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


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 A Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:21.8 occ:1.00 O B:HOH2068 2.2 16.9 1.0 OD1 B:ASP139 2.3 22.1 1.0 O B:PHE141 2.4 25.7 1.0 OD2 B:ASP150 2.4 24.2 1.0 OD1 B:ASN147 2.4 28.8 1.0 O B:HOH2082 2.5 15.2 1.0 OD2 B:ASP139 2.6 20.2 1.0 CG B:ASP139 2.8 20.5 1.0 CG B:ASN147 3.4 29.8 1.0 CG B:ASP150 3.5 24.8 1.0 C B:PHE141 3.6 25.6 1.0 OD1 B:ASP150 3.9 22.5 1.0 CB B:ASN147 4.1 28.2 1.0 O B:GLY115 4.3 16.8 1.0 MN B:MN300 4.3 21.9 1.0 CB B:ASP139 4.3 21.1 1.0 NE1 B:TRP149 4.4 25.8 1.0 CA B:PHE141 4.5 24.6 1.0 ND2 B:ASN147 4.5 29.0 1.0 O B:HOH2096 4.5 17.3 1.0 N B:PHE142 4.5 26.7 1.0 N B:PHE141 4.5 23.8 1.0 CA B:GLY115 4.6 19.0 1.0 CA B:PHE142 4.6 28.1 1.0 CB B:PHE141 4.7 23.9 1.0 OD1 B:ASP95 4.7 16.4 1.0 O B:ASP95 4.7 16.2 1.0 CB B:ASP150 4.8 25.1 1.0 CD2 B:PHE141 4.9 24.6 1.0 C B:GLY115 4.9 18.4 1.0 CE1 B:HIS155 4.9 19.5 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