Calcium in PDB 1fyu: Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form

The structure of Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form, PDB code: 1fyu was solved by S.Elgavish, B.Shaanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.16 / 2.60
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	135.850, 135.850, 82.630, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.2

The structure of Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form (pdb code 1fyu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form, PDB code: 1fyu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca290 b:27.1 occ:1.00 OD1 A:ASN133 2.3 28.5 1.0 O A:PHE131 2.3 26.4 1.0 OD2 A:ASP136 2.3 25.5 1.0 O A:HOH405 2.4 24.7 1.0 OD2 A:ASP129 2.4 23.1 1.0 O A:HOH424 2.5 10.6 1.0 OD1 A:ASP129 2.5 23.1 1.0 CG A:ASP129 2.8 23.1 1.0 CG A:ASP136 3.4 25.5 1.0 CG A:ASN133 3.4 28.5 1.0 C A:PHE131 3.5 26.4 1.0 OD1 A:ASP136 3.8 25.5 1.0 N A:ASN133 3.9 27.5 1.0 CB A:ASN133 4.2 28.5 1.0 MN A:MN289 4.2 26.2 1.0 O A:HOH482 4.2 23.9 1.0 CB A:ASP129 4.3 23.1 1.0 CA A:PHE131 4.4 26.4 1.0 N A:PHE131 4.4 26.4 1.0 N A:SER132 4.4 20.6 1.0 NE1 A:TRP135 4.5 25.8 1.0 ND2 A:ASN133 4.5 28.5 1.0 CA A:SER132 4.5 20.6 1.0 CB A:ASP136 4.6 25.5 1.0 CB A:PHE131 4.6 28.3 1.0 CA A:GLY107 4.6 20.8 1.0 O A:GLY107 4.6 20.8 1.0 C A:SER132 4.7 20.6 1.0 CA A:ASN133 4.7 27.5 1.0 OD2 A:ASP89 4.7 19.7 1.0 CD1 A:PHE131 4.8 28.3 1.0 O A:ASP89 4.8 27.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Erythrina Corallodendron Lectin in Hexagonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca290 b:20.0 occ:1.00 O B:PHE131 2.3 19.3 1.0 OD2 B:ASP129 2.3 23.1 1.0 OD2 B:ASP136 2.3 16.0 1.0 OD1 B:ASN133 2.4 24.1 1.0 O B:HOH410 2.4 23.7 1.0 O B:HOH414 2.5 16.6 1.0 OD1 B:ASP129 2.6 23.1 1.0 CG B:ASP129 2.8 23.1 1.0 CG B:ASP136 3.4 16.0 1.0 C B:PHE131 3.5 19.3 1.0 CG B:ASN133 3.5 24.1 1.0 OD1 B:ASP136 3.9 16.0 1.0 N B:ASN133 4.0 21.4 1.0 CB B:ASN133 4.2 24.1 1.0 MN B:MN289 4.2 23.8 1.0 CB B:ASP129 4.3 23.1 1.0 CA B:PHE131 4.3 19.3 1.0 N B:PHE131 4.3 19.3 1.0 NE1 B:TRP135 4.4 18.3 1.0 O B:HOH411 4.4 16.4 1.0 N B:SER132 4.5 20.1 1.0 CB B:PHE131 4.5 19.1 1.0 CA B:GLY107 4.6 20.4 1.0 ND2 B:ASN133 4.6 24.1 1.0 O B:GLY107 4.6 20.4 1.0 CA B:SER132 4.6 20.1 1.0 OD2 B:ASP89 4.6 24.7 1.0 CB B:ASP136 4.7 16.0 1.0 O B:ASP89 4.7 21.9 1.0 CD1 B:PHE131 4.7 19.1 1.0 CA B:ASN133 4.7 21.4 1.0 C B:SER132 4.7 20.1 1.0 CZ2 B:TRP135 4.8 18.3 1.0 CE2 B:TRP135 4.9 18.3 1.0

S.Elgavish, B.Shaanan. Chemical Characteristics of Dimer Interfaces in the Legume Lectin Family. Protein Sci. V. 10 753 2001.
ISSN: ISSN 0961-8368
PubMed: 11274466
DOI: 10.1110/PS.44001