Calcium in PDB 4xxa: Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin

The structure of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin, PDB code: 4xxa was solved by B.L.Sousa, J.C.Silva-Filho, P.Kumar, A.Lyskowski, G.A.Bezerra, P.Delatorre, B.A.M.Rocha, R.M.S.Cunha, C.S.Nagano, K.Gruber, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.21 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.083, 96.083, 85.099, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.5

The structure of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin (pdb code 4xxa). 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 A Recombinant Vatairea Macrocarpa Seed Lectin, PDB code: 4xxa:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin


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 A Recombinant Vatairea Macrocarpa Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:35.2 occ:1.00 OD2 A:ASP126 2.2 31.9 1.0 O A:HOH433 2.3 30.0 1.0 OD2 A:ASP133 2.3 41.3 1.0 O A:PHE128 2.4 40.0 1.0 ND2 A:ASN130 2.5 34.7 1.0 OD1 A:ASP126 2.5 33.4 1.0 O A:HOH429 2.5 30.0 1.0 CG A:ASP126 2.7 31.4 1.0 CG A:ASP133 3.5 41.6 1.0 C A:PHE128 3.6 39.5 1.0 CG A:ASN130 3.7 44.1 1.0 OD1 A:ASP133 4.0 37.3 1.0 N A:ASN130 4.0 44.6 1.0 MN A:MN302 4.1 35.2 1.0 CB A:ASP126 4.2 30.5 1.0 CB A:ASN130 4.2 42.7 1.0 O A:HOH465 4.3 30.0 1.0 N A:PHE128 4.4 35.2 1.0 CA A:PHE128 4.4 38.9 1.0 NE1 A:TRP132 4.4 42.4 1.0 O A:ASP88 4.5 34.1 1.0 O A:GLY106 4.5 35.3 1.0 CB A:PHE128 4.6 39.3 1.0 N A:SER129 4.6 42.3 1.0 OD1 A:ASP88 4.6 35.5 1.0 OD1 A:ASN130 4.6 44.0 1.0 CE1 A:HIS138 4.6 40.6 1.0 CB A:ASP133 4.7 44.8 1.0 CA A:SER129 4.7 42.2 1.0 CA A:ASN130 4.8 45.7 1.0 CA A:GLY106 4.8 37.3 1.0 C A:SER129 4.8 44.9 1.0 CD2 A:PHE128 4.9 41.3 1.0 NE2 A:HIS138 5.0 39.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin


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 A Recombinant Vatairea Macrocarpa Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:35.2 occ:1.00 OD2 B:ASP126 2.1 31.1 1.0 O B:PHE128 2.3 36.9 1.0 OD2 B:ASP133 2.4 32.2 1.0 O B:HOH427 2.4 30.0 1.0 OD1 B:ASP126 2.5 26.3 1.0 ND2 B:ASN130 2.5 26.0 1.0 O B:HOH442 2.6 30.0 1.0 CG B:ASP126 2.6 26.7 1.0 CG B:ASP133 3.5 34.0 1.0 C B:PHE128 3.5 33.3 1.0 CG B:ASN130 3.7 35.4 1.0 N B:ASN130 4.0 36.4 1.0 OD1 B:ASP133 4.0 29.0 1.0 MN B:MN302 4.1 35.2 1.0 CB B:ASP126 4.1 28.3 1.0 CB B:ASN130 4.2 32.2 1.0 O B:HOH472 4.2 27.4 1.0 CA B:PHE128 4.4 34.5 1.0 N B:PHE128 4.4 33.4 1.0 NE1 B:TRP132 4.4 40.3 1.0 O B:GLY106 4.5 31.6 1.0 N B:SER129 4.5 37.5 1.0 O B:ASP88 4.5 31.3 1.0 CA B:GLY106 4.7 29.6 1.0 CA B:SER129 4.7 34.4 1.0 CB B:ASP133 4.7 33.3 1.0 CB B:PHE128 4.7 35.6 1.0 OD1 B:ASN130 4.7 33.7 1.0 OD1 B:ASP88 4.7 35.8 1.0 CA B:ASN130 4.7 35.4 1.0 C B:SER129 4.8 36.3 1.0 CE1 B:HIS138 4.8 30.6 1.0 CD2 B:PHE128 4.9 38.0 1.0

B.L.Sousa, J.C.Silva-Filho, P.Kumar, A.Lyskowski, G.A.Bezerra, P.Delatorre, B.A.M.Rocha, R.M.S.Cunha, C.S.Nagano, K.Gruber, B.S.Cavada. Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Int.J.Biochem.Cell Biol. 2016.
ISSN: ISSN 1357-2725