Calcium in PDB 2gnd: One Hour Edta Treatment, P. Angolensis Lectin

The structure of One Hour Edta Treatment, P. Angolensis Lectin, PDB code: 2gnd was solved by A.Garcia-Pino, L.Buts, L.Wyns, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.850, 83.370, 123.437, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.9

The structure of One Hour Edta Treatment, P. Angolensis Lectin also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the One Hour Edta Treatment, P. Angolensis Lectin (pdb code 2gnd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the One Hour Edta Treatment, P. Angolensis Lectin, PDB code: 2gnd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the One Hour Edta Treatment, P. Angolensis Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of One Hour Edta Treatment, P. Angolensis Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca256 b:24.5 occ:1.00 OD2 A:ASP141 2.3 20.4 1.0 O A:PHE132 2.4 26.9 1.0 OD1 A:ASN138 2.4 26.1 1.0 OD2 A:ASP130 2.4 15.9 1.0 O A:HOH259 2.5 22.4 1.0 OD1 A:ASP130 2.5 26.6 1.0 O A:HOH261 2.6 21.0 1.0 CG A:ASP130 2.8 21.9 1.0 CG A:ASN138 3.5 36.2 1.0 CG A:ASP141 3.5 23.3 1.0 C A:PHE132 3.6 29.4 1.0 CB A:ASN138 4.0 26.8 1.0 OD1 A:ASP141 4.1 28.8 1.0 MN A:MN255 4.2 21.7 1.0 CB A:ASP130 4.3 27.2 1.0 NE1 A:TRP140 4.4 29.1 1.0 CA A:PHE132 4.5 29.1 1.0 N A:TYR133 4.5 29.8 1.0 N A:PHE132 4.5 29.2 1.0 CA A:TYR133 4.5 29.8 1.0 O A:HOH257 4.5 19.7 1.0 CA A:GLY106 4.5 22.9 1.0 O A:GLY106 4.6 25.1 1.0 ND2 A:ASN138 4.6 33.3 1.0 CB A:ASP141 4.6 26.2 1.0 CB A:PHE132 4.7 33.4 1.0 O A:ASP86 4.7 23.4 1.0 OD1 A:ASP86 4.7 25.0 1.0

Calcium binding site 2 out of 2 in the One Hour Edta Treatment, P. Angolensis Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of One Hour Edta Treatment, P. Angolensis Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca254 b:24.4 occ:1.00 O B:PHE132 2.4 26.4 1.0 OD2 B:ASP141 2.4 26.4 1.0 O B:HOH256 2.5 27.2 1.0 OD2 B:ASP130 2.5 21.1 1.0 OD1 B:ASP130 2.5 22.4 1.0 O B:HOH257 2.5 23.4 1.0 OD1 B:ASN138 2.5 32.6 1.0 CG B:ASP130 2.8 21.2 1.0 CG B:ASP141 3.5 26.0 1.0 CG B:ASN138 3.5 38.4 1.0 C B:PHE132 3.6 29.2 1.0 CB B:ASN138 3.9 39.2 1.0 OD1 B:ASP141 4.0 29.9 1.0 MN B:MN255 4.2 26.2 1.0 CB B:ASP130 4.3 21.1 1.0 NE1 B:TRP140 4.3 33.1 1.0 CA B:PHE132 4.5 24.6 1.0 N B:PHE132 4.5 26.6 1.0 N B:TYR133 4.5 30.2 1.0 CA B:TYR133 4.6 30.8 1.0 CB B:PHE132 4.6 29.8 1.0 O B:HOH258 4.6 15.6 1.0 CB B:ASP141 4.6 28.3 1.0 O B:GLY106 4.7 27.2 1.0 O B:ASP86 4.7 22.8 1.0 CA B:GLY106 4.7 18.5 1.0 ND2 B:ASN138 4.7 30.6 1.0 OD1 B:ASP86 4.9 22.6 1.0 CE1 B:HIS146 5.0 18.1 1.0

A.Garcia-Pino, L.Buts, L.Wyns, R.Loris. Interplay Between Metal Binding and Cis/Trans Isomerization in Legume Lectins: Structural and Thermodynamic Study of P. Angolensis Lectin. J.Mol.Biol. V. 361 153 2006.
ISSN: ISSN 0022-2836
PubMed: 16824540
DOI: 10.1016/J.JMB.2006.06.006