Calcium in PDB 2gnt: Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment)

The structure of Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment), PDB code: 2gnt 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 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.192, 83.682, 123.830, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.4

The binding sites of Calcium atom in the Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment) (pdb code 2gnt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment), PDB code: 2gnt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca253 b:22.4 occ:1.00 OD2 A:ASP141 2.3 26.4 1.0 OD1 A:ASN138 2.4 28.0 1.0 O A:HOH256 2.4 22.6 1.0 OD2 A:ASP130 2.4 22.1 1.0 O A:PHE132 2.4 26.8 1.0 O A:HOH255 2.5 22.6 1.0 OD1 A:ASP130 2.5 25.6 1.0 CG A:ASP130 2.8 25.1 1.0 CG A:ASP141 3.4 17.5 1.0 CG A:ASN138 3.5 38.3 1.0 C A:PHE132 3.6 31.4 1.0 OD1 A:ASP141 3.9 22.1 1.0 CB A:ASN138 4.0 26.9 1.0 CA A:CA254 4.2 29.2 1.0 CB A:ASP130 4.3 19.2 1.0 NE1 A:TRP140 4.5 34.8 1.0 CA A:PHE132 4.5 31.6 1.0 N A:PHE132 4.6 28.6 1.0 N A:TYR133 4.6 30.4 1.0 CA A:TYR133 4.6 25.2 1.0 ND2 A:ASN138 4.6 37.9 1.0 CA A:GLY106 4.6 24.2 1.0 CB A:ASP141 4.6 27.7 1.0 O A:GLY106 4.7 26.6 1.0 O A:HOH261 4.7 21.2 1.0 CB A:PHE132 4.7 29.4 1.0 O A:ASP86 4.7 21.5 1.0 OD1 A:ASP86 4.8 28.2 1.0

Calcium binding site 2 out of 4 in the Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca254 b:29.2 occ:1.00 OD1 A:ASP141 2.3 22.1 1.0 OE1 A:GLU128 2.3 22.4 1.0 O A:HOH262 2.3 26.5 1.0 OD2 A:ASP130 2.3 22.1 1.0 O A:HOH261 2.5 21.2 1.0 NE2 A:HIS146 2.5 21.3 1.0 CG A:ASP141 3.2 17.5 1.0 CD A:GLU128 3.3 24.7 1.0 CG A:ASP130 3.3 25.1 1.0 CE1 A:HIS146 3.4 21.3 1.0 OE2 A:GLU128 3.6 26.4 1.0 CD2 A:HIS146 3.6 20.0 1.0 OD2 A:ASP141 3.6 26.4 1.0 CB A:ASP130 3.6 19.2 1.0 O A:HOH255 3.9 22.6 1.0 CA A:CA253 4.2 22.4 1.0 OG A:SER156 4.4 22.4 1.0 CB A:ASP141 4.4 27.7 1.0 OD1 A:ASP130 4.4 25.6 1.0 CD1 A:TRP140 4.5 26.4 1.0 O A:ILE154 4.6 23.3 1.0 ND1 A:HIS146 4.6 22.8 1.0 NE1 A:TRP140 4.6 34.8 1.0 O A:HOH259 4.6 33.0 1.0 CG A:GLU128 4.7 14.3 1.0 CG A:HIS146 4.7 21.7 1.0 CA A:ASP141 4.8 30.0 1.0

Calcium binding site 3 out of 4 in the Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca253 b:21.4 occ:1.00 O B:PHE132 2.4 22.1 1.0 OD2 B:ASP141 2.4 28.0 1.0 OD1 B:ASN138 2.4 24.7 1.0 O B:HOH256 2.4 24.4 1.0 OD2 B:ASP130 2.4 18.1 1.0 O B:HOH255 2.5 21.2 1.0 OD1 B:ASP130 2.6 20.9 1.0 CG B:ASP130 2.8 23.1 1.0 CG B:ASP141 3.5 20.5 1.0 CG B:ASN138 3.5 37.5 1.0 C B:PHE132 3.6 32.4 1.0 OD1 B:ASP141 4.0 22.9 1.0 CB B:ASN138 4.0 31.4 1.0 CA B:CA254 4.3 27.3 1.0 CB B:ASP130 4.3 22.3 1.0 CA B:PHE132 4.4 24.6 1.0 N B:PHE132 4.5 25.2 1.0 N B:TYR133 4.5 30.2 1.0 NE1 B:TRP140 4.5 31.2 1.0 CB B:PHE132 4.6 25.0 1.0 CA B:TYR133 4.6 30.9 1.0 ND2 B:ASN138 4.6 30.8 1.0 O B:ASP86 4.6 17.1 1.0 CB B:ASP141 4.7 25.6 1.0 CA B:GLY106 4.7 21.2 1.0 O B:GLY106 4.7 23.1 1.0 O B:HOH260 4.8 24.6 1.0 OD1 B:ASP86 4.8 21.5 1.0

Calcium binding site 4 out of 4 in the Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Edta Treated P. Angolensis Lectin (Pal) Remetallized with Calcium (1 Hour Treatment) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca254 b:27.3 occ:1.00 OD1 B:ASP141 2.3 22.9 1.0 OE1 B:GLU128 2.3 16.1 1.0 O B:HOH260 2.3 24.6 1.0 O B:HOH259 2.4 20.4 1.0 OD2 B:ASP130 2.4 18.1 1.0 NE2 B:HIS146 2.6 19.4 1.0 CG B:ASP141 3.2 20.5 1.0 CD B:GLU128 3.3 22.5 1.0 CG B:ASP130 3.4 23.1 1.0 CE1 B:HIS146 3.4 19.6 1.0 OE2 B:GLU128 3.6 18.4 1.0 CD2 B:HIS146 3.6 20.1 1.0 CB B:ASP130 3.7 22.3 1.0 OD2 B:ASP141 3.7 28.0 1.0 O B:HOH255 3.9 21.2 1.0 CA B:CA253 4.3 21.4 1.0 OG B:SER156 4.3 22.8 1.0 CB B:ASP141 4.4 25.6 1.0 NE1 B:TRP140 4.5 31.2 1.0 OD1 B:ASP130 4.5 20.9 1.0 CD1 B:TRP140 4.5 26.7 1.0 ND1 B:HIS146 4.6 18.9 1.0 O B:ILE154 4.6 23.7 1.0 O B:HOH261 4.6 33.3 1.0 CG B:GLU128 4.7 14.9 1.0 CG B:HIS146 4.7 21.6 1.0 CA B:ASP141 4.8 26.5 1.0 CD B:PRO142 5.0 30.6 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