Calcium in PDB 2gnm: P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours

The structure of P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours, PDB code: 2gnm 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 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.196, 82.974, 123.781, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.3

The structure of P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours (pdb code 2gnm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours, PDB code: 2gnm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca254 b:28.9 occ:0.50 OD2 A:ASP130 2.3 49.0 1.0 O A:HOH258 2.3 17.2 0.5 O A:HOH257 2.4 21.7 0.5 OE1 A:GLU128 2.5 51.6 1.0 NE2 A:HIS146 2.7 39.2 1.0 O A:HOH336 2.9 52.3 1.0 CE1 A:HIS146 3.1 37.8 1.0 CG A:ASP130 3.1 50.8 1.0 CD A:GLU128 3.3 36.9 1.0 CB A:ASP130 3.3 34.6 1.0 OE2 A:GLU128 3.7 34.9 1.0 O A:HOH321 3.8 30.3 0.5 CD2 A:HIS146 3.8 39.1 1.0 OD1 A:ASP130 4.2 51.9 1.0 ND1 A:HIS146 4.3 39.5 1.0 MN A:MN255 4.3 39.6 0.5 CG A:GLU128 4.5 25.6 1.0 OG A:SER156 4.5 35.5 1.0 O A:HOH276 4.6 45.1 1.0 CD1 A:TRP140 4.6 35.0 0.5 NE1 A:TRP140 4.6 36.5 0.5 CG A:HIS146 4.7 40.3 1.0 CA A:ASP130 4.8 33.5 1.0 O A:ILE154 4.9 39.7 1.0

Calcium binding site 2 out of 2 in the P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of P. Angolensis Lectin (Pal) Treated with Edta For 39 Hours within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca253 b:57.7 occ:0.50 O B:HOH268 2.4 22.3 0.5 NE2 B:HIS146 2.4 26.6 1.0 OE1 B:GLU128 2.5 50.9 1.0 O B:HOH267 2.5 20.5 0.5 OD2 B:ASP130 2.7 64.6 1.0 CE1 B:HIS146 3.0 28.0 1.0 CG B:ASP130 3.1 54.5 1.0 CD B:GLU128 3.6 35.0 1.0 O B:HOH266 3.6 28.2 0.5 OD1 B:ASP130 3.6 67.5 1.0 CB B:ASP130 3.7 37.2 1.0 CD2 B:HIS146 3.7 29.1 1.0 MN B:MN254 4.0 47.4 0.5 OE2 B:GLU128 4.1 31.4 1.0 NE1 B:TRP140 4.2 88.2 1.0 ND1 B:HIS146 4.3 30.7 1.0 CD1 B:TRP140 4.4 87.2 1.0 OG B:SER156 4.5 30.3 1.0 CA B:ASP141 4.6 76.3 1.0 CG B:HIS146 4.6 22.1 1.0 CG B:GLU128 4.8 28.3 1.0 O B:ILE154 5.0 37.5 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