Calcium in PDB 1fat: Phytohemagglutinin-L

The structure of Phytohemagglutinin-L, PDB code: 1fat was solved by T.Hamelryck, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.300, 121.200, 90.800, 90.00, 93.70, 90.00
R / Rfree (%)	20 / 23

The structure of Phytohemagglutinin-L also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Phytohemagglutinin-L (pdb code 1fat). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Phytohemagglutinin-L, PDB code: 1fat:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Phytohemagglutinin-L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca255 b:27.8 occ:1.00 O A:HOH306 2.0 87.7 1.0 OD1 A:ASN128 2.2 40.7 1.0 OD1 A:ASP124 2.3 19.7 1.0 O A:HOH305 2.4 33.7 1.0 O A:LEU126 2.4 20.5 1.0 OD2 A:ASP124 2.5 11.8 1.0 OD2 A:ASP132 2.5 36.6 1.0 CG A:ASP124 2.7 14.4 1.0 CG A:ASN128 3.4 34.5 1.0 CG A:ASP132 3.6 35.1 1.0 C A:LEU126 3.6 21.9 1.0 OD1 A:ASP132 4.0 40.9 1.0 OD1 A:ASP86 4.0 29.7 1.0 CB A:ASP124 4.2 6.3 1.0 O A:HOH307 4.2 25.7 1.0 ND2 A:ASN128 4.2 27.0 1.0 O A:ASP86 4.3 24.9 1.0 N A:LEU126 4.3 22.6 1.0 CA A:LEU126 4.4 20.7 1.0 MN A:MN254 4.4 36.7 1.0 CB A:ASN128 4.5 37.1 1.0 CB A:LEU126 4.5 22.5 1.0 N A:ASN128 4.6 28.5 1.0 O A:GLY104 4.6 19.3 1.0 NE1 A:TRP131 4.6 15.8 1.0 N A:TYR127 4.7 26.8 1.0 CA A:GLY104 4.7 20.4 1.0 C A:TYR127 4.8 26.6 1.0 CA A:ASP124 4.8 6.5 1.0 CB A:ASP132 4.9 30.7 1.0 CE1 A:HIS137 4.9 9.0 1.0 CA A:TYR127 4.9 29.3 1.0 NE2 A:HIS137 5.0 3.2 1.0

Calcium binding site 2 out of 4 in the Phytohemagglutinin-L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca255 b:15.6 occ:1.00 O B:HOH301 1.7 50.0 1.0 OD1 B:ASN128 2.1 36.4 1.0 O B:LEU126 2.3 17.1 1.0 OD2 B:ASP132 2.3 36.9 1.0 O B:HOH302 2.3 2.9 1.0 OD1 B:ASP124 2.4 12.4 1.0 OD2 B:ASP124 2.5 17.4 1.0 CG B:ASP124 2.7 12.8 1.0 CG B:ASN128 3.3 32.3 1.0 CG B:ASP132 3.4 31.0 1.0 C B:LEU126 3.5 23.4 1.0 OD1 B:ASP132 3.8 34.8 1.0 O B:HOH303 4.1 13.5 1.0 ND2 B:ASN128 4.1 27.7 1.0 OD1 B:ASP86 4.2 33.3 1.0 CB B:ASP124 4.2 5.5 1.0 N B:LEU126 4.3 12.1 1.0 CB B:ASN128 4.3 33.0 1.0 CA B:LEU126 4.3 19.7 1.0 N B:ASN128 4.3 27.2 1.0 O B:ASP86 4.4 24.7 1.0 N B:TYR127 4.5 26.2 1.0 CB B:LEU126 4.5 21.6 1.0 NE1 B:TRP131 4.5 16.7 1.0 MN B:MN254 4.5 42.7 1.0 C B:TYR127 4.7 24.5 1.0 CB B:ASP132 4.7 28.7 1.0 O B:GLY104 4.7 15.9 1.0 CA B:TYR127 4.7 25.4 1.0 CA B:GLY104 4.8 10.4 1.0 CE1 B:HIS137 4.9 4.3 1.0 CA B:ASP124 5.0 10.6 1.0 CA B:ASN128 5.0 33.1 1.0

Calcium binding site 3 out of 4 in the Phytohemagglutinin-L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca255 b:19.2 occ:1.00 OD1 C:ASN128 1.9 33.4 1.0 O C:HOH314 2.0 31.2 1.0 OD2 C:ASP132 2.4 31.8 1.0 O C:LEU126 2.5 27.4 1.0 OD2 C:ASP124 2.7 2.8 1.0 OD1 C:ASP124 2.7 13.3 1.0 O C:HOH313 2.7 57.1 1.0 CG C:ASP124 3.0 8.8 1.0 CG C:ASN128 3.1 32.9 1.0 CG C:ASP132 3.5 31.6 1.0 C C:LEU126 3.7 24.7 1.0 ND2 C:ASN128 3.8 32.8 1.0 OD1 C:ASP132 3.9 43.1 1.0 OD1 C:ASP86 4.0 31.8 1.0 CB C:ASN128 4.1 32.5 1.0 N C:ASN128 4.3 27.8 1.0 NE1 C:TRP131 4.4 19.8 1.0 O C:ASP86 4.4 20.2 1.0 CB C:ASP124 4.4 5.0 1.0 CA C:LEU126 4.5 17.8 1.0 N C:LEU126 4.5 18.2 1.0 MN C:MN254 4.5 40.0 1.0 O C:GLY104 4.6 26.9 1.0 CA C:GLY104 4.6 24.2 1.0 CB C:LEU126 4.6 24.0 1.0 C C:TYR127 4.6 24.3 1.0 N C:TYR127 4.7 25.9 1.0 CB C:ASP132 4.7 24.3 1.0 O C:HOH315 4.8 34.3 1.0 CA C:ASN128 4.8 33.4 1.0 CA C:TYR127 4.8 24.1 1.0

Calcium binding site 4 out of 4 in the Phytohemagglutinin-L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca255 b:15.4 occ:1.00 O D:HOH309 2.1 26.9 1.0 OD1 D:ASN128 2.1 35.6 1.0 OD2 D:ASP132 2.4 30.3 1.0 OD2 D:ASP124 2.4 6.8 1.0 OD1 D:ASP124 2.5 10.6 1.0 O D:LEU126 2.5 24.7 1.0 O D:HOH310 2.7 25.0 1.0 CG D:ASP124 2.7 13.5 1.0 CG D:ASN128 3.3 33.7 1.0 CG D:ASP132 3.4 30.2 1.0 O D:HOH311 3.7 74.3 1.0 C D:LEU126 3.7 20.4 1.0 OD1 D:ASP132 3.8 41.9 1.0 MN D:MN254 4.1 42.5 1.0 ND2 D:ASN128 4.2 36.7 1.0 CB D:ASP124 4.2 7.2 1.0 OD1 D:ASP86 4.2 31.7 1.0 CB D:ASN128 4.4 34.2 1.0 NE1 D:TRP131 4.4 17.1 1.0 O D:ASP86 4.4 20.9 1.0 N D:LEU126 4.5 16.8 1.0 N D:ASN128 4.5 25.7 1.0 CA D:LEU126 4.5 17.6 1.0 O D:GLY104 4.5 20.3 1.0 CB D:ASP132 4.7 26.9 1.0 CB D:LEU126 4.7 23.0 1.0 CA D:GLY104 4.7 21.0 1.0 N D:TYR127 4.7 22.8 1.0 C D:TYR127 4.8 25.8 1.0 CE1 D:HIS137 4.9 19.1 1.0 CA D:TYR127 4.9 24.8 1.0 CA D:ASP124 4.9 10.6 1.0 NE2 D:HIS137 4.9 7.6 1.0

T.W.Hamelryck, M.H.Dao-Thi, F.Poortmans, M.J.Chrispeels, L.Wyns, R.Loris. The Crystallographic Structure of Phytohemagglutinin-L. J.Biol.Chem. V. 271 20479 1996.
ISSN: ISSN 0021-9258
PubMed: 8702788
DOI: 10.1074/JBC.271.34.20479