Calcium in PDB 1g8w: Improved Structure of Phytohemagglutinin-L From the Kidney Bean

The structure of Improved Structure of Phytohemagglutinin-L From the Kidney Bean, PDB code: 1g8w was solved by L.Buts, T.W.Hamelryck, M.Dao-Thi, R.Loris, L.Wyns, M.E.Etzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.479, 121.278, 89.957, 90.00, 93.18, 90.00
R / Rfree (%)	18.1 / 21.2

The structure of Improved Structure of Phytohemagglutinin-L From the Kidney Bean also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean (pdb code 1g8w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean, PDB code: 1g8w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca256 b:37.2 occ:1.00 OD1 A:ASP124 2.2 35.5 1.0 OD1 A:ASN128 2.3 51.2 1.0 O A:HOH1257 2.3 30.4 1.0 O A:HOH1258 2.4 35.9 1.0 O A:LEU126 2.4 43.5 1.0 OD2 A:ASP132 2.4 46.7 1.0 OD2 A:ASP124 2.7 29.0 1.0 CG A:ASP124 2.7 31.6 1.0 CG A:ASN128 3.5 42.3 1.0 C A:LEU126 3.6 40.7 1.0 CG A:ASP132 3.6 46.6 1.0 OD1 A:ASP132 4.1 50.9 1.0 CB A:ASP124 4.2 27.0 1.0 O A:HOH1254 4.2 25.8 1.0 N A:LEU126 4.2 36.1 1.0 CA A:LEU126 4.3 38.0 1.0 OD1 A:ASP86 4.3 35.3 1.0 O A:ASP86 4.3 30.9 1.0 ND2 A:ASN128 4.4 39.1 1.0 CB A:ASN128 4.4 44.8 1.0 N A:ASN128 4.4 40.8 1.0 CB A:LEU126 4.5 40.0 1.0 N A:TYR127 4.6 40.8 1.0 CA A:GLY104 4.6 32.5 1.0 O A:GLY104 4.6 36.4 1.0 MN A:MN253 4.7 41.4 1.0 NE1 A:TRP131 4.7 24.8 1.0 CB A:ASP132 4.7 40.7 1.0 C A:TYR127 4.8 39.4 1.0 CA A:TYR127 4.8 42.4 1.0 CA A:ASP124 4.9 26.4 1.0

Calcium binding site 2 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca256 b:22.1 occ:1.00 OD1 B:ASN128 2.2 44.9 1.0 OD1 B:ASP124 2.2 27.9 1.0 O B:HOH2257 2.2 27.1 1.0 O B:HOH2258 2.3 7.9 1.0 OD2 B:ASP132 2.4 37.6 1.0 O B:LEU126 2.4 31.0 1.0 OD2 B:ASP124 2.7 32.1 1.0 CG B:ASP124 2.8 25.8 1.0 CG B:ASN128 3.4 34.0 1.0 CG B:ASP132 3.5 35.7 1.0 C B:LEU126 3.6 32.3 1.0 OD1 B:ASP132 4.1 37.6 1.0 CB B:ASP124 4.2 21.2 1.0 N B:LEU126 4.3 26.5 1.0 ND2 B:ASN128 4.3 31.8 1.0 CA B:LEU126 4.3 29.3 1.0 OD1 B:ASP86 4.3 31.1 1.0 CB B:ASN128 4.3 31.5 1.0 O B:HOH2254 4.4 23.3 1.0 O B:ASP86 4.4 28.0 1.0 N B:ASN128 4.4 33.9 1.0 CB B:LEU126 4.5 30.5 1.0 N B:TYR127 4.6 31.7 1.0 CA B:GLY104 4.6 21.3 1.0 O B:GLY104 4.6 25.8 1.0 NE1 B:TRP131 4.6 27.5 1.0 CB B:ASP132 4.7 34.6 1.0 MN B:MN253 4.7 46.0 1.0 C B:TYR127 4.7 33.5 1.0 CA B:TYR127 4.8 33.0 1.0 CA B:ASP124 4.9 23.8 1.0 CA B:ASN128 5.0 35.4 1.0

Calcium binding site 3 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca256 b:33.9 occ:1.00 OD1 C:ASN128 2.2 46.8 1.0 OD1 C:ASP124 2.3 31.0 1.0 O C:HOH3258 2.4 35.2 1.0 O C:HOH3257 2.4 35.4 1.0 OD2 C:ASP132 2.5 42.6 1.0 O C:LEU126 2.6 37.8 1.0 OD2 C:ASP124 2.7 18.7 1.0 CG C:ASP124 2.8 24.6 1.0 CG C:ASN128 3.4 38.9 1.0 CG C:ASP132 3.6 43.9 1.0 C C:LEU126 3.8 37.1 1.0 OD1 C:ASP132 4.1 54.1 1.0 CB C:ASP124 4.3 21.8 1.0 OD1 C:ASP86 4.3 40.9 1.0 O C:HOH3254 4.3 26.8 1.0 ND2 C:ASN128 4.3 39.8 1.0 O C:ASP86 4.3 31.5 1.0 CB C:ASN128 4.4 40.1 1.0 O C:GLY104 4.4 42.3 1.0 N C:LEU126 4.4 30.3 1.0 CA C:GLY104 4.5 35.3 1.0 CA C:LEU126 4.5 32.0 1.0 N C:ASN128 4.6 38.6 1.0 NE1 C:TRP131 4.6 36.5 1.0 CB C:LEU126 4.6 37.8 1.0 MN C:MN253 4.6 44.1 1.0 N C:TYR127 4.8 37.5 1.0 CB C:ASP132 4.8 37.1 1.0 CA C:ASP124 4.9 27.7 1.0 C C:TYR127 4.9 36.4 1.0 C C:GLY104 4.9 36.6 1.0

Calcium binding site 4 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca256 b:34.7 occ:1.00 OD1 D:ASN128 2.1 46.9 1.0 O D:HOH4257 2.3 34.0 1.0 OD2 D:ASP132 2.4 41.7 1.0 OD1 D:ASP124 2.4 22.0 1.0 O D:HOH4258 2.4 26.1 1.0 O D:LEU126 2.6 31.8 1.0 OD2 D:ASP124 2.7 23.2 1.0 CG D:ASP124 2.8 27.1 1.0 CG D:ASN128 3.3 42.3 1.0 CG D:ASP132 3.5 41.6 1.0 C D:LEU126 3.7 32.7 1.0 OD1 D:ASP132 4.0 46.5 1.0 ND2 D:ASN128 4.2 44.5 1.0 CB D:ASN128 4.3 41.7 1.0 OD1 D:ASP86 4.3 41.6 1.0 CB D:ASP124 4.3 25.9 1.0 N D:ASN128 4.4 36.2 1.0 O D:GLY104 4.4 33.5 1.0 O D:ASP86 4.4 30.2 1.0 NE1 D:TRP131 4.5 40.0 1.0 O D:HOH4254 4.5 50.9 1.0 MN D:MN253 4.5 48.8 1.0 CA D:GLY104 4.5 33.2 1.0 N D:LEU126 4.5 33.3 1.0 CA D:LEU126 4.5 33.9 1.0 CB D:LEU126 4.7 35.4 1.0 CB D:ASP132 4.7 40.2 1.0 N D:TYR127 4.7 33.4 1.0 C D:TYR127 4.8 37.5 1.0 CA D:TYR127 4.9 37.3 1.0 C D:GLY104 5.0 32.8 1.0 CA D:ASN128 5.0 40.0 1.0

L.Buts, M.H.Dao-Thi, R.Loris, L.Wyns, M.Etzler, T.Hamelryck. Weak Protein-Protein Interactions in Lectins: the Crystal Structure of A Vegetative Lectin From the Legume Dolichos Biflorus. J.Mol.Biol. V. 309 193 2001.
ISSN: ISSN 0022-2836
PubMed: 11491289
DOI: 10.1006/JMBI.2001.4639