Manganese 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:

Calcium

(Ca)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn254 b:36.7 occ:1.00 O A:HOH308 1.5 58.7 1.0 O A:HOH307 1.7 25.7 1.0 OE2 A:GLU122 2.0 29.7 1.0 NE2 A:HIS137 2.1 3.2 1.0 OD2 A:ASP124 2.3 11.8 1.0 OD1 A:ASP132 2.4 40.9 1.0 CD A:GLU122 3.1 25.2 1.0 CD2 A:HIS137 3.1 3.9 1.0 CE1 A:HIS137 3.2 9.0 1.0 CG A:ASP132 3.3 35.1 1.0 CG A:ASP124 3.3 14.4 1.0 OE1 A:GLU122 3.5 20.3 1.0 OD2 A:ASP132 3.6 36.6 1.0 O A:HOH305 3.6 33.7 1.0 OG A:SER147 3.7 20.9 1.0 CB A:ASP124 3.7 6.3 1.0 O A:ILE145 4.2 28.1 1.0 CG A:HIS137 4.3 3.2 1.0 ND1 A:HIS137 4.3 9.4 1.0 CG A:GLU122 4.4 22.5 1.0 CA A:CA255 4.4 27.8 1.0 OD1 A:ASP124 4.5 19.7 1.0 CB A:ASP132 4.6 30.7 1.0 CD1 A:TRP131 4.7 18.2 1.0 NE1 A:TRP131 4.7 15.8 1.0 CD A:PRO133 4.7 27.7 1.0 CA A:ASP132 4.9 29.4 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn254 b:42.7 occ:1.00 O B:HOH304 1.5 61.7 1.0 NE2 B:HIS137 2.0 2.0 1.0 O B:HOH303 2.0 13.5 1.0 OE2 B:GLU122 2.1 18.8 1.0 OD1 B:ASP132 2.3 34.8 1.0 OD2 B:ASP124 2.5 17.4 1.0 CD2 B:HIS137 3.0 2.0 1.0 CE1 B:HIS137 3.1 4.3 1.0 CD B:GLU122 3.2 19.8 1.0 CG B:ASP132 3.3 31.0 1.0 CG B:ASP124 3.4 12.8 1.0 OG B:SER147 3.5 24.4 1.0 OE1 B:GLU122 3.6 16.8 1.0 OD2 B:ASP132 3.7 36.9 1.0 CB B:ASP124 3.7 5.5 1.0 O B:HOH302 4.0 2.9 1.0 CG B:HIS137 4.2 2.0 1.0 ND1 B:HIS137 4.2 2.0 1.0 O B:ILE145 4.3 21.7 1.0 CB B:ASP132 4.5 28.7 1.0 CG B:GLU122 4.5 16.2 1.0 CA B:CA255 4.5 15.6 1.0 OD1 B:ASP124 4.6 12.4 1.0 CD B:PRO133 4.6 25.3 1.0 CD1 B:TRP131 4.7 23.5 1.0 CA B:ASP132 4.7 25.0 1.0 NE1 B:TRP131 4.8 16.7 1.0 CB B:SER147 4.9 12.0 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn254 b:40.0 occ:1.00 O C:HOH316 1.5 50.4 1.0 NE2 C:HIS137 1.8 13.1 1.0 OE2 C:GLU122 2.2 31.8 1.0 OD2 C:ASP124 2.2 2.8 1.0 O C:HOH315 2.4 34.3 1.0 OD1 C:ASP132 2.4 43.1 1.0 CD2 C:HIS137 2.8 15.4 1.0 CE1 C:HIS137 2.9 15.8 1.0 CG C:ASP124 3.2 8.8 1.0 CG C:ASP132 3.2 31.6 1.0 CD C:GLU122 3.4 21.4 1.0 CB C:ASP124 3.5 5.0 1.0 O C:HOH313 3.5 57.1 1.0 OD2 C:ASP132 3.6 31.8 1.0 OG C:SER147 3.8 29.0 1.0 OE1 C:GLU122 3.8 24.0 1.0 CG C:HIS137 4.0 8.2 1.0 ND1 C:HIS137 4.0 9.5 1.0 OD1 C:ASP124 4.4 13.3 1.0 CB C:ASP132 4.4 24.3 1.0 CD C:PRO133 4.4 34.6 1.0 CA C:CA255 4.5 19.2 1.0 O C:ILE145 4.6 27.9 1.0 CG C:GLU122 4.6 16.9 1.0 CA C:ASP132 4.7 26.0 1.0 CD1 C:TRP131 4.8 13.8 1.0 NE1 C:TRP131 4.9 19.8 1.0 CA C:ASP124 4.9 16.0 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Phytohemagglutinin-L within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn254 b:42.5 occ:1.00 O D:HOH311 1.5 74.3 1.0 O D:HOH312 1.5 87.4 1.0 OE2 D:GLU122 2.2 35.0 1.0 OD2 D:ASP124 2.3 6.8 1.0 OD1 D:ASP132 2.3 41.9 1.0 NE2 D:HIS137 2.4 7.6 1.0 CD D:GLU122 3.2 27.7 1.0 CG D:ASP132 3.2 30.2 1.0 CG D:ASP124 3.4 13.5 1.0 CD2 D:HIS137 3.4 16.8 1.0 OE1 D:GLU122 3.4 30.5 1.0 CE1 D:HIS137 3.4 19.1 1.0 OD2 D:ASP132 3.5 30.3 1.0 O D:HOH310 3.6 25.0 1.0 OG D:SER147 3.7 25.6 1.0 CB D:ASP124 3.8 7.2 1.0 O D:ILE145 4.0 25.2 1.0 CA D:CA255 4.1 15.4 1.0 NE1 D:TRP131 4.4 17.1 1.0 CD1 D:TRP131 4.4 17.0 1.0 CB D:ASP132 4.5 26.9 1.0 OD1 D:ASP124 4.5 10.6 1.0 CG D:GLU122 4.5 19.9 1.0 ND1 D:HIS137 4.6 17.1 1.0 CG D:HIS137 4.6 7.7 1.0 CA D:ASP132 4.8 26.6 1.0 CD D:PRO133 4.8 35.2 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