Title : Structure of human diferric
lactoferrin refined at 2.2 A resolution
Abstract :
- The three-dimensional structure of the diferric form of human lactoferrin has been refined at 2.2 A resolution, using synchrotron data combined with a lower resolution (3.2 A) diffractometer data set
- Following restrained least-squares refinement and model rebuilding the final model comprises 5330 protein atoms (691 residues ), 2Fe(3+) and 2CO(3)(2-) ions, 469 solvent molecules and 98 carbohydrate atoms (eight sugar residues).
- Root-mean-square deviations from standard geometry are 0.015 A for bond lengths and 0.038 A for angle (1-3) distances, and the final crystallographic R-factor is 0.179 for all 39 113 reflections in the resolution range 8.0-2.2 A
- A close structural similarity is seen between the two lobes of the molecule, with differences mainly in loops and turns
- The two binding sites are extremely similar, the only apparent differences being a slightly more asymmetric bidentate binding of the carbonate ion to the metal, and a slightly longer Fe-O bond to one of the Tyr ligands, in the N-lobe site relative to the C-lobe site
- Distinct differences are seen in the interactions made by two cationic groups, Arg210 and Lys546 , behind the iron site , and these may influence the stability of the two metal sites
- Analysis of interdomain and interlobe interactions shows that these are few in number which is consistent with the known flexibility of the molecule with respect to domain and lobe movements
- Internal water molecules are found in discrete sites and in two large clusters (in the two interdomain clefts) and one tightly bound water molecule is present 3.8 A from the Fe atom in each lobe
- The carbohydrate is weakly defined and has been modelled to a limited extent; two sugar residues of the N-lobe glycan and six of the C-lobe glycan
- Only one direct protein-carbohydrate contact can be found