Ytterbium in PDB 4x1d: Ytterbium-Bound Human Serum Transferrin

The structure of Ytterbium-Bound Human Serum Transferrin, PDB code: 4x1d was solved by M.Wang, H.Zhang, H.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.502, 136.863, 107.843, 90.00, 90.41, 90.00
R / Rfree (%)	19.8 / 23.1

The binding sites of Ytterbium atom in the Ytterbium-Bound Human Serum Transferrin (pdb code 4x1d). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 2 binding sites of Ytterbium where determined in the Ytterbium-Bound Human Serum Transferrin, PDB code: 4x1d:
Jump to Ytterbium binding site number: 1; 2;

Ytterbium binding site 1 out of 2 in the Ytterbium-Bound Human Serum Transferrin


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Ytterbium-Bound Human Serum Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb701 b:49.9 occ:1.00 O9 A:MLI702 2.2 37.4 1.0 O7 A:MLI702 2.2 36.8 1.0 OD1 A:ASP392 2.2 62.6 1.0 NE2 A:HIS585 2.4 45.3 1.0 OH A:TYR426 2.4 62.6 1.0 OH A:TYR517 2.4 56.8 1.0 C2 A:MLI702 3.0 38.4 1.0 C3 A:MLI702 3.1 35.8 1.0 CD2 A:HIS585 3.2 51.6 1.0 CG A:ASP392 3.3 49.2 1.0 CZ A:TYR426 3.3 73.6 1.0 CZ A:TYR517 3.4 48.0 1.0 CE1 A:HIS585 3.4 49.1 1.0 C1 A:MLI702 3.4 33.4 1.0 CE1 A:TYR517 3.8 43.9 1.0 CE2 A:TYR426 3.9 70.6 1.0 CB A:ASP392 4.0 44.8 1.0 O8 A:MLI702 4.2 37.4 1.0 O6 A:MLI702 4.2 38.6 1.0 OD2 A:ASP392 4.2 48.8 1.0 CE1 A:TYR426 4.3 74.4 1.0 CB A:THR457 4.3 56.7 1.0 NH2 A:ARG632 4.3 70.5 1.0 OG1 A:THR457 4.3 53.9 1.0 CG A:HIS585 4.4 52.6 1.0 ND1 A:HIS585 4.5 49.6 1.0 CE2 A:TYR517 4.5 44.3 1.0 CA A:ASP392 4.6 45.0 1.0 N A:ALA458 4.9 46.0 1.0 N A:THR457 4.9 44.7 1.0

Ytterbium binding site 2 out of 2 in the Ytterbium-Bound Human Serum Transferrin


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Ytterbium-Bound Human Serum Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Yb701 b:47.5 occ:1.00 O9 B:MLI702 2.2 34.5 1.0 O7 B:MLI702 2.2 36.0 1.0 OD1 B:ASP392 2.2 56.0 1.0 NE2 B:HIS585 2.3 40.4 1.0 OH B:TYR426 2.4 58.9 1.0 OH B:TYR517 2.4 55.5 1.0 C3 B:MLI702 3.0 38.6 1.0 C2 B:MLI702 3.0 38.7 1.0 CD2 B:HIS585 3.2 43.0 1.0 C1 B:MLI702 3.3 35.9 1.0 CZ B:TYR426 3.3 73.1 1.0 CG B:ASP392 3.3 42.8 1.0 CZ B:TYR517 3.4 44.5 1.0 CE1 B:HIS585 3.4 44.8 1.0 CE1 B:TYR517 3.8 40.1 1.0 CE2 B:TYR426 3.9 73.5 1.0 CB B:ASP392 4.0 41.2 1.0 O8 B:MLI702 4.1 41.0 1.0 O6 B:MLI702 4.2 40.4 1.0 OD2 B:ASP392 4.3 41.1 1.0 NH2 B:ARG632 4.3 39.0 0.5 CB B:THR457 4.3 53.8 1.0 CE1 B:TYR426 4.3 73.6 1.0 OG1 B:THR457 4.3 51.6 1.0 CG B:HIS585 4.4 45.7 1.0 ND1 B:HIS585 4.5 45.2 1.0 CE2 B:TYR517 4.5 44.1 1.0 CA B:ASP392 4.6 41.4 1.0 N B:ALA458 4.9 44.4 1.0 N B:THR457 4.9 41.7 1.0

M.Wang, T.P.Lai, L.Wang, H.Zhang, N.Yang, P.J.Sadler, H.Sun. "Anion Clamp" Allows Flexible Protein to Impose Coordination Geometry on Metal Ions Chem.Commun.(Camb.) 2015.
ISSN: ESSN 1364-548X
DOI: 10.1039/C4CC09642H