Sodium in PDB 6xr0: Crystal Structure of Human Melanotransferrin in Complex with SC57.32 Fab

The structure of Crystal Structure of Human Melanotransferrin in Complex with SC57.32 Fab, PDB code: 6xr0 was solved by K.Hayashi, K.L.Longenecker, S.Vivona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	111.10 / 3.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.829, 136.91, 111.135, 90, 91.46, 90
R / Rfree (%)	20.2 / 22.5

The structure of Crystal Structure of Human Melanotransferrin in Complex with SC57.32 Fab also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Iron	(Fe)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Melanotransferrin in Complex with SC57.32 Fab (pdb code 6xr0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Melanotransferrin in Complex with SC57.32 Fab, PDB code: 6xr0:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Melanotransferrin in Complex with SC57.32 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Melanotransferrin in Complex with SC57.32 Fab within 5.0Å range: probe atom residue distance (Å) B Occ M:Na807 b:40.4 occ:1.00 OD2 M:ASP652 2.3 71.4 1.0 O M:ASP675 2.4 51.7 1.0 O M:PHE661 2.5 55.5 1.0 CG M:ASP652 3.0 69.1 1.0 OD1 M:ASP652 3.1 70.8 1.0 C M:ASP675 3.5 51.0 1.0 C M:PHE661 3.7 54.2 1.0 O M:THR677 4.1 50.7 1.0 CB M:PHE661 4.2 49.2 1.0 CA M:ASP675 4.2 51.6 1.0 CB M:ASP652 4.5 63.2 1.0 CB M:ASP675 4.5 53.5 1.0 N M:ASP662 4.6 54.5 1.0 CA M:PHE661 4.6 51.1 1.0 N M:ALA676 4.6 49.7 1.0 CA M:ASP662 4.7 54.1 1.0 CB M:ASP662 4.8 56.9 1.0 CA M:ALA676 4.9 49.0 1.0 C M:ALA676 5.0 48.3 1.0

K.Hayashi, K.L.Longenecker, L.Y.Liu, B.Faust, A.Prashar, J.Hampl, V.Stoll, S.Vivona. Complex of Human Melanotransferrin and SC57.32 Fab Fragment Reveals Novel Interdomain Arrangement with Ferric N-Lobe and Open C-Lobe. Sci Rep V. 11 566 2021.
ISSN: ESSN 2045-2322
DOI: 10.1038/S41598-020-79090-8