Sodium in PDB 4irz: Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab, PDB code: 4irz was solved by Y.Yu, T.Schurpf, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.62 / 2.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.610, 77.890, 217.740, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 28.7

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab (pdb code 4irz). 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 A4B7 Headpiece Complexed with Fab Natalizumab, PDB code: 4irz:

Sodium binding site 1 out of 1 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab


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 A4B7 Headpiece Complexed with Fab Natalizumab within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:57.7 occ:1.00 O H:GLN65 2.2 0.1 1.0 O H:PHE64 3.0 93.6 1.0 HG3 H:ARG67 3.0 0.1 1.0 H H:ARG67 3.1 0.1 1.0 O H:LYS63 3.2 91.3 1.0 C H:GLN65 3.3 0.5 1.0 C H:PHE64 3.4 91.0 1.0 HD3 H:ARG67 3.5 0.7 1.0 HA3 H:GLY66 3.7 0.2 1.0 CG H:ARG67 3.8 85.1 1.0 N H:ARG67 3.9 84.3 1.0 N H:GLN65 3.9 0.6 1.0 HA H:PHE64 4.0 0.8 1.0 CD H:ARG67 4.0 84.8 1.0 HB2 H:ARG67 4.0 96.8 1.0 HD2 H:ARG67 4.1 0.7 1.0 CA H:GLN65 4.1 0.3 1.0 C H:LYS63 4.1 88.3 1.0 N H:GLY66 4.2 0.8 1.0 CA H:PHE64 4.2 87.3 1.0 HB3 H:GLN65 4.3 0.1 1.0 CA H:GLY66 4.3 0.3 1.0 CB H:ARG67 4.4 80.7 1.0 H H:GLN65 4.5 0.8 1.0 HG2 H:ARG67 4.6 0.1 1.0 N H:PHE64 4.6 87.8 1.0 C H:GLY66 4.6 0.5 1.0 CA H:ARG67 4.8 81.8 1.0 CB H:GLN65 4.8 1.0 1.0 H H:GLY66 4.9 0.3 1.0 HA H:GLN65 5.0 0.8 1.0 O H:PRO62 5.0 91.0 1.0

Y.Yu, T.Schurpf, T.A.Springer. How Natalizumab Binds and Antagonizes Alpha 4 Integrins. J.Biol.Chem. V. 288 32314 2013.
ISSN: ISSN 0021-9258
PubMed: 24047894
DOI: 10.1074/JBC.M113.501668