Sodium in PDB 6o9h: Mouse Ecd with FAB1

The structure of Mouse Ecd with FAB1, PDB code: 6o9h was solved by X.Min, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.078, 48.974, 150.908, 90.00, 101.08, 90.00
R / Rfree (%)	20.3 / 24.8

The binding sites of Sodium atom in the Mouse Ecd with FAB1 (pdb code 6o9h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mouse Ecd with FAB1, PDB code: 6o9h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mouse Ecd with FAB1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse Ecd with FAB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:29.6 occ:1.00 O C:LEU21 2.3 27.5 1.0 O C:THR24 2.4 25.8 1.0 OG A:SER31 2.4 31.4 1.0 O A:SER31 2.4 25.7 1.0 OH C:TYR44 2.5 33.9 1.0 O A:HOH495 2.8 38.4 1.0 C A:SER31 3.3 25.3 1.0 CB A:SER31 3.3 28.9 1.0 C C:LEU21 3.5 28.4 1.0 CZ C:TYR44 3.5 38.7 1.0 C C:THR24 3.6 28.1 1.0 CA A:SER31 3.6 26.2 1.0 O C:HOH208 3.7 45.5 1.0 CE2 C:TYR44 3.9 34.1 1.0 O A:HOH414 4.1 36.0 1.0 CA C:GLU25 4.1 33.1 1.0 CA C:LEU21 4.3 28.2 1.0 N C:GLU25 4.3 29.3 1.0 N C:GLU22 4.5 27.3 1.0 N C:THR24 4.5 24.0 1.0 N A:PHE32 4.6 25.2 1.0 CD C:PRO26 4.6 32.0 1.0 CA C:GLU22 4.6 27.7 1.0 CE1 C:TYR44 4.6 32.4 1.0 CA C:THR24 4.6 27.3 1.0 CB C:LEU21 4.7 27.5 1.0 OG1 C:THR24 4.7 26.2 1.0 C C:GLU22 4.9 26.9 1.0 CB C:GLU25 4.9 32.5 1.0

Sodium binding site 2 out of 2 in the Mouse Ecd with FAB1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mouse Ecd with FAB1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:19.9 occ:1.00 O D:LEU21 2.3 22.5 1.0 O H:SER31 2.3 21.3 1.0 OG H:SER31 2.3 20.8 1.0 OH D:TYR44 2.4 26.1 1.0 O D:THR24 2.4 18.8 1.0 O H:HOH339 2.8 29.4 1.0 C H:SER31 3.3 21.5 1.0 CZ D:TYR44 3.3 26.4 1.0 CB H:SER31 3.4 22.5 1.0 C D:LEU21 3.5 22.8 1.0 CE2 D:TYR44 3.6 24.7 1.0 C D:THR24 3.6 21.0 1.0 CA H:SER31 3.6 20.8 1.0 CA D:GLU25 4.3 26.8 1.0 CA D:LEU21 4.3 21.7 1.0 O H:HOH387 4.3 30.2 1.0 N D:GLU25 4.4 19.2 1.0 N D:GLU22 4.4 17.1 1.0 N D:THR24 4.5 22.4 1.0 N H:PHE32 4.5 21.5 1.0 CA D:GLU22 4.5 21.6 1.0 CE1 D:TYR44 4.5 27.4 1.0 CA D:THR24 4.6 20.5 1.0 OG1 D:THR24 4.7 20.0 1.0 O D:HOH346 4.7 49.7 1.0 CB D:LEU21 4.7 24.0 1.0 C D:GLU22 4.8 18.9 1.0 CD2 D:TYR44 4.9 21.6 1.0 CD D:PRO26 4.9 28.6 1.0 CA H:PHE32 5.0 20.7 1.0

X.Min, J.Yie, J.Wang, B.C.Chung, C.S.Huang, H.Xu, J.Yang, L.Deng, J.Lin, Q.Chen, C.M.Abbott, C.Gundel, S.A.Thibault, T.Meng, D.L.Bates, D.J.Lloyd, M.M.Veniant, Z.Wang. Molecular Mechanism of An Antagonistic Antibody Against Glucose-Dependent Insulinotropic Polypeptide Receptor. Mabs V. 12 10047 2020.
ISSN: ESSN 1942-0870
PubMed: 31905038
DOI: 10.1080/19420862.2019.1710047