Sodium in PDB 9dpu: Bmp-9 G389S Dimer in Acidic pH

The structure of Bmp-9 G389S Dimer in Acidic pH, PDB code: 9dpu was solved by T.A.Schwartze, A.P.Hinck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.66 / 2.10
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.589, 71.589, 146.719, 90, 90, 90
R / Rfree (%)	19.2 / 22.4

The structure of Bmp-9 G389S Dimer in Acidic pH also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Bmp-9 G389S Dimer in Acidic pH (pdb code 9dpu). 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 Bmp-9 G389S Dimer in Acidic pH, PDB code: 9dpu:

Sodium binding site 1 out of 1 in the Bmp-9 G389S Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bmp-9 G389S Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:57.6 occ:0.99 OG1 A:THR386 2.5 81.8 1.0 H A:THR386 2.6 66.9 1.0 HA A:PHE384 2.9 61.7 1.0 HD2 A:PRO385 3.1 71.7 1.0 HG3 A:LYS387 3.3 97.8 1.0 HG23 A:THR386 3.3 100.9 1.0 N A:THR386 3.4 55.6 1.0 HB3 A:PHE384 3.5 63.3 1.0 O A:HOH700 3.5 68.7 0.9 HE3 A:LYS387 3.5 176.1 1.0 CA A:PHE384 3.6 51.3 1.0 C A:PHE384 3.6 53.6 1.0 CB A:THR386 3.6 69.3 1.0 N A:PRO385 3.6 45.6 1.0 H A:LYS387 3.7 90.2 1.0 CD A:PRO385 3.8 59.7 1.0 CG2 A:THR386 3.8 84.0 1.0 HD1 A:PHE384 3.9 80.0 1.0 HG2 A:PRO385 4.0 62.6 1.0 HG21 A:THR386 4.0 100.9 1.0 CB A:PHE384 4.0 52.7 1.0 CA A:THR386 4.0 88.6 1.0 O A:PHE384 4.2 57.4 1.0 CG A:LYS387 4.2 81.4 1.0 N A:LYS387 4.3 75.1 1.0 CE A:LYS387 4.4 146.7 1.0 HD2 A:LYS387 4.4 175.1 1.0 HB A:THR386 4.4 83.3 1.0 CG A:PRO385 4.4 52.0 1.0 C A:PRO385 4.4 45.8 1.0 CD A:LYS387 4.6 145.8 1.0 HD3 A:PRO385 4.6 71.7 1.0 CA A:PRO385 4.6 44.8 1.0 C A:THR386 4.7 67.4 1.0 CD1 A:PHE384 4.7 66.6 1.0 O A:LYS383 4.7 58.7 1.0 HG22 A:THR386 4.7 100.9 1.0 HB2 A:LYS387 4.7 83.1 1.0 HB2 A:PHE384 4.8 63.3 1.0 HG2 A:LYS387 4.8 97.8 1.0 N A:PHE384 4.8 52.5 1.0 CG A:PHE384 4.9 72.3 1.0 HA A:THR386 4.9 106.4 1.0 HZ1 A:LYS387 4.9 132.7 1.0 CB A:LYS387 5.0 69.2 1.0 HE2 A:LYS387 5.0 176.1 1.0

T.A.Schwartze, S.A.Morosky, T.L.Rosato, A.Henrickson, G.Lin, C.S.Hinck, A.B.Taylor, S.K.Olsen, G.Calero, B.Demeler, B.L.Roman, A.P.Hinck. Molecular Basis of Interchain Disulfide Bond Formation in Bmp-9 and Bmp-10. J.Mol.Biol. V. 437 68935 2025.
ISSN: ESSN 1089-8638
PubMed: 39793884
DOI: 10.1016/J.JMB.2025.168935