Sodium in PDB 9dpx: Bmp-9 G389S K357R Dimer in Acidic pH

The structure of Bmp-9 G389S K357R Dimer in Acidic pH, PDB code: 9dpx 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)	64.09 / 2.10
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.289, 71.289, 146.379, 90, 90, 90
R / Rfree (%)	22.8 / 26.8

The structure of Bmp-9 G389S K357R Dimer in Acidic pH also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Bmp-9 G389S K357R Dimer in Acidic pH (pdb code 9dpx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Bmp-9 G389S K357R Dimer in Acidic pH, PDB code: 9dpx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Bmp-9 G389S K357R 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 K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:59.1 occ:0.99 OG1 A:THR386 2.4 73.9 1.0 H A:THR386 2.5 63.5 1.0 HA A:PHE384 2.8 67.3 1.0 HD2 A:PRO385 2.9 62.0 1.0 HG3 A:LYS387 3.2 94.4 1.0 N A:THR386 3.3 52.5 1.0 C A:PHE384 3.3 54.4 1.0 CA A:PHE384 3.4 55.7 1.0 HB3 A:PHE384 3.4 64.7 1.0 H A:LYS387 3.5 76.1 1.0 N A:PRO385 3.5 40.5 1.0 HG23 A:THR386 3.5 79.1 1.0 CB A:THR386 3.5 70.0 1.0 CD A:PRO385 3.6 51.3 1.0 HD1 A:PHE384 3.8 80.4 1.0 HE3 A:LYS387 3.9 124.6 1.0 O A:PHE384 3.9 55.4 1.0 CA A:THR386 3.9 67.7 1.0 CB A:PHE384 3.9 53.5 1.0 CG2 A:THR386 3.9 65.5 1.0 N A:LYS387 4.0 63.0 1.0 HG2 A:PRO385 4.1 62.7 1.0 HG21 A:THR386 4.1 79.1 1.0 CG A:LYS387 4.2 78.2 1.0 HD2 A:LYS387 4.3 108.6 1.0 C A:PRO385 4.3 54.0 1.0 HD3 A:PRO385 4.3 62.0 1.0 HB A:THR386 4.3 84.5 1.0 C A:THR386 4.4 69.8 1.0 CA A:PRO385 4.4 46.1 1.0 CG A:PRO385 4.5 51.8 1.0 HB2 A:LYS387 4.5 84.8 1.0 CD A:LYS387 4.6 90.1 1.0 CD1 A:PHE384 4.6 66.6 1.0 HB2 A:PHE384 4.7 64.7 1.0 CE A:LYS387 4.7 103.5 1.0 N A:PHE384 4.7 50.0 1.0 O A:LYS383 4.7 57.1 1.0 CB A:LYS387 4.8 70.3 1.0 HG2 A:LYS387 4.8 94.4 1.0 HA A:THR386 4.8 81.8 1.0 CG A:PHE384 4.8 59.5 1.0 HG22 A:THR386 4.8 79.1 1.0

Sodium binding site 2 out of 3 in the Bmp-9 G389S K357R Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bmp-9 G389S K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:66.3 occ:0.99 CL A:CL506 2.5 95.8 1.0 O A:ARG333 2.8 61.9 1.0 O A:HOH630 2.9 50.7 1.0 HA A:VAL334 3.6 58.6 1.0 HD11 A:LEU332 3.9 54.8 1.0 C A:ARG333 4.0 58.9 1.0 HD12 A:LEU332 4.1 54.8 1.0 H A:ASN335 4.2 59.0 1.0 CD1 A:LEU332 4.5 46.0 1.0 CA A:VAL334 4.5 48.4 1.0 HG22 A:VAL334 4.6 62.6 1.0 N A:VAL334 4.7 46.3 1.0 HB2 A:ARG333 4.7 89.4 1.0 HG A:LEU332 4.9 54.8 1.0 N A:ASN335 4.9 51.2 1.0 OD2 A:ASP338 4.9 74.0 1.0 H A:ARG333 4.9 69.6 1.0

Sodium binding site 3 out of 3 in the Bmp-9 G389S K357R Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bmp-9 G389S K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:36.8 occ:0.50 CL A:CL508 2.4 59.2 0.3 H A:GLU352 2.7 58.1 1.0 HB2 A:TYR351 2.8 50.8 1.0 O A:HOH641 3.0 43.9 0.5 HB3 A:GLU352 3.4 58.6 1.0 N A:GLU352 3.5 48.0 1.0 HD2 A:TYR351 3.6 49.5 1.0 CB A:TYR351 3.7 44.4 1.0 HA A:TYR351 3.8 54.5 1.0 O A:HOH666 3.9 86.3 1.0 CA A:TYR351 4.2 46.5 1.0 CB A:GLU352 4.2 48.4 1.0 O A:GLU352 4.2 55.9 1.0 HB3 A:TYR351 4.3 50.8 1.0 HG21 A:ILE401 4.3 58.3 1.0 CA A:GLU352 4.3 43.4 1.0 CD2 A:TYR351 4.3 40.8 1.0 HB2 A:GLU352 4.4 58.6 1.0 C A:TYR351 4.4 50.3 1.0 HG22 A:ILE401 4.4 58.3 1.0 CG A:TYR351 4.6 41.3 1.0 C A:GLU352 4.7 39.9 1.0 O A:HOH616 4.8 19.7 0.2 CG2 A:ILE401 4.8 48.2 1.0 HB A:ILE401 4.9 59.1 1.0 O A:HOH645 4.9 57.0 0.5 O A:HOH618 5.0 64.8 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