Sodium in PDB 9dpw: Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH

The structure of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH, PDB code: 9dpw 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)	40.08 / 2.71
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.1, 71.1, 145.548, 90, 90, 90
R / Rfree (%)	22.4 / 29.9

The structure of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Sodium atom in the Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH (pdb code 9dpw). 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 K357R G389S Dimer with Radiation Damage in Neutral pH, PDB code: 9dpw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:76.5 occ:0.98 HH A:TYR416 2.0 72.7 1.0 CL A:CL507 2.5 57.5 0.5 OH A:TYR416 2.8 60.4 1.0 HE2 A:TYR416 2.8 70.5 1.0 CE2 A:TYR416 3.4 58.6 1.0 H12 A:GOL501 3.4 100.0 1.0 CZ A:TYR416 3.5 54.3 1.0 HE1 A:HIS417 3.5 86.0 1.0 NE2 A:HIS417 3.9 62.8 1.0 CE1 A:HIS417 4.0 71.5 1.0 C1 A:GOL501 4.3 83.1 1.0 H11 A:GOL501 4.3 100.0 1.0 O2 A:GOL501 4.5 97.6 1.0 CD2 A:TYR416 4.6 54.1 1.0 CE1 A:TYR416 4.7 49.1 1.0 HO2 A:GOL501 4.9 117.3 1.0 HD2 A:TYR416 4.9 65.1 1.0

Sodium binding site 2 out of 3 in the Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na513 b:60.0 occ:0.99 OG1 A:THR386 2.7 79.4 1.0 HG1 A:THR386 2.7 95.5 1.0 HD2 A:PRO385 2.7 61.8 1.0 HA A:PHE384 2.8 69.7 1.0 H A:THR386 3.1 81.0 1.0 CD A:PRO385 3.5 51.3 1.0 HG3 A:LYS387 3.5 101.4 1.0 CA A:PHE384 3.6 57.9 1.0 HD3 A:PRO385 3.6 61.8 1.0 HD1 A:PHE384 3.7 78.4 1.0 HZ2 A:LYS387 3.7 120.2 1.0 C A:PHE384 3.8 58.8 1.0 N A:PRO385 3.8 53.0 1.0 HG23 A:THR386 3.8 74.1 1.0 HB3 A:PHE384 3.8 65.5 1.0 N A:THR386 3.8 67.3 1.0 CB A:THR386 3.9 66.6 1.0 H A:LYS387 4.0 72.6 1.0 CG2 A:THR386 4.2 61.6 1.0 CB A:PHE384 4.2 54.4 1.0 HG21 A:THR386 4.3 74.1 1.0 O A:LYS383 4.4 64.2 1.0 CA A:THR386 4.4 65.6 1.0 CG A:LYS387 4.5 84.3 1.0 O A:PHE384 4.5 50.3 1.0 CD1 A:PHE384 4.5 65.2 1.0 NZ A:LYS387 4.6 100.0 1.0 N A:LYS387 4.6 60.3 1.0 HB A:THR386 4.6 80.1 1.0 HG2 A:LYS387 4.7 101.4 1.0 N A:PHE384 4.7 57.7 1.0 HD2 A:LYS387 4.8 119.5 1.0 C A:PRO385 4.8 55.5 1.0 HZ1 A:LYS387 4.8 120.2 1.0 CG A:PRO385 4.8 47.1 1.0 CA A:PRO385 4.8 49.5 1.0 CG A:PHE384 4.9 57.9 1.0 HG2 A:PRO385 4.9 56.7 1.0 HZ3 A:LYS387 5.0 120.2 1.0 C A:THR386 5.0 58.8 1.0

Sodium binding site 3 out of 3 in the Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na514 b:69.8 occ:1.00 HD12 A:LEU332 4.1 51.0 1.0 HD11 A:LEU332 4.4 51.0 1.0 O A:ARG333 4.5 57.9 1.0 CD1 A:LEU332 4.7 42.3 1.0 O A:HOH618 4.7 66.8 1.0 CL A:CL511 4.7 135.1 1.0 O A:HOH636 4.8 66.8 0.9 HD13 A:LEU332 4.9 51.0 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