Sodium in PDB 9dpv: Bmp-9 K357R G389S Dimer Without Radiation Damage in Neutral pH

The structure of Bmp-9 K357R G389S Dimer Without Radiation Damage in Neutral pH, PDB code: 9dpv 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)	35.55 / 1.99
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.105, 71.105, 145.553, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

The structure of Bmp-9 K357R G389S Dimer Without Radiation Damage in Neutral pH also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Bmp-9 K357R G389S Dimer Without Radiation Damage in Neutral pH (pdb code 9dpv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Bmp-9 K357R G389S Dimer Without Radiation Damage in Neutral pH, PDB code: 9dpv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Bmp-9 K357R G389S Dimer Without 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 Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:38.4 occ:0.80 HH A:TYR416 2.1 55.6 1.0 CL A:CL506 2.3 63.1 0.6 HE2 A:TYR416 2.7 57.1 1.0 OH A:TYR416 2.9 46.6 1.0 CE2 A:TYR416 3.4 47.5 1.0 CZ A:TYR416 3.6 45.3 1.0 HE1 A:HIS417 3.6 57.5 1.0 O A:HOH678 4.1 35.6 0.2 NE2 A:HIS417 4.2 45.0 1.0 CE1 A:HIS417 4.2 47.9 1.0 H12 A:GOL501 4.3 52.3 0.9 CD2 A:TYR416 4.7 44.5 1.0 O2 A:GOL501 4.8 47.1 0.9 HD2 A:TYR416 5.0 53.0 1.0 CE1 A:TYR416 5.0 44.4 1.0

Sodium binding site 2 out of 4 in the Bmp-9 K357R G389S Dimer Without 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 Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:95.0 occ:0.84 HE1 A:TYR354 3.2 54.2 1.0 HE3 A:LYS329 3.5 56.5 1.0 HG2 A:LYS329 3.8 58.0 1.0 O A:LYS329 3.8 49.4 1.0 CE1 A:TYR354 3.8 45.1 1.0 HA A:THR330 3.8 45.7 1.0 HD1 A:TYR354 3.8 49.8 1.0 O A:HOH670 3.9 64.2 0.5 HE2 A:LYS329 4.1 56.5 1.0 CD1 A:TYR354 4.2 41.4 1.0 HB3 A:LYS329 4.2 59.4 1.0 CE A:LYS329 4.3 47.0 1.0 C A:LYS329 4.3 48.5 1.0 CA A:THR330 4.5 38.4 1.0 CG A:LYS329 4.6 48.2 1.0 O A:HOH671 4.6 36.3 0.2 C A:THR330 4.6 37.6 1.0 N A:THR330 4.7 35.8 1.0 N A:SER331 4.7 39.7 1.0 O A:HOH631 4.7 23.5 0.2 H A:SER331 4.8 47.2 1.0 O A:HOH651 4.8 51.0 0.8 CB A:LYS329 4.8 49.4 1.0 CZ A:TYR354 4.8 41.5 1.0 HA A:SER331 4.9 46.8 1.0 HB2 A:SER331 4.9 51.8 1.0 O A:HOH668 5.0 32.9 0.2

Sodium binding site 3 out of 4 in the Bmp-9 K357R G389S Dimer Without 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 Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:47.0 occ:0.93 H A:THR386 2.6 54.3 1.0 OG1 A:THR386 2.6 56.7 1.0 HG1 A:THR386 2.8 68.2 1.0 HA A:PHE384 3.0 47.3 1.0 HD2 A:PRO385 3.1 44.2 1.0 HZ2 A:LYS387 3.3 122.9 1.0 N A:THR386 3.4 45.2 1.0 HG3 A:LYS387 3.4 85.1 1.0 HG23 A:THR386 3.5 63.6 1.0 C A:PHE384 3.5 44.2 1.0 CA A:PHE384 3.6 39.4 1.0 CB A:THR386 3.7 48.9 1.0 N A:PRO385 3.7 42.7 1.0 HB3 A:PHE384 3.7 53.9 1.0 H A:LYS387 3.7 64.1 1.0 CD A:PRO385 3.8 37.2 1.0 HD1 A:PHE384 3.9 75.9 1.0 HG2 A:PRO385 4.0 46.5 1.0 CA A:THR386 4.0 50.3 1.0 CG2 A:THR386 4.0 52.9 1.0 O A:PHE384 4.0 43.2 1.0 NZ A:LYS387 4.1 102.4 1.0 N A:LYS387 4.2 53.4 1.0 CB A:PHE384 4.2 44.9 1.0 HG21 A:THR386 4.2 63.6 1.0 CG A:LYS387 4.3 70.8 1.0 HZ1 A:LYS387 4.3 122.9 1.0 C A:PRO385 4.4 48.1 1.0 HB2 A:LYS387 4.4 66.5 1.0 CG A:PRO385 4.4 39.0 1.0 HD2 A:LYS387 4.4 107.4 1.0 HZ3 A:LYS387 4.5 122.9 1.0 C A:THR386 4.5 52.0 1.0 HB A:THR386 4.5 58.7 1.0 HD3 A:PRO385 4.6 44.2 1.0 CA A:PRO385 4.6 37.8 1.0 CD1 A:PHE384 4.7 63.2 1.0 CB A:LYS387 4.8 55.4 1.0 CD A:LYS387 4.8 89.4 1.0 O A:LYS383 4.8 48.4 1.0 HA A:THR386 4.8 60.4 1.0 HG22 A:THR386 4.9 63.6 1.0 N A:PHE384 4.9 44.2 1.0 HG2 A:LYS387 4.9 85.1 1.0 CG A:PHE384 5.0 46.1 1.0 HB2 A:PHE384 5.0 53.9 1.0

Sodium binding site 4 out of 4 in the Bmp-9 K357R G389S Dimer Without 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 4 of Bmp-9 K357R G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:59.8 occ:0.99 H A:ASN335 2.1 54.3 1.0 N A:ASN335 2.9 45.2 1.0 HA A:VAL334 2.9 47.6 1.0 HB2 A:ASP338 3.0 72.2 1.0 OD2 A:ASP338 3.0 60.1 1.0 HB3 A:ASN335 3.1 61.6 1.0 HB3 A:ASP338 3.6 72.2 1.0 CB A:ASP338 3.6 60.1 1.0 CG A:ASP338 3.7 61.7 1.0 CB A:ASN335 3.7 51.2 1.0 O A:ASN335 3.7 48.3 1.0 CA A:ASN335 3.8 47.8 1.0 CA A:VAL334 3.8 40.0 1.0 HB2 A:ASN335 3.8 61.6 1.0 HG13 A:VAL334 3.8 46.7 1.0 C A:VAL334 3.8 42.6 1.0 O A:ARG333 4.0 42.8 1.0 HG23 A:ILE339 4.1 60.8 1.0 C A:ASN335 4.2 48.4 1.0 CG1 A:VAL334 4.5 39.2 1.0 HG22 A:VAL334 4.6 47.0 1.0 HG12 A:VAL334 4.6 46.7 1.0 HA A:ASN335 4.6 57.3 1.0 CB A:VAL334 4.7 37.9 1.0 O A:HOH609 4.7 35.3 0.3 N A:VAL334 4.7 42.3 1.0 C A:ARG333 4.8 44.0 1.0 OD1 A:ASP338 4.9 59.3 1.0 H A:ASP338 4.9 66.9 1.0 CA A:ASP338 5.0 57.8 1.0 CG2 A:ILE339 5.0 50.6 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