Sodium in PDB 9dpm: Bmp-9 Monomer Growth Factor with Cysteinylation

The structure of Bmp-9 Monomer Growth Factor with Cysteinylation, PDB code: 9dpm 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)	29.46 / 1.90
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.863, 71.863, 144.606, 90, 90, 90
R / Rfree (%)	20.5 / 24.2

The structure of Bmp-9 Monomer Growth Factor with Cysteinylation also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Bmp-9 Monomer Growth Factor with Cysteinylation (pdb code 9dpm). 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 Monomer Growth Factor with Cysteinylation, PDB code: 9dpm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Bmp-9 Monomer Growth Factor with Cysteinylation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bmp-9 Monomer Growth Factor with Cysteinylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:52.5 occ:0.99 H A:THR386 2.6 65.1 1.0 OG1 A:THR386 2.8 65.3 1.0 HA A:PHE384 2.8 61.7 1.0 HD2 A:PRO385 2.8 78.4 1.0 HG1 A:THR386 3.0 78.6 1.0 HB3 A:PHE384 3.4 66.2 1.0 N A:THR386 3.4 54.0 1.0 CA A:PHE384 3.5 51.2 1.0 CD A:PRO385 3.5 65.1 1.0 HG3 A:LYS387 3.5 91.2 1.0 N A:PRO385 3.6 48.4 1.0 C A:PHE384 3.6 56.2 1.0 HG23 A:THR386 3.7 73.9 1.0 H A:LYS387 3.8 70.5 1.0 CB A:THR386 3.8 48.9 1.0 HD3 A:PRO385 3.9 78.4 1.0 CB A:PHE384 4.0 54.9 1.0 HD2 A:PHE384 4.1 104.3 1.0 CA A:THR386 4.1 68.3 1.0 CG2 A:THR386 4.2 61.4 1.0 HE2 A:LYS387 4.2 169.9 1.0 O A:PHE384 4.3 55.8 1.0 N A:LYS387 4.3 58.6 1.0 C A:PRO385 4.4 55.3 1.0 HG21 A:THR386 4.4 73.9 1.0 CG A:LYS387 4.4 75.8 1.0 HD2 A:LYS387 4.5 155.2 1.0 CA A:PRO385 4.5 46.1 1.0 C A:THR386 4.6 52.8 1.0 HB2 A:LYS387 4.6 73.0 1.0 HB A:THR386 4.6 58.9 1.0 HB2 A:PHE384 4.7 66.2 1.0 O A:LYS383 4.7 64.9 1.0 CD2 A:PHE384 4.8 86.7 1.0 CG A:PRO385 4.8 69.4 1.0 HB2 A:PRO385 4.8 54.0 1.0 N A:PHE384 4.8 52.3 1.0 CD A:LYS387 4.8 129.1 1.0 CG A:PHE384 4.9 64.8 1.0 CB A:LYS387 5.0 60.7 1.0 CE A:LYS387 5.0 141.4 1.0 CB A:PRO385 5.0 44.8 1.0 HG2 A:PRO385 5.0 83.5 1.0 HA A:THR386 5.0 82.2 1.0

Sodium binding site 2 out of 3 in the Bmp-9 Monomer Growth Factor with Cysteinylation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bmp-9 Monomer Growth Factor with Cysteinylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:57.2 occ:0.90 HH A:TYR416 2.0 71.6 1.0 HE2 A:TYR416 2.5 80.2 1.0 OH A:TYR416 2.8 59.5 1.0 O A:HOH672 3.0 75.1 1.0 CE2 A:TYR416 3.2 66.7 1.0 CZ A:TYR416 3.5 57.7 1.0 HE1 A:HIS417 4.0 72.9 1.0 NE2 A:HIS417 4.2 89.0 1.0 CE1 A:HIS417 4.4 60.6 1.0 CD2 A:TYR416 4.5 86.7 1.0 HD2 A:TYR416 4.7 104.3 1.0 CE1 A:TYR416 4.8 55.9 1.0

Sodium binding site 3 out of 3 in the Bmp-9 Monomer Growth Factor with Cysteinylation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bmp-9 Monomer Growth Factor with Cysteinylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:54.0 occ:0.74 H A:ASN335 1.9 59.0 1.0 N A:ASN335 2.8 48.9 1.0 HA A:VAL334 2.8 52.8 1.0 HB3 A:ASN335 2.9 76.2 1.0 HB2 A:ASP338 3.1 70.1 1.0 OD2 A:ASP338 3.2 66.7 1.0 CA A:VAL334 3.6 43.8 1.0 CB A:ASN335 3.6 63.3 1.0 HG13 A:VAL334 3.6 48.5 1.0 C A:VAL334 3.6 45.2 1.0 CA A:ASN335 3.7 53.7 1.0 HB2 A:ASN335 3.7 76.2 1.0 CB A:ASP338 3.7 58.2 1.0 HB3 A:ASP338 3.8 70.1 1.0 O A:ASN335 3.8 52.3 1.0 O A:ARG333 3.8 51.4 1.0 CG A:ASP338 3.9 83.8 1.0 HG23 A:ILE339 4.2 72.0 1.0 C A:ASN335 4.2 54.5 1.0 CG1 A:VAL334 4.3 40.4 1.0 HG12 A:VAL334 4.4 48.5 1.0 HG22 A:VAL334 4.4 53.7 1.0 CB A:VAL334 4.5 45.6 1.0 HA A:ASN335 4.5 64.7 1.0 N A:VAL334 4.6 48.0 1.0 C A:ARG333 4.6 52.9 1.0 O A:VAL334 4.8 44.5 1.0 H A:ASP338 5.0 80.7 1.0 CG A:ASN335 5.0 62.6 1.0 CG2 A:VAL334 5.0 44.6 1.0 CG2 A:ILE339 5.0 59.8 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. 68935 2025.
ISSN: ESSN 1089-8638
PubMed: 39793884
DOI: 10.1016/J.JMB.2025.168935