Chlorine 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:

Sodium

(Na)

3 atoms

The binding sites of Chlorine atom in the Bmp-9 Monomer Growth Factor with Cysteinylation (pdb code 9dpm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Bmp-9 Monomer Growth Factor with Cysteinylation, PDB code: 9dpm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine 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 Chlorine with other atoms in the Cl binding site number 1 of Bmp-9 Monomer Growth Factor with Cysteinylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:67.5 occ:0.80 H A:GLU419 2.4 60.2 1.0 HA A:TYR418 3.0 62.9 1.0 HE2 A:LYS415 3.1 93.6 1.0 N A:GLU419 3.2 50.0 1.0 HG2 A:GLU419 3.3 81.6 1.0 HD1 A:TYR418 3.3 79.2 1.0 HB2 A:GLU419 3.5 78.1 1.0 HE3 A:LYS415 3.6 93.6 1.0 O A:HIS417 3.7 54.7 1.0 CE A:LYS415 3.8 77.8 1.0 CD1 A:TYR418 3.8 65.8 1.0 CA A:TYR418 3.8 52.2 1.0 CG A:GLU419 4.0 67.8 1.0 C A:TYR418 4.0 56.8 1.0 CB A:GLU419 4.0 64.9 1.0 HG3 A:GLU419 4.1 81.6 1.0 HZ1 A:LYS415 4.1 99.7 1.0 CA A:GLU419 4.2 61.1 1.0 HE1 A:TYR418 4.2 116.1 1.0 CE1 A:TYR418 4.3 96.6 1.0 HZ3 A:LYS415 4.3 99.7 1.0 NZ A:LYS415 4.3 82.9 1.0 CG A:TYR418 4.5 51.3 1.0 C A:HIS417 4.6 50.2 1.0 HG2 A:LYS415 4.6 74.6 1.0 O A:GLU419 4.7 42.8 1.0 N A:TYR418 4.7 47.4 1.0 CB A:TYR418 4.8 45.5 1.0 O A:HOH612 4.8 55.1 0.7 C A:GLU419 4.9 51.8 1.0 HB3 A:GLU419 4.9 78.1 1.0 HA A:GLU419 4.9 73.6 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 2 of Bmp-9 Monomer Growth Factor with Cysteinylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:49.7 occ:0.89 H A:LYS372 2.4 51.4 1.0 HA A:THR371 2.9 52.5 1.0 HG3 A:LYS372 2.9 55.9 1.0 O A:HOH623 3.0 65.9 0.9 O A:HOH684 3.0 60.4 0.9 HB A:THR371 3.2 53.8 1.0 N A:LYS372 3.3 43.8 1.0 HG22 A:THR371 3.6 53.0 1.0 CA A:THR371 3.6 44.7 1.0 CB A:THR371 3.8 44.6 1.0 CG A:LYS372 3.8 47.6 1.0 HB2 A:LYS372 3.9 57.6 1.0 C A:THR371 3.9 43.5 1.0 HZ2 A:LYS372 4.0 64.6 1.0 HG2 A:LYS372 4.1 55.9 1.0 CG2 A:THR371 4.2 45.1 1.0 CB A:LYS372 4.2 47.8 1.0 CA A:LYS372 4.3 42.9 1.0 HZ3 A:LYS372 4.5 64.6 1.0 NZ A:LYS372 4.6 54.8 1.0 H A:HIS373 4.6 49.9 1.0 HG21 A:THR371 4.6 53.0 1.0 HA A:LYS372 4.9 50.7 1.0 HE3 A:LYS372 4.9 110.4 1.0 N A:THR371 4.9 45.4 1.0 HG23 A:THR371 4.9 53.0 1.0 CD A:LYS372 4.9 81.1 1.0 O A:PRO370 5.0 48.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 3 of Bmp-9 Monomer Growth Factor with Cysteinylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:71.6 occ:0.81 H A:HIS417 2.2 64.5 1.0 HZ2 A:LYS415 2.8 99.7 1.0 N A:HIS417 3.0 53.5 1.0 HD2 A:LYS415 3.1 87.3 1.0 HB3 A:TYR416 3.1 75.9 1.0 HB2 A:HIS417 3.1 68.3 1.0 O A:HOH635 3.1 57.9 0.9 H A:TYR416 3.1 61.7 1.0 HZ1 A:LYS415 3.1 99.7 1.0 HE3 A:LYS415 3.1 93.6 1.0 NZ A:LYS415 3.2 82.9 1.0 CE A:LYS415 3.5 77.8 1.0 N A:TYR416 3.6 51.2 1.0 CD A:LYS415 3.7 72.6 1.0 CA A:HIS417 3.8 45.5 1.0 CB A:HIS417 3.8 56.7 1.0 O A:HIS417 3.9 54.7 1.0 CB A:TYR416 3.9 63.1 1.0 C A:TYR416 4.0 48.3 1.0 CA A:TYR416 4.0 50.6 1.0 C A:HIS417 4.1 50.2 1.0 HZ3 A:LYS415 4.1 99.7 1.0 HD2 A:HIS417 4.1 67.1 1.0 HB2 A:TYR416 4.2 75.9 1.0 O A:HOH612 4.2 55.1 0.7 HG3 A:LYS415 4.3 74.6 1.0 HA A:LYS415 4.4 83.2 1.0 HD3 A:LYS415 4.4 87.3 1.0 HE2 A:LYS415 4.4 93.6 1.0 C A:LYS415 4.5 50.2 1.0 CG A:HIS417 4.5 52.6 1.0 HB3 A:HIS417 4.6 68.3 1.0 CD2 A:HIS417 4.6 55.7 1.0 CG A:LYS415 4.6 61.9 1.0 HD2 A:TYR416 4.6 104.3 1.0 HA A:HIS417 4.7 53.4 1.0 CA A:LYS415 4.9 69.1 1.0 HA A:TYR416 5.0 59.6 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. 68935 2025.
ISSN: ESSN 1089-8638
PubMed: 39793884
DOI: 10.1016/J.JMB.2025.168935