Chlorine in PDB 9dpu: Bmp-9 G389S Dimer in Acidic pH

The structure of Bmp-9 G389S Dimer in Acidic pH, PDB code: 9dpu 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)	41.66 / 2.10
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.589, 71.589, 146.719, 90, 90, 90
R / Rfree (%)	19.2 / 22.4

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

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Bmp-9 G389S Dimer in Acidic pH (pdb code 9dpu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Bmp-9 G389S Dimer in Acidic pH, PDB code: 9dpu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Bmp-9 G389S Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bmp-9 G389S Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:45.4 occ:0.66 H A:LYS372 2.4 47.9 1.0 HA A:THR371 2.7 38.4 1.0 O A:HOH706 2.9 52.5 0.7 O A:HOH622 3.0 57.2 0.8 HG3 A:LYS372 3.1 54.6 1.0 HB A:THR371 3.2 52.2 1.0 N A:LYS372 3.2 39.8 1.0 CA A:THR371 3.5 31.9 1.0 O A:HOH676 3.6 74.2 1.0 HG22 A:THR371 3.7 60.3 1.0 CB A:THR371 3.7 43.4 1.0 HZ2 A:LYS372 3.8 66.9 1.0 C A:THR371 3.9 29.4 1.0 HB2 A:LYS372 3.9 54.5 1.0 CG A:LYS372 4.0 45.4 1.0 CG2 A:THR371 4.2 50.1 1.0 CB A:LYS372 4.2 45.4 1.0 CA A:LYS372 4.3 28.2 1.0 HG2 A:LYS372 4.5 54.6 1.0 H A:HIS373 4.5 39.3 1.0 O A:PRO370 4.5 80.0 1.0 NZ A:LYS372 4.5 55.6 1.0 HZ3 A:LYS372 4.6 66.9 1.0 HD2 A:LYS372 4.6 101.6 1.0 HG21 A:THR371 4.7 60.3 1.0 N A:THR371 4.7 46.8 1.0 CD A:LYS372 4.8 84.5 1.0 HA A:LYS372 4.9 33.9 1.0 HG23 A:THR371 4.9 60.3 1.0 HE3 A:LYS372 5.0 97.8 1.0

Chlorine binding site 2 out of 5 in the Bmp-9 G389S Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bmp-9 G389S Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:56.8 occ:0.43 H A:LEU364 2.4 67.9 1.0 HD1 A:PHE362 3.0 60.1 1.0 HA A:PRO363 3.2 61.5 1.0 N A:LEU364 3.3 56.5 1.0 HB2 A:LEU364 3.3 71.1 1.0 CD1 A:PHE362 3.9 50.0 1.0 HG A:LEU364 3.9 98.5 1.0 CA A:PRO363 3.9 51.1 1.0 CB A:LEU364 4.0 59.2 1.0 C A:PRO363 4.1 64.9 1.0 HB2 A:PRO363 4.1 55.5 1.0 HD12 A:LEU364 4.1 90.7 1.0 HE1 A:PHE362 4.1 50.5 1.0 CA A:LEU364 4.2 106.6 1.0 HB3 A:PRO363 4.2 55.5 1.0 CB A:PRO363 4.3 46.2 1.0 O A:LEU364 4.3 82.7 1.0 CG A:LEU364 4.4 82.0 1.0 HB3 A:PHE362 4.4 56.1 1.0 CE1 A:PHE362 4.4 42.0 1.0 HA A:PHE362 4.6 48.9 1.0 CD1 A:LEU364 4.8 75.5 1.0 C A:LEU364 4.8 102.6 1.0 HB3 A:LEU364 4.8 71.1 1.0 CG A:PHE362 4.9 38.1 1.0

Chlorine binding site 3 out of 5 in the Bmp-9 G389S Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bmp-9 G389S Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:77.1 occ:0.66 H A:HIS417 2.1 73.2 1.0 HZ1 A:LYS415 2.8 89.4 1.0 N A:HIS417 2.9 60.9 1.0 HB3 A:TYR416 3.0 67.6 1.0 HE3 A:LYS415 3.0 60.4 1.0 H A:TYR416 3.1 69.9 1.0 HB2 A:HIS417 3.1 67.7 1.0 HD2 A:LYS415 3.2 69.2 1.0 O A:HOH640 3.2 50.3 0.7 NZ A:LYS415 3.3 74.4 1.0 HZ2 A:LYS415 3.4 89.4 1.0 CE A:LYS415 3.5 50.2 1.0 N A:TYR416 3.5 58.1 1.0 O A:HIS417 3.6 52.7 1.0 CA A:HIS417 3.7 54.0 1.0 CD A:LYS415 3.8 57.5 1.0 CB A:TYR416 3.8 56.2 1.0 CB A:HIS417 3.8 56.3 1.0 C A:TYR416 3.9 53.5 1.0 CA A:TYR416 3.9 51.5 1.0 C A:HIS417 3.9 59.3 1.0 HB2 A:TYR416 4.1 67.6 1.0 HZ3 A:LYS415 4.2 89.4 1.0 O A:HOH655 4.2 67.2 0.8 HG3 A:LYS415 4.3 68.8 1.0 HD1 A:HIS417 4.3 94.4 1.0 HE2 A:LYS415 4.4 60.4 1.0 C A:LYS415 4.4 53.7 1.0 HA A:LYS415 4.4 72.8 1.0 HD3 A:LYS415 4.5 69.2 1.0 O A:HOH705 4.6 80.2 1.0 HB3 A:HIS417 4.6 67.7 1.0 CG A:HIS417 4.6 85.1 1.0 HA A:HIS417 4.6 64.8 1.0 CG A:LYS415 4.6 57.2 1.0 HD2 A:TYR416 4.7 70.2 1.0 ND1 A:HIS417 4.7 78.6 1.0 HA A:TYR416 4.9 61.9 1.0 CA A:LYS415 4.9 60.6 1.0 N A:TYR418 5.0 51.3 1.0

Chlorine binding site 4 out of 5 in the Bmp-9 G389S Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bmp-9 G389S Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:50.6 occ:0.52 HH A:TYR416 2.1 66.5 1.0 HE2 A:TYR416 2.5 106.3 1.0 OH A:TYR416 2.9 55.4 1.0 CE2 A:TYR416 3.3 88.5 1.0 CZ A:TYR416 3.5 55.6 1.0 HE1 A:HIS417 3.8 69.7 1.0 H12 A:GOL507 4.3 137.7 1.0 O3 A:GOL507 4.3 114.5 1.0 NE2 A:HIS417 4.4 111.7 1.0 CE1 A:HIS417 4.4 58.0 1.0 CD2 A:TYR416 4.5 58.5 1.0 HO3 A:GOL507 4.7 137.5 1.0 HD2 A:TYR416 4.7 70.2 1.0 H31 A:GOL507 4.8 137.5 1.0 CE1 A:TYR416 4.9 54.1 1.0

Chlorine binding site 5 out of 5 in the Bmp-9 G389S Dimer in Acidic pH


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bmp-9 G389S Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:46.1 occ:0.60 H A:CYS428 2.2 49.5 1.0 HG22 A:VAL368 2.6 157.1 1.0 HG21 A:VAL368 2.9 157.1 1.0 HA A:PRO370 3.0 63.6 1.0 HH12 A:ARG429 3.1 44.5 1.0 N A:CYS428 3.1 41.2 1.0 HB2 A:CYS428 3.1 45.1 1.0 HA2 A:GLY427 3.2 49.9 1.0 CG2 A:VAL368 3.2 130.8 1.0 O A:HOH605 3.3 59.8 0.8 HB3 A:PRO370 3.3 56.1 1.0 O A:THR369 3.5 93.4 1.0 CA A:PRO370 3.6 52.9 1.0 HA3 A:GLY427 3.7 49.9 1.0 C A:THR369 3.7 56.6 1.0 NH1 A:ARG429 3.8 37.0 1.0 CA A:GLY427 3.8 41.5 1.0 HG13 A:VAL368 3.8 106.4 1.0 N A:PRO370 3.8 79.2 1.0 HH11 A:ARG429 3.8 44.5 1.0 HG23 A:VAL368 3.8 157.1 1.0 CB A:CYS428 3.9 37.5 1.0 C A:GLY427 3.9 45.0 1.0 CB A:PRO370 4.0 46.7 1.0 CA A:CYS428 4.0 36.4 1.0 HG11 A:VAL368 4.0 106.4 1.0 O A:CYS428 4.0 39.3 1.0 H A:THR369 4.1 179.8 1.0 CG1 A:VAL368 4.2 88.6 1.0 CB A:VAL368 4.3 130.0 1.0 N A:THR369 4.3 149.7 1.0 HD3 A:PRO370 4.4 113.3 1.0 C A:CYS428 4.5 38.2 1.0 SG A:CYS428 4.6 48.5 1.0 CD A:PRO370 4.6 94.4 1.0 HB2 A:PRO370 4.6 56.1 1.0 HB3 A:CYS428 4.6 45.1 1.0 CA A:THR369 4.7 145.5 1.0 C A:VAL368 4.8 85.4 1.0 HG1 A:THR369 4.8 154.8 1.0 HA A:CYS428 4.8 43.7 1.0 HH22 A:ARG429 4.8 43.8 1.0 H A:THR371 4.9 56.3 1.0 CG A:PRO370 4.9 64.4 1.0 CZ A:ARG429 5.0 48.5 1.0 C A:PRO370 5.0 61.8 1.0 HB A:VAL368 5.0 156.1 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