Chlorine in PDB 9dpt: Bmp-9 G389S Dimer with Radiation Damage in Neutral pH

The structure of Bmp-9 G389S Dimer with Radiation Damage in Neutral pH, PDB code: 9dpt 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)	50.04 / 2.49
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.771, 70.771, 145.523, 90, 90, 90
R / Rfree (%)	23.9 / 27.9

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

Sodium

(Na)

4 atoms

The binding sites of Chlorine atom in the Bmp-9 G389S Dimer with Radiation Damage in Neutral pH (pdb code 9dpt). 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 with Radiation Damage in Neutral pH, PDB code: 9dpt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Bmp-9 G389S Dimer with Radiation Damage in Neutral 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 with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:20.0 occ:0.65 H A:GLU419 2.6 27.0 1.0 HA A:TYR418 3.1 30.6 1.0 HE3 A:LYS415 3.1 57.3 1.0 HD1 A:TYR418 3.3 34.5 1.0 N A:GLU419 3.4 22.5 1.0 HE2 A:LYS415 3.6 57.3 1.0 HZ1 A:LYS415 3.6 63.3 1.0 O A:HIS417 3.7 29.0 1.0 HG2 A:GLU419 3.7 31.4 1.0 HB2 A:GLU419 3.7 29.0 1.0 CE A:LYS415 3.7 47.8 1.0 CD1 A:TYR418 3.8 28.7 1.0 HG3 A:GLU419 3.9 31.4 1.0 CA A:TYR418 3.9 25.5 1.0 HE1 A:TYR418 4.1 45.0 1.0 CG A:GLU419 4.2 26.2 1.0 C A:TYR418 4.2 20.7 1.0 NZ A:LYS415 4.2 52.7 1.0 CB A:GLU419 4.2 24.2 1.0 CE1 A:TYR418 4.3 37.5 1.0 CA A:GLU419 4.4 21.3 1.0 C A:HIS417 4.6 24.8 1.0 CG A:TYR418 4.6 26.5 1.0 O A:GLU419 4.7 21.0 1.0 HZ2 A:LYS415 4.7 63.3 1.0 N A:TYR418 4.8 26.8 1.0 HZ3 A:LYS415 4.8 63.3 1.0 CB A:TYR418 4.9 21.5 1.0 HG2 A:LYS415 4.9 48.7 1.0

Chlorine binding site 2 out of 5 in the Bmp-9 G389S Dimer with Radiation Damage in Neutral 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 with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:49.5 occ:0.69 HE2 A:HIS417 2.3 41.7 1.0 NA A:NA506 2.7 30.4 1.0 HE2 A:TYR416 2.8 33.0 1.0 NE2 A:HIS417 3.1 34.7 1.0 CE2 A:TYR416 3.7 27.5 1.0 CE1 A:HIS417 4.0 30.9 1.0 HE1 A:HIS417 4.0 37.1 1.0 HD2 A:TYR416 4.1 38.0 1.0 CD2 A:HIS417 4.1 36.0 1.0 HH A:TYR416 4.1 30.6 1.0 HD2 A:HIS417 4.3 43.1 1.0 CD2 A:TYR416 4.4 31.6 1.0 CZ A:TYR416 4.8 25.2 1.0 OH A:TYR416 4.8 25.5 1.0

Chlorine binding site 3 out of 5 in the Bmp-9 G389S Dimer with Radiation Damage in Neutral 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 with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:54.5 occ:0.94 H A:HIS417 2.1 31.1 1.0 HB2 A:HIS417 2.8 45.0 1.0 HZ2 A:LYS415 2.8 63.3 1.0 HB3 A:TYR416 2.9 34.6 1.0 N A:HIS417 2.9 25.9 1.0 O A:HOH621 3.2 25.3 1.0 H A:TYR416 3.2 34.6 1.0 HD2 A:LYS415 3.3 42.8 1.0 CB A:HIS417 3.5 37.5 1.0 N A:TYR416 3.6 28.8 1.0 CA A:HIS417 3.6 24.4 1.0 NZ A:LYS415 3.7 52.7 1.0 CB A:TYR416 3.7 28.9 1.0 C A:TYR416 3.8 24.5 1.0 HD2 A:HIS417 3.9 43.1 1.0 O A:HIS417 3.9 29.0 1.0 CA A:TYR416 3.9 26.6 1.0 HZ1 A:LYS415 4.1 63.3 1.0 HB2 A:TYR416 4.1 34.6 1.0 C A:HIS417 4.1 24.8 1.0 CG A:HIS417 4.1 33.9 1.0 CD A:LYS415 4.1 35.7 1.0 HZ3 A:LYS415 4.2 63.3 1.0 CD2 A:HIS417 4.2 36.0 1.0 HB3 A:HIS417 4.3 45.0 1.0 CE A:LYS415 4.3 47.8 1.0 HE3 A:LYS415 4.3 57.3 1.0 HD2 A:TYR416 4.4 38.0 1.0 HA A:HIS417 4.5 29.3 1.0 C A:LYS415 4.5 27.8 1.0 HA A:LYS415 4.5 54.5 1.0 HD3 A:LYS415 4.7 42.8 1.0 HG3 A:LYS415 4.8 48.7 1.0 HA A:TYR416 4.9 31.9 1.0 CG A:TYR416 4.9 27.3 1.0 O A:TYR416 4.9 26.4 1.0 CD2 A:TYR416 5.0 31.6 1.0

Chlorine binding site 4 out of 5 in the Bmp-9 G389S Dimer with Radiation Damage in Neutral 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 with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:34.8 occ:0.38 H A:LEU364 2.6 36.1 1.0 HD1 A:PHE362 2.9 24.5 1.0 HA A:PRO363 3.2 33.7 1.0 N A:LEU364 3.4 30.1 1.0 HG A:LEU364 3.5 43.3 1.0 HB2 A:LEU364 3.6 41.0 1.0 CD1 A:PHE362 3.7 20.4 1.0 CA A:PRO363 3.9 28.1 1.0 HE1 A:PHE362 4.0 23.3 1.0 HB2 A:PRO363 4.1 36.1 1.0 HD12 A:LEU364 4.1 51.1 1.0 C A:PRO363 4.1 30.4 1.0 HB3 A:PRO363 4.1 36.1 1.0 CB A:LEU364 4.2 34.2 1.0 CG A:LEU364 4.2 36.0 1.0 CB A:PRO363 4.3 30.1 1.0 CE1 A:PHE362 4.3 19.4 1.0 CA A:LEU364 4.3 37.9 1.0 HB3 A:PHE362 4.3 27.2 1.0 HA A:PHE362 4.6 29.3 1.0 CD1 A:LEU364 4.7 42.6 1.0 O A:LEU364 4.7 47.1 1.0 CG A:PHE362 4.8 21.0 1.0 CB A:PHE362 4.9 22.7 1.0 C A:LEU364 5.0 53.8 1.0

Chlorine binding site 5 out of 5 in the Bmp-9 G389S Dimer with Radiation Damage in Neutral 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 with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:48.1 occ:0.75 HG22 A:THR371 2.8 38.4 1.0 O A:HOH668 3.3 50.8 0.9 HG23 A:THR371 3.5 38.4 1.0 CG2 A:THR371 3.6 32.0 1.0 O A:THR369 3.6 52.6 1.0 HA A:THR371 3.7 34.1 1.0 HH22 A:ARG429 4.0 29.9 1.0 HB A:THR369 4.0 96.7 1.0 NH2 A:ARG429 4.1 24.9 1.0 HH21 A:ARG429 4.2 29.9 1.0 HG21 A:THR371 4.2 38.4 1.0 O A:PRO370 4.4 44.0 1.0 CA A:THR371 4.4 28.4 1.0 NA A:NA509 4.4 22.8 1.0 N A:THR371 4.4 29.6 1.0 CZ A:ARG429 4.4 21.6 1.0 C A:PRO370 4.5 31.1 1.0 C A:THR369 4.5 40.0 1.0 CB A:THR371 4.6 28.4 1.0 HH12 A:ARG429 4.7 32.4 1.0 H A:THR371 4.7 35.6 1.0 NH1 A:ARG429 4.7 27.0 1.0 HB A:THR371 4.9 34.1 1.0 CB A:THR369 4.9 80.6 1.0 HG1 A:THR369 4.9 80.5 1.0 NE A:ARG429 5.0 24.6 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