Chlorine 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:

Sodium

(Na)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Bmp-9 K357R G389S Dimer Without Radiation Damage in Neutral pH, PDB code: 9dpv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Bmp-9 K357R G389S Dimer Without 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 K357R G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:55.4 occ:0.99 H A:GLU419 2.4 54.0 1.0 HA A:TYR418 3.1 49.4 1.0 HE2 A:LYS415 3.2 68.6 1.0 N A:GLU419 3.2 44.9 1.0 HE3 A:LYS415 3.3 68.6 1.0 HB2 A:GLU419 3.3 63.5 1.0 HG2 A:GLU419 3.3 68.3 1.0 HD1 A:TYR418 3.5 70.0 1.0 HZ1 A:LYS415 3.6 81.9 1.0 CE A:LYS415 3.6 57.1 1.0 O A:HIS417 3.7 48.6 1.0 CB A:GLU419 3.9 52.9 1.0 CA A:TYR418 3.9 41.1 1.0 CG A:GLU419 3.9 56.9 1.0 CD1 A:TYR418 3.9 58.2 1.0 HG3 A:GLU419 4.0 68.3 1.0 C A:TYR418 4.0 35.7 1.0 NZ A:LYS415 4.0 68.2 1.0 CA A:GLU419 4.1 43.9 1.0 O A:HOH652 4.2 34.3 0.3 HZ3 A:LYS415 4.3 81.9 1.0 HE1 A:TYR418 4.4 157.8 1.0 CE1 A:TYR418 4.4 131.5 1.0 C A:HIS417 4.7 45.1 1.0 O A:GLU419 4.7 35.0 1.0 CG A:TYR418 4.7 46.2 1.0 HB3 A:GLU419 4.8 63.5 1.0 N A:TYR418 4.8 39.1 1.0 HZ2 A:LYS415 4.8 81.9 1.0 HA A:GLU419 4.9 52.7 1.0 CB A:TYR418 4.9 35.5 1.0 C A:GLU419 4.9 37.6 1.0 HG2 A:LYS415 5.0 65.2 1.0

Chlorine binding site 2 out of 5 in the Bmp-9 K357R G389S Dimer Without 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 K357R G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:36.2 occ:0.75 H A:LYS372 2.5 43.7 1.0 HA A:THR371 2.8 44.4 1.0 HG3 A:LYS372 3.1 47.7 1.0 O A:HOH610 3.2 27.7 0.2 HB A:THR371 3.2 41.7 1.0 N A:LYS372 3.3 36.4 1.0 HZ2 A:LYS372 3.5 53.7 1.0 CA A:THR371 3.5 36.9 1.0 HG22 A:THR371 3.5 40.8 1.0 CB A:THR371 3.8 34.7 1.0 C A:THR371 3.9 30.4 1.0 HB2 A:LYS372 4.0 42.6 1.0 CG A:LYS372 4.0 39.7 1.0 CG2 A:THR371 4.2 34.0 1.0 CB A:LYS372 4.3 35.4 1.0 NZ A:LYS372 4.3 44.7 1.0 CA A:LYS372 4.4 35.4 1.0 O A:HOH658 4.5 40.0 0.3 HG2 A:LYS372 4.5 47.7 1.0 HZ1 A:LYS372 4.7 53.7 1.0 HG21 A:THR371 4.7 40.8 1.0 H A:HIS373 4.7 33.9 1.0 HZ3 A:LYS372 4.7 53.7 1.0 N A:THR371 4.7 41.8 1.0 HG23 A:THR371 4.9 40.8 1.0 O A:PRO370 4.9 45.0 1.0 CD A:LYS372 5.0 40.7 1.0 HA A:LYS372 5.0 42.5 1.0 HD2 A:LYS372 5.0 49.0 1.0

Chlorine binding site 3 out of 5 in the Bmp-9 K357R G389S Dimer Without 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 K357R G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:67.7 occ:0.45 H A:LEU364 2.5 68.1 1.0 HD1 A:PHE362 3.0 45.9 1.0 HA A:PRO363 3.2 55.0 1.0 N A:LEU364 3.4 56.7 1.0 HB2 A:LEU364 3.4 71.2 1.0 CD1 A:PHE362 3.8 38.2 1.0 HG A:LEU364 3.9 60.8 1.0 HB2 A:PRO363 3.9 60.1 1.0 CA A:PRO363 3.9 46.1 1.0 HE1 A:PHE362 4.0 41.3 1.0 HB3 A:PRO363 4.1 60.1 1.0 C A:PRO363 4.1 48.7 1.0 CB A:LEU364 4.1 59.3 1.0 CB A:PRO363 4.2 50.4 1.0 HD12 A:LEU364 4.3 55.2 1.0 CA A:LEU364 4.3 67.7 1.0 CE1 A:PHE362 4.3 34.4 1.0 HB3 A:PHE362 4.5 46.3 1.0 CG A:LEU364 4.5 50.6 1.0 HA A:PHE362 4.5 56.3 1.0 O A:LEU364 4.6 72.6 1.0 CG A:PHE362 4.8 38.4 1.0 C A:LEU364 4.9 83.4 1.0 CD1 A:LEU364 4.9 45.9 1.0 HB3 A:LEU364 5.0 71.2 1.0

Chlorine binding site 4 out of 5 in the Bmp-9 K357R G389S Dimer Without 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 K357R G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:68.7 occ:0.99 H A:HIS417 2.1 50.5 1.0 HZ2 A:LYS415 2.3 81.9 1.0 N A:HIS417 3.0 42.0 1.0 HB2 A:HIS417 3.1 48.4 1.0 HD2 A:LYS415 3.1 70.2 1.0 NZ A:LYS415 3.1 68.2 1.0 HB3 A:TYR416 3.1 51.8 1.0 H A:TYR416 3.2 50.0 1.0 O A:HOH648 3.2 40.6 0.8 HZ1 A:LYS415 3.3 81.9 1.0 N A:TYR416 3.6 42.0 1.0 CA A:HIS417 3.7 39.4 1.0 HZ3 A:LYS415 3.7 81.9 1.0 HE3 A:LYS415 3.8 68.6 1.0 O A:HIS417 3.8 48.6 1.0 CE A:LYS415 3.8 57.1 1.0 CB A:HIS417 3.8 40.3 1.0 CD A:LYS415 3.9 58.5 1.0 C A:TYR416 4.0 39.2 1.0 CB A:TYR416 4.0 43.5 1.0 C A:HIS417 4.0 45.1 1.0 CA A:TYR416 4.0 44.1 1.0 O A:HOH652 4.2 34.3 0.3 HD2 A:HIS417 4.2 55.4 1.0 HB2 A:TYR416 4.4 51.8 1.0 HD3 A:LYS415 4.4 70.2 1.0 CG A:HIS417 4.5 45.7 1.0 C A:LYS415 4.5 46.3 1.0 HA A:LYS415 4.5 53.9 1.0 CD2 A:HIS417 4.5 46.1 1.0 HD2 A:TYR416 4.6 53.0 1.0 HB3 A:HIS417 4.6 48.4 1.0 HA A:HIS417 4.6 47.3 1.0 HE2 A:LYS415 4.7 68.6 1.0 HG3 A:LYS415 4.7 65.2 1.0 CG A:LYS415 4.9 54.3 1.0 HA A:TYR416 5.0 53.0 1.0

Chlorine binding site 5 out of 5 in the Bmp-9 K357R G389S Dimer Without 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 K357R G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:63.1 occ:0.58 NA A:NA507 2.3 38.4 0.8 HE2 A:TYR416 2.8 57.1 1.0 NE2 A:HIS417 3.3 45.0 1.0 O A:HOH678 3.4 35.6 0.2 CE2 A:TYR416 3.7 47.5 1.0 HH A:TYR416 3.8 55.6 1.0 HE1 A:HIS417 4.0 57.5 1.0 CE1 A:HIS417 4.1 47.9 1.0 HD2 A:TYR416 4.3 53.0 1.0 CD2 A:HIS417 4.4 46.1 1.0 CD2 A:TYR416 4.5 44.5 1.0 OH A:TYR416 4.5 46.6 1.0 HD2 A:HIS417 4.6 55.4 1.0 CZ A:TYR416 4.6 45.3 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