Chlorine in PDB 9dps: Bmp-9 G389S Dimer Without Radiation Damage in Neutral pH

The structure of Bmp-9 G389S Dimer Without Radiation Damage in Neutral pH, PDB code: 9dps 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)	31.82 / 2.06
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.774, 70.774, 145.525, 90, 90, 90
R / Rfree (%)	21.6 / 24.9

The structure of Bmp-9 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 G389S Dimer Without Radiation Damage in Neutral pH (pdb code 9dps). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Bmp-9 G389S Dimer Without Radiation Damage in Neutral pH, PDB code: 9dps:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Bmp-9 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 G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:47.0 occ:0.61 H A:GLU419 2.3 55.9 1.0 HA A:TYR418 3.0 56.8 1.0 HE3 A:LYS415 3.1 75.8 1.0 N A:GLU419 3.2 46.5 1.0 HD1 A:TYR418 3.2 68.5 1.0 HB2 A:GLU419 3.3 58.1 1.0 HG2 A:GLU419 3.4 61.1 1.0 HE2 A:LYS415 3.6 75.8 1.0 O A:HIS417 3.7 50.5 1.0 CE A:LYS415 3.7 63.1 1.0 CD1 A:TYR418 3.8 57.1 1.0 CA A:TYR418 3.9 47.2 1.0 CB A:GLU419 3.9 48.3 1.0 HZ1 A:LYS415 4.0 81.5 1.0 C A:TYR418 4.0 44.4 1.0 CG A:GLU419 4.0 50.9 1.0 CA A:GLU419 4.1 44.8 1.0 HE1 A:TYR418 4.2 83.5 1.0 HG3 A:GLU419 4.2 61.1 1.0 HZ3 A:LYS415 4.2 81.5 1.0 NZ A:LYS415 4.2 67.8 1.0 CE1 A:TYR418 4.3 69.5 1.0 C A:HIS417 4.6 47.6 1.0 O A:GLU419 4.6 40.2 1.0 CG A:TYR418 4.6 52.0 1.0 N A:TYR418 4.7 46.0 1.0 HG2 A:LYS415 4.8 73.9 1.0 HB3 A:GLU419 4.8 58.1 1.0 CB A:TYR418 4.8 47.5 1.0 C A:GLU419 4.8 47.0 1.0 HA A:GLU419 4.9 53.8 1.0

Chlorine binding site 2 out of 6 in the Bmp-9 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 G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:31.7 occ:0.55 H A:LYS372 2.4 46.2 1.0 HA A:THR371 2.8 45.0 1.0 HG3 A:LYS372 3.0 50.3 1.0 N A:LYS372 3.2 38.5 1.0 O A:HOH607 3.3 62.0 1.0 HB A:THR371 3.3 45.4 1.0 CA A:THR371 3.5 37.5 1.0 HG22 A:THR371 3.6 46.3 1.0 CB A:THR371 3.8 37.8 1.0 C A:THR371 3.9 36.5 1.0 CG A:LYS372 3.9 41.9 1.0 HZ2 A:LYS372 3.9 54.6 1.0 HB2 A:LYS372 3.9 39.8 1.0 CG2 A:THR371 4.2 38.5 1.0 HG2 A:LYS372 4.2 50.3 1.0 CB A:LYS372 4.2 33.1 1.0 O A:HOH673 4.3 62.6 1.0 CA A:LYS372 4.3 31.6 1.0 HZ1 A:LYS372 4.4 54.6 1.0 NZ A:LYS372 4.5 45.5 1.0 H A:HIS373 4.7 33.5 1.0 HG21 A:THR371 4.7 46.3 1.0 O A:PRO370 4.7 53.5 1.0 N A:THR371 4.8 43.6 1.0 HA A:LYS372 4.9 38.0 1.0 HG23 A:THR371 4.9 46.3 1.0 CD A:LYS372 5.0 44.9 1.0

Chlorine binding site 3 out of 6 in the Bmp-9 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 G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:53.0 occ:0.47 NA A:NA507 2.5 47.6 1.0 HE2 A:TYR416 2.7 70.4 1.0 NE2 A:HIS417 3.2 54.7 1.0 CE2 A:TYR416 3.6 58.6 1.0 HH A:TYR416 4.0 57.1 1.0 HD2 A:TYR416 4.1 61.5 1.0 CE1 A:HIS417 4.1 53.2 1.0 CD2 A:HIS417 4.2 55.6 1.0 HE1 A:HIS417 4.2 64.0 1.0 HD2 A:HIS417 4.2 66.8 1.0 CD2 A:TYR416 4.4 51.2 1.0 OH A:TYR416 4.6 47.5 1.0 CZ A:TYR416 4.6 48.8 1.0

Chlorine binding site 4 out of 6 in the Bmp-9 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 G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:61.1 occ:0.69 H A:HIS417 2.1 59.4 1.0 HZ2 A:LYS415 2.7 81.5 1.0 HB3 A:TYR416 2.9 64.7 1.0 HB2 A:HIS417 2.9 57.4 1.0 HZ1 A:LYS415 2.9 81.5 1.0 N A:HIS417 2.9 49.5 1.0 O A:HOH659 3.1 40.4 0.7 H A:TYR416 3.2 65.2 1.0 NZ A:LYS415 3.2 67.8 1.0 HD2 A:LYS415 3.3 76.2 1.0 N A:TYR416 3.6 54.2 1.0 CB A:HIS417 3.7 47.8 1.0 CA A:HIS417 3.7 46.1 1.0 CB A:TYR416 3.7 53.8 1.0 C A:TYR416 3.9 47.0 1.0 O A:HIS417 3.9 50.5 1.0 CA A:TYR416 3.9 52.1 1.0 HZ3 A:LYS415 3.9 81.5 1.0 CD A:LYS415 4.1 63.4 1.0 CE A:LYS415 4.1 63.1 1.0 C A:HIS417 4.1 47.6 1.0 HB2 A:TYR416 4.1 64.7 1.0 HE3 A:LYS415 4.2 75.8 1.0 CG A:HIS417 4.3 51.4 1.0 HD2 A:TYR416 4.3 61.5 1.0 HD2 A:HIS417 4.3 66.8 1.0 HB3 A:HIS417 4.4 57.4 1.0 C A:LYS415 4.5 50.6 1.0 HG3 A:LYS415 4.5 73.9 1.0 HA A:LYS415 4.5 77.2 1.0 CD2 A:HIS417 4.6 55.6 1.0 HA A:HIS417 4.6 55.4 1.0 HD3 A:LYS415 4.7 76.2 1.0 CG A:LYS415 4.8 61.5 1.0 CG A:TYR416 4.8 57.9 1.0 HA A:TYR416 4.9 62.6 1.0 CD2 A:TYR416 5.0 51.2 1.0 HE2 A:LYS415 5.0 75.8 1.0 CA A:LYS415 5.0 64.2 1.0

Chlorine binding site 5 out of 6 in the Bmp-9 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 G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:65.7 occ:0.42 H A:LEU364 2.6 62.9 1.0 HD1 A:PHE362 3.0 51.0 1.0 HA A:PRO363 3.2 64.0 1.0 N A:LEU364 3.4 52.3 1.0 HB2 A:LEU364 3.6 70.8 1.0 CD1 A:PHE362 3.9 42.4 1.0 CA A:PRO363 3.9 53.2 1.0 HB2 A:PRO363 4.1 65.5 1.0 HG A:LEU364 4.2 68.5 1.0 C A:PRO363 4.2 55.5 1.0 HB3 A:PRO363 4.2 65.5 1.0 HE1 A:PHE362 4.3 45.2 1.0 CB A:PRO363 4.3 54.9 1.0 CB A:LEU364 4.3 59.0 1.0 HB3 A:PHE362 4.3 50.0 1.0 HD12 A:LEU364 4.4 75.2 1.0 CA A:LEU364 4.4 64.3 1.0 HA A:PHE362 4.6 51.8 1.0 CE1 A:PHE362 4.6 37.6 1.0 O A:LEU364 4.6 68.2 1.0 CG A:LEU364 4.7 57.0 1.0 C A:LEU364 4.9 73.1 1.0 CG A:PHE362 4.9 39.1 1.0 CB A:PHE362 5.0 41.6 1.0

Chlorine binding site 6 out of 6 in the Bmp-9 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 6 of Bmp-9 G389S Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:83.3 occ:0.67 NA A:NA509 2.6 83.5 1.0 HZ3 A:TRP344 3.4 94.4 1.0 HE1 A:TYR418 3.7 83.5 1.0 HH2 A:TRP344 3.8 97.0 1.0 CZ3 A:TRP344 4.1 78.6 1.0 HG2 A:LYS415 4.2 73.9 1.0 HD3 A:LYS415 4.3 76.2 1.0 CH2 A:TRP344 4.3 80.8 1.0 CE1 A:TYR418 4.3 69.5 1.0 HE2 A:LYS415 4.4 75.8 1.0 O A:HOH624 4.4 55.0 0.6 CE1 A:TYR405 4.4 76.5 1.0 CZ A:TYR405 4.4 83.2 1.0 HB2 A:LYS415 4.4 62.7 1.0 HE1 A:TYR405 4.6 91.8 1.0 HD1 A:TYR418 4.6 68.5 1.0 CD1 A:TYR405 4.7 70.2 1.0 CE2 A:TYR405 4.7 83.5 1.0 OH A:TYR405 4.8 97.0 1.0 CD1 A:TYR418 4.8 57.1 1.0 CG A:LYS415 4.9 61.5 1.0 HH A:TYR405 4.9 116.5 1.0 CD A:LYS415 4.9 63.4 1.0 CG A:TYR405 4.9 77.0 1.0 CD2 A:TYR405 4.9 79.2 1.0 HD1 A:TYR405 5.0 84.3 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