Chlorine in PDB 9dpn: Bmp-9 Wild-Type Dimer Without Radiation Damage in Neutral pH

The structure of Bmp-9 Wild-Type Dimer Without Radiation Damage in Neutral pH, PDB code: 9dpn 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)	41.50 / 2.24
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.203, 71.203, 146.541, 90, 90, 90
R / Rfree (%)	19.5 / 20.6

The structure of Bmp-9 Wild-Type 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 Wild-Type Dimer Without Radiation Damage in Neutral pH (pdb code 9dpn). 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 Wild-Type Dimer Without Radiation Damage in Neutral pH, PDB code: 9dpn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:63.8 occ:1.00 H A:GLU419 2.2 44.3 1.0 HD1 A:TYR418 2.9 84.5 1.0 HA A:TYR418 2.9 57.8 1.0 N A:GLU419 3.0 37.3 1.0 HB2 A:GLU419 3.2 45.0 1.0 HE2 A:LYS415 3.3 76.8 1.0 HG2 A:GLU419 3.3 51.9 1.0 HE3 A:LYS415 3.4 76.8 1.0 CD1 A:TYR418 3.6 70.3 1.0 O A:HIS417 3.6 43.7 1.0 CA A:TYR418 3.7 48.1 1.0 CE A:LYS415 3.8 63.9 1.0 CB A:GLU419 3.8 37.9 1.0 CG A:GLU419 3.8 43.1 1.0 HG3 A:GLU419 3.8 51.9 1.0 C A:TYR418 3.8 36.9 1.0 HE1 A:TYR418 3.9 69.2 1.0 CA A:GLU419 4.0 51.2 1.0 CE1 A:TYR418 4.1 57.5 1.0 HZ1 A:LYS415 4.2 95.4 1.0 HZ3 A:LYS415 4.4 95.4 1.0 NZ A:LYS415 4.4 79.4 1.0 CG A:TYR418 4.5 39.2 1.0 O A:GLU419 4.5 35.0 1.0 C A:HIS417 4.5 49.0 1.0 N A:TYR418 4.6 41.3 1.0 O A:HOH644 4.6 81.1 1.0 HB3 A:GLU419 4.7 45.0 1.0 HG2 A:LYS415 4.7 53.1 1.0 CB A:TYR418 4.7 37.8 1.0 HA A:GLU419 4.7 61.6 1.0 C A:GLU419 4.8 36.9 1.0 O A:TYR418 5.0 41.4 1.0

Chlorine binding site 2 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:50.0 occ:1.00 H A:LYS372 2.4 42.7 1.0 HG2 A:LYS372 2.7 56.0 1.0 HA A:THR371 2.9 35.3 1.0 O A:HOH602 3.1 72.7 1.0 HB A:THR371 3.2 34.1 1.0 O A:HOH665 3.2 58.9 1.0 N A:LYS372 3.2 35.5 1.0 HG22 A:THR371 3.5 36.2 1.0 HZ2 A:LYS372 3.5 102.7 1.0 CA A:THR371 3.6 29.8 1.0 CG A:LYS372 3.6 46.6 1.0 HZ3 A:LYS372 3.7 102.7 1.0 CB A:THR371 3.7 28.6 1.0 C A:THR371 3.9 32.4 1.0 HG3 A:LYS372 3.9 56.0 1.0 HB2 A:LYS372 4.0 45.0 1.0 NZ A:LYS372 4.0 85.5 1.0 CG2 A:THR371 4.1 30.6 1.0 CB A:LYS372 4.2 37.4 1.0 CA A:LYS372 4.3 30.5 1.0 HG21 A:THR371 4.6 36.2 1.0 H A:HIS373 4.7 46.9 1.0 HZ1 A:LYS372 4.7 102.7 1.0 CD A:LYS372 4.7 92.6 1.0 HD3 A:LYS372 4.8 111.2 1.0 HG23 A:THR371 4.8 36.2 1.0 N A:THR371 4.8 30.6 1.0 HA A:LYS372 4.9 36.1 1.0 CE A:LYS372 4.9 111.8 1.0 O A:PRO370 4.9 39.7 1.0

Chlorine binding site 3 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:65.6 occ:0.52 H A:LEU364 2.5 60.2 1.0 HD1 A:PHE362 3.1 52.6 1.0 HA A:PRO363 3.2 45.1 1.0 N A:LEU364 3.4 50.1 1.0 HD12 A:LEU364 3.6 53.4 1.0 HB2 A:LEU364 3.6 54.9 1.0 HG A:LEU364 3.8 61.2 1.0 CD1 A:PHE362 3.9 43.7 1.0 HE1 A:PHE362 3.9 39.8 1.0 CA A:PRO363 4.0 37.5 1.0 HB2 A:PRO363 4.0 56.3 1.0 HB3 A:PRO363 4.1 56.3 1.0 C A:PRO363 4.2 45.1 1.0 CB A:LEU364 4.2 45.6 1.0 CB A:PRO363 4.2 46.9 1.0 CE1 A:PHE362 4.3 33.1 1.0 CG A:LEU364 4.3 51.0 1.0 CA A:LEU364 4.3 55.5 1.0 CD1 A:LEU364 4.3 44.4 1.0 O A:LEU364 4.6 60.7 1.0 HA A:PHE362 4.7 52.1 1.0 HB3 A:PHE362 4.8 42.3 1.0 HD11 A:LEU364 4.8 53.4 1.0 C A:LEU364 4.9 60.6 1.0 CG A:PHE362 5.0 33.0 1.0

Chlorine binding site 4 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:71.0 occ:1.00 H A:HIS417 2.1 51.3 1.0 HZ2 A:LYS415 2.7 95.4 1.0 HB3 A:TYR416 2.8 65.1 1.0 HZ1 A:LYS415 2.9 95.4 1.0 N A:HIS417 2.9 43.1 1.0 H A:TYR416 3.0 59.0 1.0 HB2 A:HIS417 3.1 58.0 1.0 O A:HOH631 3.1 43.5 1.0 NZ A:LYS415 3.2 79.4 1.0 HD2 A:LYS415 3.2 74.3 1.0 N A:TYR416 3.4 49.1 1.0 CB A:TYR416 3.6 54.1 1.0 HE3 A:LYS415 3.7 76.8 1.0 CE A:LYS415 3.8 63.9 1.0 CA A:HIS417 3.8 53.5 1.0 CA A:TYR416 3.8 51.4 1.0 CB A:HIS417 3.8 48.3 1.0 C A:TYR416 3.8 43.2 1.0 CD A:LYS415 3.9 61.9 1.0 HB2 A:TYR416 3.9 65.1 1.0 HZ3 A:LYS415 3.9 95.4 1.0 O A:HIS417 4.0 43.7 1.0 C A:HIS417 4.1 49.0 1.0 HG3 A:LYS415 4.2 53.1 1.0 O A:HOH644 4.3 81.1 1.0 HA A:LYS415 4.3 53.9 1.0 C A:LYS415 4.3 44.2 1.0 CG A:HIS417 4.5 48.3 1.0 O A:HOH664 4.5 74.5 1.0 HD2 A:HIS417 4.5 66.6 1.0 HD2 A:TYR416 4.5 58.0 1.0 HB3 A:HIS417 4.6 58.0 1.0 CG A:LYS415 4.6 44.1 1.0 HD3 A:LYS415 4.6 74.3 1.0 HA A:HIS417 4.7 64.3 1.0 HE2 A:LYS415 4.7 76.8 1.0 CD2 A:HIS417 4.8 55.4 1.0 HA A:TYR416 4.8 61.7 1.0 CA A:LYS415 4.8 45.3 1.0 CG A:TYR416 4.8 56.4 1.0

Chlorine binding site 5 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer Without Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:87.8 occ:1.00 HE2 A:TYR416 2.8 65.5 1.0 NA A:NA507 2.9 43.0 1.0 NE2 A:HIS417 3.2 47.2 1.0 CE2 A:TYR416 3.7 54.5 1.0 HD2 A:TYR416 4.0 58.0 1.0 CD2 A:HIS417 4.1 55.4 1.0 HD2 A:HIS417 4.1 66.6 1.0 CE1 A:HIS417 4.2 55.4 1.0 HE1 A:HIS417 4.2 66.5 1.0 HH A:TYR416 4.3 60.2 1.0 CD2 A:TYR416 4.3 48.7 1.0 CZ A:TYR416 4.8 59.7 1.0 OH A:TYR416 4.9 50.6 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