Chlorine in PDB 9dpo: Bmp-9 Wild-Type Dimer with Radiation Damage in Neutral pH

The structure of Bmp-9 Wild-Type Dimer with Radiation Damage in Neutral pH, PDB code: 9dpo 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)	41.49 / 2.34
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.203, 71.203, 146.515, 90, 90, 90
R / Rfree (%)	19.9 / 24.5

The structure of Bmp-9 Wild-Type 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 Wild-Type Dimer with Radiation Damage in Neutral pH (pdb code 9dpo). 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 with Radiation Damage in Neutral pH, PDB code: 9dpo:
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 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 Wild-Type Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:63.7 occ:1.00 H A:GLU419 2.6 44.9 1.0 HE2 A:LYS415 2.9 57.9 1.0 HA A:TYR418 3.0 51.3 1.0 HD1 A:TYR418 3.3 80.4 1.0 N A:GLU419 3.4 37.3 1.0 HE3 A:LYS415 3.5 57.9 1.0 HG2 A:GLU419 3.6 53.7 1.0 CE A:LYS415 3.6 48.1 1.0 HB2 A:GLU419 3.6 49.0 1.0 HZ1 A:LYS415 3.7 101.3 1.0 CD1 A:TYR418 3.8 66.9 1.0 O A:HIS417 3.8 50.0 1.0 CA A:TYR418 3.9 42.7 1.0 C A:TYR418 4.1 41.8 1.0 HE1 A:TYR418 4.1 84.5 1.0 NZ A:LYS415 4.2 84.3 1.0 CB A:GLU419 4.2 40.7 1.0 CE1 A:TYR418 4.2 70.3 1.0 CG A:GLU419 4.2 44.6 1.0 CA A:GLU419 4.4 43.9 1.0 HG3 A:GLU419 4.4 53.7 1.0 CG A:TYR418 4.5 37.4 1.0 HG2 A:LYS415 4.6 52.9 1.0 HZ2 A:LYS415 4.7 101.3 1.0 C A:HIS417 4.7 40.3 1.0 O A:GLU419 4.8 38.6 1.0 CB A:TYR418 4.8 38.2 1.0 N A:TYR418 4.8 38.7 1.0 HZ3 A:LYS415 4.8 101.3 1.0 CD A:LYS415 4.9 53.2 1.0

Chlorine binding site 2 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:57.8 occ:1.00 H A:LYS372 2.5 38.2 1.0 HG3 A:LYS372 2.8 54.0 1.0 HA A:THR371 2.9 46.5 1.0 O A:HOH651 3.0 64.8 1.0 HB A:THR371 3.1 46.1 1.0 O A:HOH643 3.3 64.2 1.0 N A:LYS372 3.3 32.4 1.0 HG22 A:THR371 3.5 50.0 1.0 CA A:THR371 3.6 39.4 1.0 CB A:THR371 3.7 39.0 1.0 CG A:LYS372 3.8 44.8 1.0 HB2 A:LYS372 4.0 46.3 1.0 C A:THR371 4.0 36.6 1.0 HE2 A:LYS372 4.1 78.2 1.0 CG2 A:THR371 4.1 42.2 1.0 HG2 A:LYS372 4.2 54.0 1.0 CB A:LYS372 4.2 38.5 1.0 CA A:LYS372 4.4 32.1 1.0 HG21 A:THR371 4.6 50.0 1.0 H A:HIS373 4.6 50.6 1.0 HZ3 A:LYS372 4.7 122.5 1.0 CD A:LYS372 4.7 70.4 1.0 HD2 A:LYS372 4.7 84.6 1.0 CE A:LYS372 4.8 65.1 1.0 HG23 A:THR371 4.9 50.0 1.0 O A:PRO370 4.9 43.8 1.0 N A:THR371 4.9 46.1 1.0 HA A:LYS372 5.0 37.9 1.0

Chlorine binding site 3 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:59.6 occ:0.45 H A:LEU364 2.6 67.6 1.0 HD1 A:PHE362 2.8 56.9 1.0 HA A:PRO363 3.2 58.9 1.0 N A:LEU364 3.4 56.2 1.0 HB2 A:LEU364 3.6 73.0 1.0 CD1 A:PHE362 3.7 47.3 1.0 HE1 A:PHE362 3.8 44.9 1.0 HG A:LEU364 3.9 70.4 1.0 CA A:PRO363 4.0 49.7 1.0 HB2 A:PRO363 4.0 64.8 1.0 HB3 A:PRO363 4.1 64.8 1.0 CE1 A:PHE362 4.1 38.0 1.0 C A:PRO363 4.2 51.5 1.0 CB A:LEU364 4.2 60.7 1.0 CB A:PRO363 4.3 53.9 1.0 HD12 A:LEU364 4.3 71.5 1.0 CA A:LEU364 4.3 68.5 1.0 O A:LEU364 4.5 83.4 1.0 CG A:LEU364 4.5 58.6 1.0 HB3 A:PHE362 4.5 49.6 1.0 HA A:PHE362 4.7 54.1 1.0 CG A:PHE362 4.8 39.4 1.0 C A:LEU364 4.8 74.3 1.0 CD1 A:LEU364 4.9 59.5 1.0

Chlorine binding site 4 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:76.9 occ:1.00 H A:HIS417 2.1 55.0 1.0 HB2 A:HIS417 2.8 57.0 1.0 HZ2 A:LYS415 2.8 101.3 1.0 N A:HIS417 2.9 45.7 1.0 HB3 A:TYR416 3.0 71.5 1.0 HD2 A:LYS415 3.2 64.0 1.0 O A:HOH624 3.2 57.3 1.0 H A:TYR416 3.2 53.1 1.0 HE3 A:LYS415 3.3 57.9 1.0 CB A:HIS417 3.6 47.4 1.0 NZ A:LYS415 3.6 84.3 1.0 CA A:HIS417 3.6 41.5 1.0 N A:TYR416 3.6 44.8 1.0 O A:HIS417 3.6 50.0 1.0 CE A:LYS415 3.7 48.1 1.0 C A:TYR416 3.8 43.0 1.0 CB A:TYR416 3.8 59.5 1.0 CD A:LYS415 3.9 53.2 1.0 C A:HIS417 3.9 40.3 1.0 CA A:TYR416 3.9 44.8 1.0 HZ3 A:LYS415 4.0 101.3 1.0 HZ1 A:LYS415 4.2 101.3 1.0 HB2 A:TYR416 4.2 71.5 1.0 HB3 A:HIS417 4.2 57.0 1.0 O A:HOH650 4.3 66.1 1.0 HA A:LYS415 4.4 67.2 1.0 HG3 A:LYS415 4.4 52.9 1.0 CG A:HIS417 4.4 49.2 1.0 C A:LYS415 4.4 43.3 1.0 HD2 A:TYR416 4.5 71.7 1.0 HA A:HIS417 4.5 49.5 1.0 HD3 A:LYS415 4.6 64.0 1.0 HE2 A:LYS415 4.6 57.9 1.0 HD2 A:HIS417 4.7 63.3 1.0 CG A:LYS415 4.7 43.9 1.0 CD2 A:HIS417 4.8 52.7 1.0 CA A:LYS415 4.9 55.9 1.0 HA A:TYR416 4.9 53.5 1.0 N A:TYR418 4.9 38.7 1.0 O A:TYR416 5.0 42.2 1.0 CG A:TYR416 5.0 51.5 1.0

Chlorine binding site 5 out of 5 in the Bmp-9 Wild-Type 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 Wild-Type Dimer with Radiation Damage in Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:103.5 occ:1.00 HE2 A:HIS417 2.8 62.6 1.0 HE2 A:TYR416 2.8 74.4 1.0 NA A:NA506 2.9 47.0 1.0 NE2 A:HIS417 3.5 52.0 1.0 CE2 A:TYR416 3.7 61.9 1.0 HH A:TYR416 4.0 72.9 1.0 HD2 A:TYR416 4.1 71.7 1.0 CD2 A:TYR416 4.3 59.6 1.0 HD2 A:HIS417 4.3 63.3 1.0 CD2 A:HIS417 4.3 52.7 1.0 CE1 A:HIS417 4.5 71.1 1.0 HE1 A:HIS417 4.6 85.4 1.0 CZ A:TYR416 4.6 51.1 1.0 OH A:TYR416 4.7 60.6 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