Chlorine in PDB 9dpx: Bmp-9 G389S K357R Dimer in Acidic pH

The structure of Bmp-9 G389S K357R Dimer in Acidic pH, PDB code: 9dpx 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)	64.09 / 2.10
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.289, 71.289, 146.379, 90, 90, 90
R / Rfree (%)	22.8 / 26.8

The structure of Bmp-9 G389S K357R Dimer in Acidic pH also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Chlorine atom in the Bmp-9 G389S K357R Dimer in Acidic pH (pdb code 9dpx). 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 K357R Dimer in Acidic pH, PDB code: 9dpx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Bmp-9 G389S K357R Dimer in Acidic 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 K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:78.9 occ:0.99 H A:GLU419 2.4 57.8 1.0 HG2 A:GLU419 3.0 68.4 1.0 HA A:TYR418 3.1 62.6 1.0 N A:GLU419 3.2 47.7 1.0 HB2 A:GLU419 3.2 60.9 1.0 HD1 A:TYR418 3.2 72.1 1.0 HE2 A:LYS415 3.4 72.4 1.0 HZ1 A:LYS415 3.7 87.9 1.0 CG A:GLU419 3.7 56.6 1.0 HE3 A:LYS415 3.7 72.4 1.0 O A:HIS417 3.7 55.2 1.0 CB A:GLU419 3.8 50.4 1.0 CD1 A:TYR418 3.8 59.6 1.0 HG3 A:GLU419 3.9 68.4 1.0 CA A:TYR418 3.9 51.8 1.0 CE A:LYS415 3.9 59.9 1.0 O A:HOH663 4.0 46.0 0.3 O A:HOH603 4.0 10.0 0.1 C A:TYR418 4.0 48.7 1.0 CA A:GLU419 4.0 45.9 1.0 HE1 A:TYR418 4.2 84.9 1.0 NZ A:LYS415 4.3 72.9 1.0 CE1 A:TYR418 4.4 70.3 1.0 HZ2 A:LYS415 4.7 87.9 1.0 HB3 A:GLU419 4.7 60.9 1.0 C A:HIS417 4.7 59.4 1.0 CG A:TYR418 4.7 54.6 1.0 O A:GLU419 4.8 47.5 1.0 N A:TYR418 4.8 45.2 1.0 HA A:GLU419 4.8 55.6 1.0 C A:GLU419 4.9 46.2 1.0 CB A:TYR418 4.9 45.9 1.0 HZ3 A:LYS415 5.0 87.9 1.0

Chlorine binding site 2 out of 6 in the Bmp-9 G389S K357R Dimer in Acidic 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 K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:56.0 occ:0.99 H A:LYS372 2.4 55.9 1.0 HA A:THR371 2.7 42.6 1.0 O A:HOH612 3.0 42.6 0.5 HG3 A:LYS372 3.1 49.0 1.0 HB A:THR371 3.2 43.8 1.0 N A:LYS372 3.2 46.2 1.0 HZ2 A:LYS372 3.4 77.5 1.0 CA A:THR371 3.5 35.5 1.0 CB A:THR371 3.7 36.1 1.0 HG22 A:THR371 3.8 49.5 1.0 HB2 A:LYS372 3.8 54.0 1.0 O A:HOH647 3.9 39.0 0.3 C A:THR371 3.9 33.5 1.0 CG A:LYS372 3.9 40.5 1.0 CB A:LYS372 4.2 44.6 1.0 CA A:LYS372 4.3 33.1 1.0 NZ A:LYS372 4.3 64.2 1.0 CG2 A:THR371 4.3 40.8 1.0 HG2 A:LYS372 4.5 49.0 1.0 O A:PRO370 4.5 86.5 1.0 H A:HIS373 4.5 45.4 1.0 HZ1 A:LYS372 4.5 77.5 1.0 N A:THR371 4.7 45.1 1.0 HZ3 A:LYS372 4.8 77.5 1.0 HG21 A:THR371 4.8 49.5 1.0 CD A:LYS372 4.9 72.4 1.0 HA A:LYS372 4.9 40.2 1.0 HD2 A:LYS372 4.9 87.4 1.0

Chlorine binding site 3 out of 6 in the Bmp-9 G389S K357R Dimer in Acidic 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 K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:58.5 occ:0.50 H A:LEU364 2.4 75.6 1.0 HG A:LEU364 2.8 80.0 1.0 HD1 A:PHE362 3.1 59.6 1.0 HA A:PRO363 3.2 72.0 1.0 N A:LEU364 3.3 62.6 1.0 HD12 A:LEU364 3.5 84.8 1.0 CG A:LEU364 3.6 66.3 1.0 HB2 A:PRO363 3.7 63.7 1.0 HB2 A:LEU364 3.7 62.8 1.0 CA A:PRO363 3.8 59.6 1.0 CD1 A:PHE362 3.9 49.2 1.0 HB3 A:PRO363 3.9 63.7 1.0 CD1 A:LEU364 4.0 70.2 1.0 CB A:PRO363 4.0 55.1 1.0 CB A:LEU364 4.0 51.9 1.0 C A:PRO363 4.1 60.3 1.0 HD11 A:LEU364 4.1 84.8 1.0 HE1 A:PHE362 4.2 49.5 1.0 CA A:LEU364 4.3 64.4 1.0 HB3 A:PHE362 4.4 52.5 1.0 CE1 A:PHE362 4.4 40.8 1.0 HA A:PHE362 4.5 58.4 1.0 CD2 A:LEU364 4.8 49.3 1.0 CG A:PHE362 4.8 37.1 1.0 HD13 A:LEU364 4.9 84.8 1.0 O A:LEU364 4.9 69.7 1.0 HA A:LEU364 4.9 77.8 1.0 CB A:PHE362 4.9 43.3 1.0 HD23 A:LEU364 5.0 59.7 1.0 HD21 A:LEU364 5.0 59.7 1.0 HB3 A:LEU364 5.0 62.8 1.0

Chlorine binding site 4 out of 6 in the Bmp-9 G389S K357R Dimer in Acidic 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 K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:95.8 occ:0.99 NA A:NA510 2.5 66.3 1.0 O A:HOH652 4.1 69.2 1.0 HD12 A:LEU332 4.2 54.8 1.0 O A:ARG333 4.4 61.9 1.0 HD11 A:LEU332 4.5 54.8 1.0 O A:HOH669 4.5 75.7 1.0 CD1 A:LEU332 4.8 46.0 1.0

Chlorine binding site 5 out of 6 in the Bmp-9 G389S K357R Dimer in Acidic 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 K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:113.5 occ:0.99 HD2 A:PRO363 3.0 66.7 1.0 HE2 A:PHE361 3.2 103.5 1.0 HG2 A:PRO363 3.7 77.5 1.0 CD A:PRO363 3.8 55.3 1.0 CE2 A:PHE361 4.1 85.8 1.0 NE2 A:HIS326 4.1 78.3 1.0 HD3 A:PRO363 4.2 66.7 1.0 CG A:PRO363 4.2 64.2 1.0 HG3 A:PRO363 4.4 77.5 1.0 HD2 A:HIS326 4.5 92.8 1.0 O A:PRO363 4.7 52.7 1.0 HZ A:PHE361 4.7 106.2 1.0 CD2 A:HIS326 4.7 76.9 1.0 HD2 A:PHE361 4.8 89.1 1.0 CZ A:PHE361 4.9 88.1 1.0 N A:PRO363 4.9 52.5 1.0 CD2 A:PHE361 5.0 73.8 1.0

Chlorine binding site 6 out of 6 in the Bmp-9 G389S K357R Dimer in Acidic 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 K357R Dimer in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl508 b:59.2 occ:0.30 NA A:NA511 2.4 36.8 0.5 H A:GLU352 2.8 58.1 1.0 O A:HOH666 3.1 86.3 1.0 HH12 A:ARG333 3.3 116.5 1.0 HB3 A:GLU352 3.3 58.6 1.0 HA A:TYR351 3.3 54.5 1.0 HB2 A:GLU352 3.3 58.6 1.0 N A:GLU352 3.5 48.0 1.0 O A:HOH618 3.6 64.8 1.0 CB A:GLU352 3.7 48.4 1.0 HB2 A:TYR351 3.9 50.8 1.0 NH1 A:ARG333 4.0 96.7 1.0 CA A:TYR351 4.1 46.5 1.0 C A:TYR351 4.2 50.3 1.0 CA A:GLU352 4.2 43.4 1.0 HH11 A:ARG333 4.4 116.5 1.0 HH22 A:ARG333 4.4 105.0 1.0 CB A:TYR351 4.5 44.4 1.0 O A:HOH641 4.7 43.9 0.5 HA A:GLU352 4.9 51.9 1.0 O A:GLU350 4.9 54.2 1.0 CZ A:ARG333 5.0 99.8 1.0 HB3 A:TYR351 5.0 50.8 1.0 NH2 A:ARG333 5.0 87.1 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