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Chlorine in PDB 9dpw: Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH

Protein crystallography data

The structure of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH, PDB code: 9dpw 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) 40.08 / 2.71
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.1, 71.1, 145.548, 90, 90, 90
R / Rfree (%) 22.4 / 29.9

Other elements in 9dpw:

The structure of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH (pdb code 9dpw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH, PDB code: 9dpw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 9dpw

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Chlorine binding site 1 out of 9 in the Bmp-9 K357R G389S 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:61.2
occ:0.73
 H A:GLU419 2.6 53.3 1.0
HB2 A:GLU419 3.2 64.7 1.0
HE2 A:LYS415 3.2 71.1 1.0
HD1 A:TYR418 3.4 73.2 1.0
HA A:TYR418 3.4 63.6 1.0
N A:GLU419 3.4 44.3 1.0
HE3 A:LYS415 3.7 71.1 1.0
HG2 A:GLU419 3.8 78.4 1.0
CD1 A:TYR418 3.9 60.9 1.0
CE A:LYS415 3.9 59.1 1.0
CB A:GLU419 4.0 53.7 1.0
HE1 A:TYR418 4.0 83.8 1.0
O A:HIS417 4.1 47.1 1.0
HZ1 A:LYS415 4.1 85.3 1.0
O A:HOH642 4.2 60.0 0.8
CA A:TYR418 4.2 52.8 1.0
C A:TYR418 4.3 46.0 1.0
CE1 A:TYR418 4.3 69.6 1.0
CA A:GLU419 4.3 46.8 1.0
CG A:GLU419 4.3 65.2 1.0
HG3 A:GLU419 4.3 78.4 1.0
NZ A:LYS415 4.5 70.9 1.0
O A:GLU419 4.7 45.4 1.0
HB3 A:GLU419 4.8 64.7 1.0
CG A:TYR418 4.8 52.6 1.0
HG2 A:LYS415 4.9 65.6 1.0
HZ2 A:LYS415 5.0 85.3 1.0
C A:HIS417 5.0 45.3 1.0

Chlorine binding site 2 out of 9 in 9dpw

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Chlorine binding site 2 out of 9 in the Bmp-9 K357R G389S 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:41.8
occ:0.49
 H A:LYS372 2.4 41.5 1.0
HZ3 A:LYS372 2.8 83.7 1.0
HA A:THR371 2.8 41.7 1.0
HG3 A:LYS372 3.0 61.1 1.0
HZ2 A:LYS372 3.1 83.7 1.0
N A:LYS372 3.2 34.5 1.0
NZ A:LYS372 3.4 69.6 1.0
HB A:THR371 3.4 43.2 1.0
CA A:THR371 3.6 34.6 1.0
HB2 A:LYS372 3.7 50.8 1.0
CG A:LYS372 3.8 50.7 1.0
HZ1 A:LYS372 3.9 83.7 1.0
O A:HOH637 3.9 52.7 1.0
C A:THR371 3.9 38.5 1.0
CB A:THR371 4.0 35.8 1.0
HG22 A:THR371 4.0 52.1 1.0
CB A:LYS372 4.1 42.1 1.0
CA A:LYS372 4.3 28.5 1.0
HG2 A:LYS372 4.5 61.1 1.0
HD2 A:LYS372 4.5 77.5 1.0
CE A:LYS372 4.5 74.3 1.0
CD A:LYS372 4.5 64.4 1.0
CG2 A:THR371 4.5 43.2 1.0
H A:HIS373 4.7 49.0 1.0
O A:PRO370 4.7 56.3 1.0
HA A:LYS372 4.8 34.4 1.0
N A:THR371 4.8 39.0 1.0
O A:HOH629 4.9 56.1 0.9
HE3 A:LYS372 5.0 89.3 1.0

Chlorine binding site 3 out of 9 in 9dpw

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Chlorine binding site 3 out of 9 in the Bmp-9 K357R G389S 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:46.2
occ:0.46
 H A:LEU364 2.5 86.9 1.0
HB2 A:LEU364 2.8 86.5 1.0
HD1 A:PHE362 2.9 50.6 1.0
N A:LEU364 3.4 72.2 1.0
HA A:PRO363 3.6 57.8 1.0
CD1 A:PHE362 3.7 42.0 1.0
CB A:LEU364 3.7 71.9 1.0
HE1 A:PHE362 4.0 56.2 1.0
CA A:LEU364 4.1 77.3 1.0
HD12 A:LEU364 4.2 71.7 1.0
HG A:LEU364 4.2 79.8 1.0
HB3 A:PHE362 4.2 62.5 1.0
HB3 A:LEU364 4.3 86.5 1.0
CE1 A:PHE362 4.3 46.7 1.0
C A:PRO363 4.3 62.5 1.0
CA A:PRO363 4.4 48.0 1.0
CG A:LEU364 4.5 66.4 1.0
O A:LEU364 4.6 91.3 1.0
HA A:PHE362 4.6 56.3 1.0
CG A:PHE362 4.7 44.1 1.0
HB2 A:PRO363 4.8 56.2 1.0
C A:LEU364 4.8 92.7 1.0
CD1 A:LEU364 4.8 59.6 1.0
CB A:PHE362 4.8 51.9 1.0
HB3 A:PRO363 4.9 56.2 1.0
CB A:PRO363 4.9 46.7 1.0
HA A:LEU364 5.0 93.0 1.0

Chlorine binding site 4 out of 9 in 9dpw

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Chlorine binding site 4 out of 9 in the Bmp-9 K357R G389S 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:59.7
occ:0.54
 HZ2 A:LYS415 2.1 85.3 1.0
H A:HIS417 2.3 62.2 1.0
NZ A:LYS415 2.9 70.9 1.0
HB2 A:HIS417 3.1 72.8 1.0
N A:HIS417 3.1 51.6 1.0
HB3 A:TYR416 3.1 73.4 1.0
HZ3 A:LYS415 3.2 85.3 1.0
O A:HOH624 3.2 54.3 0.9
H A:TYR416 3.3 56.4 1.0
HD2 A:LYS415 3.4 61.7 1.0
HZ1 A:LYS415 3.5 85.3 1.0
HE3 A:LYS415 3.5 71.1 1.0
O A:HOH646 3.6 74.1 0.9
CE A:LYS415 3.7 59.1 1.0
N A:TYR416 3.8 46.8 1.0
CB A:HIS417 3.8 60.5 1.0
CA A:HIS417 3.9 56.8 1.0
O A:HIS417 3.9 47.1 1.0
HD2 A:HIS417 3.9 64.3 1.0
CB A:TYR416 4.0 61.0 1.0
CD A:LYS415 4.0 51.2 1.0
C A:TYR416 4.1 46.1 1.0
C A:HIS417 4.1 45.3 1.0
CA A:TYR416 4.1 54.9 1.0
HB2 A:TYR416 4.4 73.4 1.0
CD2 A:HIS417 4.4 53.4 1.0
CG A:HIS417 4.5 60.3 1.0
HB3 A:HIS417 4.6 72.8 1.0
HE2 A:LYS415 4.6 71.1 1.0
HD3 A:LYS415 4.6 61.7 1.0
HD2 A:TYR416 4.6 65.1 1.0
HA A:LYS415 4.7 78.9 1.0
C A:LYS415 4.7 55.9 1.0
HA A:HIS417 4.8 68.3 1.0
HG3 A:LYS415 4.8 65.6 1.0

Chlorine binding site 5 out of 9 in 9dpw

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Chlorine binding site 5 out of 9 in the Bmp-9 K357R G389S 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 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:57.5
occ:0.48
 NA A:NA512 2.5 76.5 1.0
HE2 A:TYR416 2.5 70.5 1.0
NE2 A:HIS417 3.2 62.8 1.0
CE2 A:TYR416 3.4 58.6 1.0
HH A:TYR416 3.7 72.7 1.0
HE1 A:HIS417 4.1 86.0 1.0
HD2 A:TYR416 4.1 65.1 1.0
CE1 A:HIS417 4.1 71.5 1.0
CD2 A:TYR416 4.2 54.1 1.0
CD2 A:HIS417 4.3 53.4 1.0
OH A:TYR416 4.3 60.4 1.0
CZ A:TYR416 4.3 54.3 1.0
HD2 A:HIS417 4.4 64.3 1.0

Chlorine binding site 6 out of 9 in 9dpw

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Chlorine binding site 6 out of 9 in the Bmp-9 K357R G389S 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 6 of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:64.2
occ:0.40
 HG2 A:PRO363 2.6 77.0 1.0
HE2 A:HIS326 2.9 132.6 1.0
HD2 A:PRO363 3.1 71.5 1.0
CG A:PRO363 3.4 64.0 1.0
HG3 A:PRO363 3.6 77.0 1.0
CD A:PRO363 3.7 59.4 1.0
NE2 A:HIS326 3.7 110.3 1.0
HD2 A:HIS326 4.1 141.9 1.0
O A:PRO363 4.2 69.6 1.0
HE2 A:PHE361 4.3 96.7 1.0
HD3 A:PRO363 4.3 71.5 1.0
CD2 A:HIS326 4.3 118.1 1.0
CB A:PRO363 4.6 46.7 1.0
N A:PRO363 4.7 46.5 1.0
HB2 A:PRO363 4.8 56.2 1.0
CE1 A:HIS326 4.9 105.0 1.0
CE2 A:PHE361 4.9 80.4 1.0

Chlorine binding site 7 out of 9 in 9dpw

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Chlorine binding site 7 out of 9 in the Bmp-9 K357R G389S 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 7 of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl509

b:81.9
occ:0.69
 O A:THR386 3.5 72.5 1.0
O A:LYS387 3.9 81.3 1.0
HB2 A:SER389 4.0 104.2 1.0
O A:PRO385 4.1 56.2 1.0
O A:VAL388 4.2 53.1 1.0
C A:THR386 4.2 58.8 1.0
C A:LYS387 4.3 71.6 1.0
HA A:SER389 4.3 77.5 1.0
C A:VAL388 4.4 47.5 1.0
HA A:THR386 4.6 78.9 1.0
HA A:LYS387 4.6 66.3 1.0
N A:LYS387 4.7 60.3 1.0
N A:SER389 4.8 58.9 1.0
CB A:SER389 4.8 86.6 1.0
CA A:LYS387 4.8 55.1 1.0
N A:VAL388 4.8 62.4 1.0
CA A:SER389 4.9 64.5 1.0
CA A:THR386 5.0 65.6 1.0

Chlorine binding site 8 out of 9 in 9dpw

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Chlorine binding site 8 out of 9 in the Bmp-9 K357R G389S 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 8 of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl510

b:141.4
occ:1.00
 O A:HOH644 2.9 85.2 0.8
HD3 A:LYS415 4.0 61.7 1.0
HE2 A:LYS415 4.4 71.1 1.0
OH A:TYR405 4.8 91.2 1.0
HG2 A:LYS415 4.8 65.6 1.0
CD A:LYS415 4.9 51.2 1.0

Chlorine binding site 9 out of 9 in 9dpw

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Chlorine binding site 9 out of 9 in the Bmp-9 K357R G389S 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 9 of Bmp-9 K357R G389S Dimer with Radiation Damage in Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl511

b:135.1
occ:1.00
 H A:ARG333 2.8 58.9 1.0
HA A:LEU332 3.4 48.9 1.0
HB3 A:ARG333 3.5 78.2 1.0
N A:ARG333 3.6 48.9 1.0
HB2 A:ARG333 4.1 78.2 1.0
CA A:LEU332 4.2 40.6 1.0
CB A:ARG333 4.2 65.0 1.0
HD12 A:LEU332 4.2 51.0 1.0
HB3 A:SER331 4.3 86.0 1.0
O A:SER331 4.3 48.6 1.0
C A:LEU332 4.4 43.6 1.0
HB2 A:SER331 4.4 86.0 1.0
N A:LEU332 4.5 49.3 1.0
C A:SER331 4.5 49.5 1.0
CA A:ARG333 4.5 54.1 1.0
NA A:NA514 4.7 69.8 1.0
CB A:SER331 4.8 71.5 1.0
O A:ARG333 5.0 57.9 1.0

Reference:

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
Page generated: Sun Jul 13 16:22:16 2025

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