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Chlorine in PDB 9dpr: Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic pH

Protein crystallography data

The structure of Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic pH, PDB code: 9dpr 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) 41.34 / 2.61
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.044, 71.044, 145.564, 90, 90, 90
R / Rfree (%) 21.2 / 26.6

Other elements in 9dpr:

The structure of Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic pH also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic pH (pdb code 9dpr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic pH, PDB code: 9dpr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 9dpr

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Chlorine binding site 1 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:78.5
occ:0.94
 H A:HIS417 2.4 53.3 1.0
HB2 A:HIS417 2.7 53.6 1.0
HZ2 A:LYS415 2.8 85.7 1.0
HD2 A:LYS415 3.0 72.9 1.0
N A:HIS417 3.1 44.4 1.0
HB3 A:TYR416 3.2 73.1 1.0
H A:TYR416 3.4 53.8 1.0
O A:HOH643 3.5 49.0 1.0
CB A:HIS417 3.6 44.6 1.0
NZ A:LYS415 3.6 71.4 1.0
HZ1 A:LYS415 3.7 85.7 1.0
O A:HIS417 3.8 39.8 1.0
CA A:HIS417 3.8 39.3 1.0
CD A:LYS415 3.8 60.8 1.0
N A:TYR416 3.9 44.8 1.0
HD3 A:LYS415 4.0 72.9 1.0
CB A:TYR416 4.1 60.9 1.0
C A:TYR416 4.1 41.5 1.0
CE A:LYS415 4.1 58.4 1.0
C A:HIS417 4.1 38.1 1.0
HE3 A:LYS415 4.2 70.2 1.0
CA A:TYR416 4.2 52.7 1.0
HB3 A:HIS417 4.2 53.6 1.0
HZ3 A:LYS415 4.2 85.7 1.0
CG A:HIS417 4.3 53.5 1.0
HD2 A:HIS417 4.4 51.9 1.0
HB2 A:TYR416 4.5 73.1 1.0
HD2 A:TYR416 4.5 61.5 1.0
CD2 A:HIS417 4.6 43.5 1.0
HA A:LYS415 4.7 91.5 1.0
HA A:HIS417 4.7 47.2 1.0
C A:LYS415 4.7 47.6 1.0
HG3 A:LYS415 4.9 72.7 1.0
O A:HOH660 5.0 68.9 1.0

Chlorine binding site 2 out of 10 in 9dpr

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Chlorine binding site 2 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:49.6
occ:0.74
 H A:GLU419 2.6 47.4 1.0
HE3 A:LYS415 3.1 70.2 1.0
HA A:TYR418 3.3 50.9 1.0
HB2 A:GLU419 3.5 46.0 1.0
N A:GLU419 3.5 39.5 1.0
HG2 A:GLU419 3.6 44.6 1.0
HD1 A:TYR418 3.6 65.9 1.0
HE2 A:LYS415 3.7 70.2 1.0
HZ1 A:LYS415 3.8 85.7 1.0
CE A:LYS415 3.8 58.4 1.0
O A:HIS417 3.9 39.8 1.0
CD1 A:TYR418 4.1 54.9 1.0
CB A:GLU419 4.1 38.3 1.0
CA A:TYR418 4.2 42.4 1.0
CG A:GLU419 4.2 37.2 1.0
NZ A:LYS415 4.3 71.4 1.0
C A:TYR418 4.3 42.0 1.0
HG3 A:GLU419 4.3 44.6 1.0
HE1 A:TYR418 4.3 75.3 1.0
CA A:GLU419 4.4 51.8 1.0
CE1 A:TYR418 4.5 62.7 1.0
HZ3 A:LYS415 4.7 85.7 1.0
O A:GLU419 4.8 38.7 1.0
CG A:TYR418 4.8 49.9 1.0
C A:HIS417 4.8 38.1 1.0
HG2 A:LYS415 5.0 72.7 1.0
HB3 A:GLU419 5.0 46.0 1.0
HZ2 A:LYS415 5.0 85.7 1.0

Chlorine binding site 3 out of 10 in 9dpr

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Chlorine binding site 3 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:58.0
occ:0.77
 NA A:NA512 2.7 52.0 1.0
O A:HOH625 3.2 31.2 0.8
HG A:LEU398 3.4 42.6 1.0
HD12 A:LEU398 3.6 33.2 1.0
HD11 A:LEU398 3.9 33.2 1.0
CD1 A:LEU398 4.1 27.9 1.0
HA A:LYS397 4.1 68.4 1.0
CG A:LEU398 4.2 35.5 1.0
O A:THR396 4.2 42.0 1.0
H A:LEU398 4.4 60.3 1.0
C A:THR396 4.5 39.3 1.0
HB2 A:LEU398 4.5 33.3 1.0
O A:HOH657 4.6 62.9 1.0
HA A:THR396 4.7 53.7 1.0
N A:LEU398 4.8 50.2 1.0
CA A:LYS397 4.8 57.0 1.0
O A:PRO395 4.8 50.9 1.0
N A:LYS397 4.8 37.7 1.0
CB A:LEU398 4.9 27.9 1.0
HD13 A:LEU398 5.0 33.2 1.0

Chlorine binding site 4 out of 10 in 9dpr

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Chlorine binding site 4 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:28.7
occ:0.58
 H A:LYS372 2.4 49.7 1.0
HA A:THR371 2.7 41.5 1.0
N A:LYS372 3.2 41.4 1.0
HG3 A:LYS372 3.2 63.4 1.0
HB A:THR371 3.3 41.5 1.0
CA A:THR371 3.5 34.5 1.0
HG22 A:THR371 3.7 43.4 1.0
CB A:THR371 3.8 34.5 1.0
C A:THR371 3.8 31.3 1.0
O A:HOH610 3.8 62.5 1.0
HB2 A:LYS372 3.8 59.0 1.0
HZ2 A:LYS372 4.0 96.3 1.0
CG A:LYS372 4.0 52.8 1.0
CL A:CL507 4.1 78.3 0.8
CB A:LYS372 4.2 49.1 1.0
CG2 A:THR371 4.3 36.1 1.0
CA A:LYS372 4.3 33.6 1.0
HZ3 A:LYS372 4.3 96.3 1.0
NZ A:LYS372 4.6 80.2 1.0
O A:PRO370 4.6 54.2 1.0
HG2 A:LYS372 4.6 63.4 1.0
H A:HIS373 4.6 38.2 1.0
N A:THR371 4.7 58.5 1.0
HD2 A:LYS372 4.8 80.6 1.0
HG21 A:THR371 4.8 43.4 1.0
HA A:LYS372 4.8 40.3 1.0
CD A:LYS372 4.9 67.1 1.0
HG23 A:THR371 5.0 43.4 1.0

Chlorine binding site 5 out of 10 in 9dpr

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Chlorine binding site 5 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:92.0
occ:0.73
 H A:LEU364 2.3 92.4 1.0
HD1 A:PHE362 2.9 55.3 1.0
HB2 A:LEU364 2.9 64.7 1.0
N A:LEU364 3.2 77.0 1.0
HA A:PRO363 3.3 69.4 1.0
CD1 A:PHE362 3.7 46.3 1.0
CB A:LEU364 3.7 53.9 1.0
CA A:LEU364 4.0 56.8 1.0
HE1 A:PHE362 4.0 51.9 1.0
CA A:PRO363 4.1 58.0 1.0
C A:PRO363 4.1 57.0 1.0
HD12 A:LEU364 4.2 95.6 1.0
HG A:LEU364 4.2 65.1 1.0
HB3 A:PHE362 4.2 59.7 1.0
HB2 A:PRO363 4.2 75.0 1.0
CE1 A:PHE362 4.3 43.5 1.0
HB3 A:LEU364 4.4 64.7 1.0
O A:LEU364 4.4 86.0 1.0
CG A:LEU364 4.5 54.2 1.0
HB3 A:PRO363 4.5 75.0 1.0
CB A:PRO363 4.5 62.8 1.0
C A:LEU364 4.6 66.1 1.0
HA A:PHE362 4.6 60.9 1.0
CG A:PHE362 4.7 46.6 1.0
CD1 A:LEU364 4.8 79.6 1.0
HA A:LEU364 4.8 68.3 1.0
CB A:PHE362 4.8 49.9 1.0

Chlorine binding site 6 out of 10 in 9dpr

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Chlorine binding site 6 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:78.3
occ:0.82
 HG22 A:THR371 3.2 43.4 1.0
HA A:THR371 3.6 41.5 1.0
O A:PRO370 3.9 54.2 1.0
CL A:CL505 4.1 28.7 0.6
CG2 A:THR371 4.1 36.1 1.0
O A:THR369 4.1 70.5 1.0
HG23 A:THR371 4.1 43.4 1.0
CA A:THR371 4.4 34.5 1.0
C A:PRO370 4.4 36.0 1.0
HH22 A:ARG429 4.5 57.8 1.0
NH2 A:ARG429 4.5 48.1 1.0
HH21 A:ARG429 4.5 57.8 1.0
N A:THR371 4.6 58.5 1.0
O A:HOH653 4.6 57.2 1.0
HG21 A:THR371 4.7 43.4 1.0
CB A:THR371 4.8 34.5 1.0
HB A:THR369 4.9 125.4 1.0
CZ A:ARG429 4.9 40.4 1.0
C A:THR369 5.0 64.0 1.0

Chlorine binding site 7 out of 10 in 9dpr

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Chlorine binding site 7 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:93.4
occ:0.70
 O A:HOH617 3.1 69.9 1.0
O A:THR386 3.7 79.3 1.0
O A:LYS387 3.9 97.7 1.0
H A:GLY389 4.1 35.9 1.0
N A:GLY389 4.2 29.9 1.0
C A:LYS387 4.2 78.4 1.0
C A:VAL388 4.3 42.3 1.0
HA A:VAL388 4.4 58.5 1.0
HA2 A:GLY389 4.4 35.0 1.0
C A:THR386 4.5 74.4 1.0
HA3 A:GLY389 4.5 35.0 1.0
N A:VAL388 4.5 79.4 1.0
CA A:GLY389 4.6 29.2 1.0
CA A:VAL388 4.7 48.7 1.0
HA A:LYS387 4.7 80.0 1.0
O A:VAL388 4.8 47.0 1.0
HA A:THR386 4.9 104.8 1.0
O A:PRO385 4.9 55.3 1.0
CA A:LYS387 4.9 66.6 1.0
H A:VAL388 5.0 95.4 1.0
N A:LYS387 5.0 85.5 1.0

Chlorine binding site 8 out of 10 in 9dpr

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Chlorine binding site 8 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl509

b:86.9
occ:0.99
 HB3 A:PRO385 3.7 59.8 1.0
NE2 A:HIS381 3.7 42.9 1.0
O A:HOH620 4.1 58.5 1.0
CE1 A:HIS381 4.5 36.1 1.0
HE1 A:HIS381 4.5 43.4 1.0
CD2 A:HIS381 4.6 54.2 1.0
HG3 A:PRO385 4.6 70.9 1.0
CB A:PRO385 4.6 49.8 1.0
HD2 A:HIS381 4.6 65.1 1.0
HD12 A:LEU382 4.8 104.5 1.0
HB2 A:PRO385 4.9 59.8 1.0
CG A:PRO385 5.0 59.1 1.0

Chlorine binding site 9 out of 10 in 9dpr

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Chlorine binding site 9 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic 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 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl510

b:92.6
occ:0.99
 O A:HOH652 3.0 47.7 1.0
HG2 A:PRO363 3.0 78.1 1.0
HE2 A:HIS326 3.1 112.8 1.0
HD2 A:PRO363 3.2 74.6 1.0
HG3 A:PRO363 3.6 78.1 1.0
CG A:PRO363 3.6 65.3 1.0
CD A:PRO363 3.8 62.4 1.0
NE2 A:HIS326 4.0 94.0 1.0
HD3 A:PRO363 4.2 74.6 1.0
HA2 A:GLY324 4.3 167.3 1.0
HE1 A:PHE361 4.4 98.8 1.0
HD2 A:HIS326 4.6 112.5 1.0
CD2 A:HIS326 4.7 93.8 1.0
HA3 A:GLY324 4.8 167.3 1.0
O A:PRO363 4.8 58.3 1.0
CB A:PRO363 5.0 62.8 1.0

Chlorine binding site 10 out of 10 in 9dpr

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Chlorine binding site 10 out of 10 in the Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic pH


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Bmp-9 Wild-Type Dimer with Radiation Damage in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl511

b:61.0
occ:0.83
 HH A:TYR416 2.2 58.5 1.0
HE2 A:TYR416 2.7 57.3 1.0
OH A:TYR416 3.0 48.7 1.0
CE2 A:TYR416 3.4 47.7 1.0
HE1 A:HIS417 3.5 74.0 1.0
O A:HOH638 3.6 58.4 1.0
CZ A:TYR416 3.6 47.0 1.0
O A:HOH656 3.9 60.7 1.0
NE2 A:HIS417 4.0 44.3 1.0
CE1 A:HIS417 4.0 61.6 1.0
H12 A:GOL501 4.0 114.2 0.9
H11 A:GOL501 4.2 114.2 0.9
O A:HOH659 4.6 58.0 1.0
C1 A:GOL501 4.6 95.2 0.9
CD2 A:TYR416 4.7 51.2 1.0
O2 A:GOL501 4.9 86.4 0.9
HD2 A:TYR416 4.9 61.5 1.0
CE1 A:TYR416 5.0 49.6 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 16:19:51 2025

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