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Chlorine in PDB 9dpp: Bmp-9 Wild-Type Dimer in Acidic pH

Protein crystallography data

The structure of Bmp-9 Wild-Type Dimer in Acidic pH, PDB code: 9dpp 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) 35.47 / 2.12
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.94, 70.94, 145.86, 90, 90, 90
R / Rfree (%) 22 / 25.8

Other elements in 9dpp:

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

Sodium (Na) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bmp-9 Wild-Type Dimer in Acidic pH (pdb code 9dpp). 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 Wild-Type Dimer in Acidic pH, PDB code: 9dpp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 9dpp

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Chlorine binding site 1 out of 9 in the Bmp-9 Wild-Type 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 Wild-Type Dimer in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:74.4
occ:0.87
 H A:HIS417 2.1 65.4 1.0
HZ1 A:LYS415 2.8 92.5 1.0
N A:HIS417 2.9 55.4 1.0
HZ2 A:LYS415 3.0 92.5 1.0
HB2 A:HIS417 3.0 64.0 1.0
HB3 A:TYR416 3.2 72.7 1.0
H A:TYR416 3.2 69.4 1.0
O A:HOH629 3.2 61.5 1.0
HD2 A:LYS415 3.2 70.1 1.0
NZ A:LYS415 3.3 76.9 1.0
HE3 A:LYS415 3.5 73.5 1.0
CA A:HIS417 3.6 54.9 1.0
N A:TYR416 3.7 58.8 1.0
O A:HIS417 3.7 51.9 1.0
CB A:HIS417 3.7 54.3 1.0
CE A:LYS415 3.7 61.1 1.0
C A:HIS417 3.9 51.2 1.0
CD A:LYS415 3.9 58.2 1.0
C A:TYR416 4.0 58.8 1.0
CB A:TYR416 4.0 61.4 1.0
CA A:TYR416 4.1 58.3 1.0
HZ3 A:LYS415 4.1 92.5 1.0
HD2 A:HIS417 4.2 69.9 1.0
HB2 A:TYR416 4.4 72.7 1.0
HA A:LYS415 4.4 71.6 1.0
CG A:HIS417 4.4 65.6 1.0
C A:LYS415 4.5 56.9 1.0
HB3 A:HIS417 4.5 64.0 1.0
HG3 A:LYS415 4.5 85.2 1.0
HA A:HIS417 4.5 66.1 1.0
CD2 A:HIS417 4.6 59.1 1.0
HD3 A:LYS415 4.6 70.1 1.0
HD2 A:TYR416 4.6 73.8 1.0
HE2 A:LYS415 4.7 73.5 1.0
CG A:LYS415 4.8 70.8 1.0
CA A:LYS415 5.0 59.5 1.0

Chlorine binding site 2 out of 9 in 9dpp

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Chlorine binding site 2 out of 9 in the Bmp-9 Wild-Type 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 Wild-Type Dimer in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:56.3
occ:0.83
 H A:GLU419 2.5 53.6 1.0
HE2 A:LYS415 3.1 73.5 1.0
HA A:TYR418 3.2 56.0 1.0
HB2 A:GLU419 3.3 53.9 1.0
N A:GLU419 3.3 45.6 1.0
HD1 A:TYR418 3.4 80.0 1.0
HG2 A:GLU419 3.5 60.9 1.0
HE3 A:LYS415 3.6 73.5 1.0
CE A:LYS415 3.7 61.1 1.0
HZ3 A:LYS415 3.8 92.5 1.0
O A:HIS417 3.9 51.9 1.0
CD1 A:TYR418 3.9 66.5 1.0
CB A:GLU419 3.9 45.8 1.0
HZ1 A:LYS415 4.0 92.5 1.0
CA A:TYR418 4.0 47.6 1.0
CG A:GLU419 4.1 50.6 1.0
NZ A:LYS415 4.1 76.9 1.0
HG3 A:GLU419 4.1 60.9 1.0
C A:TYR418 4.2 52.0 1.0
CA A:GLU419 4.2 44.3 1.0
HE1 A:TYR418 4.2 73.7 1.0
CE1 A:TYR418 4.4 61.3 1.0
CG A:TYR418 4.7 48.0 1.0
O A:GLU419 4.8 49.6 1.0
HB3 A:GLU419 4.8 53.9 1.0
C A:HIS417 4.8 51.2 1.0
HG2 A:LYS415 4.9 85.2 1.0
N A:TYR418 4.9 49.2 1.0
HZ2 A:LYS415 4.9 92.5 1.0
C A:GLU419 5.0 51.8 1.0
HA A:GLU419 5.0 53.3 1.0
CB A:TYR418 5.0 47.0 1.0

Chlorine binding site 3 out of 9 in 9dpp

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Chlorine binding site 3 out of 9 in the Bmp-9 Wild-Type 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 Wild-Type Dimer in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:81.2
occ:1.00
 NA A:NA512 2.8 46.9 0.6
O A:HOH621 3.7 57.3 1.0
HD12 A:LEU398 3.7 42.4 1.0
HG A:LEU398 3.8 51.3 1.0
HD11 A:LEU398 4.2 42.4 1.0
HA A:LYS397 4.2 65.2 1.0
CD1 A:LEU398 4.3 36.3 1.0
O A:THR396 4.4 64.2 1.0
HA A:THR396 4.5 62.8 1.0
CG A:LEU398 4.5 42.6 1.0
C A:THR396 4.5 47.3 1.0
H A:LEU398 4.7 57.1 1.0
HB2 A:LEU398 4.9 46.7 1.0
O A:HOH639 4.9 51.4 0.5
CA A:LYS397 4.9 55.2 1.0
N A:LYS397 4.9 62.0 1.0
O A:HOH651 5.0 67.5 1.0
O A:PRO395 5.0 41.3 1.0

Chlorine binding site 4 out of 9 in 9dpp

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Chlorine binding site 4 out of 9 in the Bmp-9 Wild-Type 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 Wild-Type Dimer in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:46.3
occ:0.82
 H A:LYS372 2.4 48.3 1.0
HA A:THR371 2.7 52.9 1.0
HG3 A:LYS372 3.0 62.9 1.0
N A:LYS372 3.2 40.0 1.0
HB A:THR371 3.3 46.6 1.0
O A:HOH608 3.4 75.4 1.0
CA A:THR371 3.5 43.9 1.0
HZ2 A:LYS372 3.6 69.5 1.0
HG22 A:THR371 3.6 52.3 1.0
CB A:THR371 3.8 39.7 1.0
C A:THR371 3.8 43.6 1.0
CG A:LYS372 3.9 52.3 1.0
HB2 A:LYS372 4.1 58.7 1.0
HZ3 A:LYS372 4.1 69.5 1.0
CG2 A:THR371 4.2 43.4 1.0
NZ A:LYS372 4.3 57.7 1.0
HG2 A:LYS372 4.3 62.9 1.0
CA A:LYS372 4.3 41.9 1.0
CB A:LYS372 4.3 48.8 1.0
CL A:CL508 4.5 93.5 1.0
H A:HIS373 4.6 37.5 1.0
HG21 A:THR371 4.7 52.3 1.0
N A:THR371 4.7 42.3 1.0
O A:PRO370 4.8 48.0 1.0
HZ1 A:LYS372 4.8 69.5 1.0
HA A:LYS372 4.9 50.4 1.0
HG23 A:THR371 4.9 52.3 1.0
CD A:LYS372 5.0 54.9 1.0

Chlorine binding site 5 out of 9 in 9dpp

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Chlorine binding site 5 out of 9 in the Bmp-9 Wild-Type 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 Wild-Type Dimer in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:71.1
occ:0.45
 H A:LEU364 2.6 68.1 1.0
HD1 A:PHE362 2.9 63.8 1.0
HA A:PRO363 3.2 71.9 1.0
N A:LEU364 3.4 57.6 1.0
HB2 A:LEU364 3.5 67.9 1.0
CD1 A:PHE362 3.7 54.1 1.0
HE1 A:PHE362 3.9 61.8 1.0
CA A:PRO363 4.0 60.8 1.0
HG A:LEU364 4.0 74.2 1.0
HB2 A:PRO363 4.1 78.6 1.0
HD12 A:LEU364 4.1 91.3 1.0
HB3 A:PRO363 4.2 78.6 1.0
CB A:LEU364 4.2 56.4 1.0
C A:PRO363 4.2 59.0 1.0
CE1 A:PHE362 4.3 52.4 1.0
CB A:PRO363 4.3 65.3 1.0
HB3 A:PHE362 4.3 66.7 1.0
CA A:LEU364 4.4 74.5 1.0
HA A:PHE362 4.4 65.5 1.0
CG A:LEU364 4.5 61.6 1.0
O A:LEU364 4.7 74.0 1.0
CG A:PHE362 4.8 54.2 1.0
CD1 A:LEU364 4.8 75.9 1.0
CB A:PHE362 4.9 56.4 1.0
HB3 A:LEU364 5.0 67.9 1.0

Chlorine binding site 6 out of 9 in 9dpp

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Chlorine binding site 6 out of 9 in the Bmp-9 Wild-Type 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 Wild-Type Dimer in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:93.5
occ:1.00
 HG22 A:THR371 3.6 52.3 1.0
HA A:THR371 3.9 52.9 1.0
O A:THR369 4.0 81.4 1.0
HH22 A:ARG429 4.0 56.8 1.0
HB A:THR369 4.1 127.2 1.0
HG23 A:THR371 4.2 52.3 1.0
NH2 A:ARG429 4.2 47.2 1.0
CG2 A:THR371 4.3 43.4 1.0
HH21 A:ARG429 4.4 56.8 1.0
O A:PRO370 4.4 48.0 1.0
CL A:CL506 4.5 46.3 0.8
CA A:THR371 4.7 43.9 1.0
C A:PRO370 4.7 45.0 1.0
HG1 A:THR369 4.7 88.0 1.0
C A:THR369 4.7 48.5 1.0
N A:THR371 4.8 42.3 1.0
CZ A:ARG429 4.8 42.8 1.0
O A:HOH647 4.9 86.7 1.0
CB A:THR369 4.9 105.9 1.0
HH12 A:ARG429 4.9 52.6 1.0
O A:HOH610 5.0 58.0 1.0

Chlorine binding site 7 out of 9 in 9dpp

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Chlorine binding site 7 out of 9 in the Bmp-9 Wild-Type Dimer 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 in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl509

b:96.6
occ:1.00
 HB3 A:PRO385 3.1 70.1 1.0
NE2 A:HIS381 3.7 56.7 1.0
CB A:PRO385 3.9 59.3 1.0
HG3 A:PRO385 3.9 99.7 1.0
HB2 A:PRO385 4.0 70.1 1.0
HE1 A:HIS381 4.2 64.0 1.0
CE1 A:HIS381 4.2 53.2 1.0
HZ1 A:LYS390 4.3 151.9 1.0
CG A:PRO385 4.4 82.9 1.0
HG2 A:PRO385 4.5 99.7 1.0
CD2 A:HIS381 4.6 55.2 1.0
HD2 A:HIS381 4.8 66.5 1.0
HD23 A:LEU382 4.8 57.6 0.5
HZ2 A:LYS390 4.9 151.9 1.0
NZ A:LYS390 4.9 126.4 1.0
HA A:LEU382 5.0 60.2 0.5
HA A:LEU382 5.0 61.6 0.5

Chlorine binding site 8 out of 9 in 9dpp

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Chlorine binding site 8 out of 9 in the Bmp-9 Wild-Type Dimer 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 in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl510

b:110.8
occ:1.00
 O A:HOH641 2.9 69.2 1.0
HE1 A:HIS326 3.4 119.1 1.0
HG2 A:PRO363 3.4 79.2 1.0
HD2 A:PRO363 3.5 75.7 1.0
HA2 A:GLY324 3.8 148.1 1.0
HA3 A:GLY324 3.8 148.1 1.0
HG3 A:PRO363 3.9 79.2 1.0
CG A:PRO363 4.0 66.2 1.0
CD A:PRO363 4.1 64.0 1.0
CA A:GLY324 4.2 123.2 1.0
CE1 A:HIS326 4.3 100.1 1.0
HD3 A:PRO363 4.5 75.7 1.0
HE1 A:PHE361 4.6 104.8 1.0
N A:GLY324 4.7 131.3 1.0

Chlorine binding site 9 out of 9 in 9dpp

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Chlorine binding site 9 out of 9 in the Bmp-9 Wild-Type Dimer 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 in Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl511

b:67.4
occ:0.86
 HH A:TYR416 2.2 75.0 1.0
O A:HOH618 2.8 61.3 1.0
HE2 A:TYR416 2.8 83.9 1.0
OH A:TYR416 2.9 63.4 1.0
NA A:NA516 3.1 66.2 0.7
HE1 A:HIS417 3.3 67.8 1.0
CE2 A:TYR416 3.5 69.8 1.0
CZ A:TYR416 3.6 62.6 1.0
CE1 A:HIS417 4.0 57.4 1.0
H12 A:GOL501 4.0 55.4 1.0
NE2 A:HIS417 4.2 60.3 1.0
O2 A:GOL501 4.4 47.0 1.0
O A:HOH650 4.7 37.2 0.3
CD2 A:TYR416 4.8 62.4 1.0
HO2 A:GOL501 4.8 56.6 1.0
O A:HOH636 4.8 81.8 1.0
C1 A:GOL501 4.8 46.0 1.0
H11 A:GOL501 4.9 55.4 1.0
CE1 A:TYR416 4.9 62.0 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 16:19:29 2025

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