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Calcium in PDB 5wdj: Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine

Enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine

All present enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine:
1.11.2.2;

Protein crystallography data

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine, PDB code: 5wdj was solved by J.A.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.51 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.925, 103.925, 242.276, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.8

Other elements in 5wdj:

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine (pdb code 5wdj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine, PDB code: 5wdj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5wdj

Go back to Calcium Binding Sites List in 5wdj
Calcium binding site 1 out of 2 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:31.9
occ:1.00
 O A:ASP96 2.2 19.9 1.0
OD1 A:ASP96 2.3 20.2 1.0
O B:PHE170 2.4 20.6 1.0
OG1 B:THR168 2.4 20.0 1.0
OG B:SER174 2.4 21.4 1.0
OD1 B:ASP172 2.5 21.6 1.0
O B:THR168 2.5 20.0 1.0
C B:THR168 3.3 20.2 1.0
C A:ASP96 3.4 19.9 1.0
CB B:SER174 3.5 21.2 1.0
CG A:ASP96 3.5 19.9 1.0
CG B:ASP172 3.5 22.4 1.0
C B:PHE170 3.6 20.4 1.0
CB B:THR168 3.7 20.0 1.0
OD2 B:ASP172 4.0 22.1 1.0
CA B:THR168 4.0 20.0 1.0
N B:PHE170 4.0 20.1 1.0
CA A:ASP96 4.0 19.6 1.0
N B:ASP172 4.0 21.1 1.0
C B:SER169 4.1 20.4 1.0
N B:SER174 4.1 21.6 1.0
N B:THR168 4.2 19.8 1.0
CB A:ASP96 4.2 19.5 1.0
N B:SER169 4.3 20.4 1.0
CA B:PHE170 4.3 20.2 1.0
OD2 A:ASP96 4.4 20.4 1.0
O B:SER169 4.4 20.1 1.0
CA B:SER174 4.4 21.4 1.0
N A:LEU97 4.4 19.9 1.0
CA B:SER169 4.6 20.4 1.0
N B:VAL171 4.6 20.4 1.0
CG2 B:THR168 4.7 19.7 1.0
CB B:ASP172 4.7 21.1 1.0
CA A:LEU97 4.7 20.2 1.0
CA B:VAL171 4.7 20.8 1.0
CA B:ASP172 4.8 21.4 1.0
N B:ALA173 4.9 21.4 1.0
C B:VAL171 4.9 21.1 1.0
CB B:PHE170 4.9 19.9 1.0
C B:ASP172 5.0 21.3 1.0
CD2 A:LEU97 5.0 19.0 1.0

Calcium binding site 2 out of 2 in 5wdj

Go back to Calcium Binding Sites List in 5wdj
Calcium binding site 2 out of 2 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-6 Aka 7-(Benzyloxy)-1H-[1,2, 3]Triazolo[4,5-D]Pyrimidin-5- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:28.8
occ:1.00
 O E:PHE170 2.3 21.4 1.0
OG E:SER174 2.4 21.8 1.0
OD1 E:ASP172 2.4 22.8 1.0
O D:ASP96 2.4 19.0 1.0
OG1 E:THR168 2.4 18.9 1.0
OD1 D:ASP96 2.5 20.5 1.0
O E:THR168 2.5 20.6 1.0
CG E:ASP172 3.4 23.0 1.0
CB E:SER174 3.4 21.6 1.0
C E:THR168 3.4 20.5 1.0
C D:ASP96 3.5 19.3 1.0
C E:PHE170 3.5 21.2 1.0
CG D:ASP96 3.6 19.5 1.0
CB E:THR168 3.7 20.0 1.0
OD2 E:ASP172 3.8 23.1 1.0
N E:ASP172 4.0 21.7 1.0
N E:PHE170 4.0 20.8 1.0
CA E:THR168 4.0 20.2 1.0
N E:SER174 4.1 21.8 1.0
C E:SER169 4.1 20.8 1.0
CA D:ASP96 4.2 19.2 1.0
N E:THR168 4.3 20.3 1.0
CA E:PHE170 4.3 20.8 1.0
CA E:SER174 4.3 21.7 1.0
O E:SER169 4.4 20.7 1.0
CB D:ASP96 4.4 19.3 1.0
N E:SER169 4.4 20.6 1.0
OD2 D:ASP96 4.5 19.8 1.0
N E:VAL171 4.5 21.3 1.0
O E:HOH787 4.6 13.7 1.0
N D:LEU97 4.6 19.5 1.0
CB E:ASP172 4.6 21.6 1.0
CA E:SER169 4.7 20.8 1.0
CA E:VAL171 4.7 21.3 1.0
CA E:ASP172 4.8 21.8 1.0
CG2 E:THR168 4.8 19.6 1.0
CA D:LEU97 4.8 20.0 1.0
N E:ALA173 4.9 21.7 1.0
C E:VAL171 4.9 21.7 1.0
CB E:PHE170 4.9 20.7 1.0
C E:ASP172 4.9 21.7 1.0

Reference:

F.Duclos, L.M.Abell, D.G.Harden, K.Pike, K.Nowak, G.A.Locke, G.J.Duke, X.Liu, G.Fernando, S.A.Shaw, B.P.Vokits, N.R.Wurtz, A.Viet, M.N.Valente, S.Stachura, P.Sleph, J.A.Khan, J.Gao, A.R.Dongre, L.Zhao, R.R.Wexler, D.A.Gordon, E.K.Kick. Triazolopyrimidines Identified As Reversible Myeloperoxidase Inhibitors. Medchemcomm V. 8 2093 2017.
ISSN: ISSN 2040-2503
PubMed: 30108726
DOI: 10.1039/C7MD00268H
Page generated: Mon Jul 15 13:08:24 2024

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