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Calcium in PDB 5qj2: Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine

Enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine

All present enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine:
1.11.2.2;

Protein crystallography data

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine, PDB code: 5qj2 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) 116.55 / 2.82
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 143.817, 150.949, 233.104, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 27.2

Other elements in 5qj2:

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine (pdb code 5qj2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine, PDB code: 5qj2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5qj2

Go back to Calcium Binding Sites List in 5qj2
Calcium binding site 1 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-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) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca614

b:43.8
occ:1.00
 OG B:SER174 2.2 56.8 1.0
O B:THR168 2.2 50.2 1.0
O B:PHE170 2.3 42.2 1.0
O A:ASP96 2.3 46.8 1.0
OG1 B:THR168 2.3 53.8 1.0
OD1 B:ASP172 2.4 53.6 1.0
OD1 A:ASP96 2.8 68.0 1.0
C B:THR168 3.3 49.3 1.0
CB B:SER174 3.3 50.0 1.0
CG B:ASP172 3.4 53.7 1.0
C B:PHE170 3.4 45.4 1.0
C A:ASP96 3.4 47.0 1.0
CB B:THR168 3.6 49.2 1.0
CG A:ASP96 3.7 65.3 1.0
N B:PHE170 3.7 41.0 1.0
OD2 B:ASP172 3.8 55.0 1.0
CA B:THR168 3.9 45.0 1.0
CA B:PHE170 4.0 41.0 1.0
N B:SER174 4.1 48.5 1.0
CA A:ASP96 4.1 43.3 1.0
C B:SER169 4.2 46.6 1.0
N B:THR168 4.2 45.3 1.0
N B:ASP172 4.2 50.4 1.0
CA B:SER174 4.3 47.4 1.0
N B:SER169 4.3 46.0 1.0
CB A:ASP96 4.4 45.6 1.0
OD2 A:ASP96 4.5 74.4 1.0
N B:VAL171 4.5 45.1 1.0
N A:LEU97 4.5 41.3 1.0
CB B:ASP172 4.6 52.0 1.0
CB B:PHE170 4.7 42.8 1.0
CA B:SER169 4.7 45.9 1.0
CG2 B:THR168 4.7 43.0 1.0
O B:SER169 4.7 46.7 1.0
CA A:LEU97 4.8 40.1 1.0
N B:ALA173 4.8 50.9 1.0
CA B:ASP172 4.9 50.6 1.0
CA B:VAL171 4.9 45.5 1.0

Calcium binding site 2 out of 4 in 5qj2

Go back to Calcium Binding Sites List in 5qj2
Calcium binding site 2 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-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) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca611

b:44.8
occ:1.00
 O D:ASP96 2.1 51.1 1.0
OG1 E:THR168 2.2 52.5 1.0
OD1 E:ASP172 2.3 53.8 1.0
O E:PHE170 2.4 46.5 1.0
OG E:SER174 2.5 42.7 1.0
OD1 D:ASP96 2.7 52.5 1.0
O E:THR168 2.9 45.9 1.0
C D:ASP96 3.2 50.1 1.0
CG E:ASP172 3.4 51.7 1.0
C E:PHE170 3.4 47.7 1.0
C E:THR168 3.5 46.2 1.0
CB E:THR168 3.5 48.8 1.0
CB E:SER174 3.5 46.5 1.0
CG D:ASP96 3.7 53.0 1.0
N E:PHE170 3.8 43.6 1.0
OD2 E:ASP172 3.8 54.2 1.0
CA D:ASP96 3.9 46.0 1.0
CA E:THR168 4.0 42.3 1.0
CA E:PHE170 4.1 43.8 1.0
N E:SER174 4.2 47.9 1.0
N E:ASP172 4.2 46.3 1.0
C E:SER169 4.2 47.0 1.0
CB D:ASP96 4.3 47.4 1.0
N D:LEU97 4.3 45.6 1.0
N E:SER169 4.3 42.2 1.0
N E:THR168 4.3 43.0 1.0
CA E:SER174 4.5 46.8 1.0
N E:VAL171 4.5 44.5 1.0
CB E:PHE170 4.6 45.7 1.0
CG2 E:THR168 4.6 42.7 1.0
OD2 D:ASP96 4.6 54.9 1.0
CB E:ASP172 4.6 47.5 1.0
CA E:SER169 4.7 41.0 1.0
CA D:LEU97 4.7 43.8 1.0
CA E:VAL171 4.8 44.5 1.0
O E:SER169 4.8 48.5 1.0
CA E:ASP172 4.9 46.6 1.0
N E:ALA173 4.9 50.6 1.0
CD2 D:LEU97 4.9 45.3 1.0
OG E:SER179 5.0 45.9 1.0

Calcium binding site 3 out of 4 in 5qj2

Go back to Calcium Binding Sites List in 5qj2
Calcium binding site 3 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca613

b:40.8
occ:1.00
 O F:ASP96 2.1 45.5 1.0
OG G:SER174 2.1 46.5 1.0
O G:PHE170 2.2 30.7 1.0
OD1 G:ASP172 2.3 40.6 1.0
O G:THR168 2.3 35.0 1.0
OG1 G:THR168 2.7 36.7 1.0
OD1 F:ASP96 2.9 49.1 1.0
CG G:ASP172 3.2 42.5 1.0
C F:ASP96 3.3 46.2 1.0
C G:PHE170 3.3 32.2 1.0
C G:THR168 3.4 34.4 1.0
CB G:SER174 3.5 41.3 1.0
N G:PHE170 3.7 25.9 1.0
CG F:ASP96 3.7 50.0 1.0
OD2 G:ASP172 3.7 50.1 1.0
CB G:THR168 3.9 41.0 1.0
N G:ASP172 4.0 32.7 1.0
CA G:PHE170 4.0 26.1 1.0
CA F:ASP96 4.0 40.8 1.0
C G:SER169 4.1 30.5 1.0
CA G:THR168 4.1 32.6 1.0
N G:SER174 4.1 40.0 1.0
N G:THR168 4.3 34.6 1.0
CB F:ASP96 4.3 41.9 1.0
N G:SER169 4.3 29.4 1.0
N F:LEU97 4.4 42.2 1.0
CB G:ASP172 4.4 34.4 1.0
CA G:SER174 4.4 39.0 1.0
O G:SER169 4.5 32.0 1.0
N G:VAL171 4.5 29.3 1.0
OD2 F:ASP96 4.6 58.3 1.0
CB G:PHE170 4.6 27.7 1.0
CA F:LEU97 4.6 41.7 1.0
CA G:SER169 4.6 28.1 1.0
CA G:ASP172 4.6 33.3 1.0
CA G:VAL171 4.7 29.4 1.0
N G:ALA173 4.8 38.0 1.0
C G:VAL171 4.9 36.2 1.0
C G:ASP172 4.9 41.3 1.0

Calcium binding site 4 out of 4 in 5qj2

Go back to Calcium Binding Sites List in 5qj2
Calcium binding site 4 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Myeloperoxidase Subform C (Mpo) Omplex with Compound-20 Aka 7-((3-(1-Methyl-1H-Pyrazol-3- Yl)Benzyl)Oxy)- 1H-[1, 2,3]Triazolo[4,5-B]Pyridin-5-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca611

b:52.0
occ:1.00
 O H:ASP96 2.1 44.0 1.0
O I:PHE170 2.2 52.5 1.0
OD1 H:ASP96 2.5 54.0 1.0
O I:THR168 2.5 49.7 1.0
OG I:SER174 2.6 55.1 1.0
OD1 I:ASP172 2.6 52.6 1.0
OG1 I:THR168 2.6 42.8 1.0
C H:ASP96 3.2 44.8 1.0
C I:THR168 3.3 49.7 1.0
C I:PHE170 3.4 54.0 1.0
CG H:ASP96 3.5 54.1 1.0
CG I:ASP172 3.6 54.2 1.0
CB I:SER174 3.7 53.5 1.0
CB I:THR168 3.7 45.4 1.0
N I:PHE170 3.9 52.5 1.0
C I:SER169 3.9 55.1 1.0
CA H:ASP96 3.9 42.8 1.0
CA I:THR168 4.0 42.5 1.0
O I:SER169 4.0 55.6 1.0
N I:ASP172 4.0 49.8 1.0
OD2 I:ASP172 4.1 61.0 1.0
CA I:PHE170 4.1 52.6 1.0
CB H:ASP96 4.2 44.3 1.0
N I:THR168 4.3 42.4 1.0
N I:SER169 4.3 48.2 1.0
N H:LEU97 4.3 39.0 1.0
N I:SER174 4.3 51.1 1.0
OD2 H:ASP96 4.4 61.1 1.0
N I:VAL171 4.5 49.6 1.0
CA H:LEU97 4.5 37.9 1.0
CA I:SER169 4.5 49.3 1.0
CA I:SER174 4.6 50.8 1.0
CA I:VAL171 4.7 48.4 1.0
CB I:ASP172 4.7 50.5 1.0
CB I:PHE170 4.7 54.8 1.0
CA I:ASP172 4.8 49.5 1.0
C I:VAL171 4.9 52.4 1.0
CD2 H:LEU97 4.9 38.9 1.0
N I:ALA173 4.9 51.4 1.0
CG2 I:THR168 4.9 45.8 1.0

Reference:

N.R.Wurtz, A.Viet, S.A.Shaw, A.Dilger, M.N.Valente, J.A.Khan, S.Jusuf, R.Narayanan, G.Fernando, F.Lo, X.Liu, G.A.Locke, L.Kopcho, L.M.Abell, P.Sleph, M.Basso, L.Zhao, R.R.Wexler, F.Duclos, E.K.Kick. Potent Triazolopyridine Myeloperoxidase Inhibitors. Acs Med Chem Lett V. 9 1175 2018.
ISSN: ISSN 1948-5875
PubMed: 30613322
DOI: 10.1021/ACSMEDCHEMLETT.8B00308
Page generated: Mon Jul 15 10:05:19 2024

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