Calcium in PDB 6wyd: Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid

Enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid

All present enzymatic activity of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid:
1.11.2.2;

Protein crystallography data

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid, PDB code: 6wyd 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) 115.53 / 2.55
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 143.683, 150.651, 231.060, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25.4

Other elements in 6wyd:

The structure of Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid (pdb code 6wyd). 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) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid, PDB code: 6wyd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6wyd

Go back to Calcium Binding Sites List in 6wyd
Calcium binding site 1 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid


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-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca612

b:32.2
occ:1.00
 OG1 B:THR168 2.2 35.4 1.0
O A:ASP96 2.2 37.8 1.0
OD1 B:ASP172 2.3 43.0 1.0
O B:PHE170 2.3 33.5 1.0
OG B:SER174 2.4 38.0 1.0
O B:THR168 2.5 32.6 1.0
OD1 A:ASP96 2.6 45.5 1.0
CG B:ASP172 3.3 41.1 1.0
C B:THR168 3.4 34.2 1.0
C A:ASP96 3.4 37.8 1.0
C B:PHE170 3.4 32.8 1.0
CB B:SER174 3.5 32.5 1.0
CB B:THR168 3.5 38.2 1.0
CG A:ASP96 3.6 42.2 1.0
OD2 B:ASP172 3.8 35.8 1.0
N B:PHE170 3.9 27.8 1.0
CA B:THR168 4.0 33.3 1.0
N B:ASP172 4.1 31.0 1.0
CA A:ASP96 4.1 32.1 1.0
N B:SER174 4.1 35.0 1.0
C B:SER169 4.2 32.9 1.0
CA B:PHE170 4.2 27.2 1.0
N B:THR168 4.2 34.4 1.0
N B:SER169 4.3 29.2 1.0
CB A:ASP96 4.3 32.7 1.0
CB B:ASP172 4.4 32.7 1.0
CA B:SER174 4.4 33.4 1.0
N A:LEU97 4.5 33.7 1.0
N B:VAL171 4.5 29.1 1.0
OD2 A:ASP96 4.5 43.5 1.0
O B:SER169 4.5 35.4 1.0
CG2 B:THR168 4.6 32.6 1.0
CA B:SER169 4.7 27.3 1.0
CA B:ASP172 4.7 30.8 1.0
CA A:LEU97 4.7 32.8 1.0
CA B:VAL171 4.8 28.0 1.0
CB B:PHE170 4.8 28.5 1.0
N B:ALA173 4.9 34.9 1.0
O A:HOH317 4.9 35.4 1.0
C B:ASP172 4.9 37.1 1.0
C B:VAL171 5.0 33.7 1.0

Calcium binding site 2 out of 4 in 6wyd

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Calcium binding site 2 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid


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-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca612

b:41.0
occ:1.00
 O D:ASP96 2.0 39.0 1.0
O E:PHE170 2.3 42.8 1.0
OD1 D:ASP96 2.4 48.2 1.0
OD1 E:ASP172 2.5 45.0 1.0
O E:THR168 2.5 48.7 1.0
OG E:SER174 2.5 53.6 1.0
OG1 E:THR168 2.6 32.5 1.0
C D:ASP96 3.2 41.6 1.0
C E:THR168 3.3 46.9 1.0
C E:PHE170 3.5 44.1 1.0
CG E:ASP172 3.5 44.9 1.0
CG D:ASP96 3.6 46.8 1.0
CB E:SER174 3.6 46.4 1.0
CB E:THR168 3.8 40.2 1.0
N E:PHE170 3.8 40.3 1.0
CA E:THR168 4.0 39.7 1.0
C E:SER169 4.0 44.5 1.0
CA D:ASP96 4.0 38.5 1.0
OD2 E:ASP172 4.0 47.9 1.0
N E:ASP172 4.1 41.6 1.0
CA E:PHE170 4.1 39.7 1.0
N E:THR168 4.2 38.7 1.0
N E:SER169 4.2 41.9 1.0
CB D:ASP96 4.3 40.0 1.0
N D:LEU97 4.3 38.1 1.0
O E:SER169 4.3 43.3 1.0
N E:SER174 4.4 43.8 1.0
OD2 D:ASP96 4.5 46.9 1.0
CA D:LEU97 4.5 36.9 1.0
CA E:SER169 4.5 41.5 1.0
CA E:SER174 4.6 43.1 1.0
N E:VAL171 4.6 41.3 1.0
CB E:ASP172 4.7 42.0 1.0
O E:HOH714 4.7 42.0 1.0
CB E:PHE170 4.8 40.7 1.0
CA E:ASP172 4.8 41.3 1.0
CA E:VAL171 4.9 41.4 1.0
CG2 E:THR168 4.9 37.9 1.0
CD2 D:LEU97 4.9 40.3 1.0
N E:ALA173 5.0 44.6 1.0

Calcium binding site 3 out of 4 in 6wyd

Go back to Calcium Binding Sites List in 6wyd
Calcium binding site 3 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid


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) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca611

b:39.7
occ:1.00
 O F:ASP96 2.2 36.4 1.0
O G:PHE170 2.3 42.0 1.0
O G:THR168 2.4 39.6 1.0
OD1 G:ASP172 2.5 40.7 1.0
OG1 G:THR168 2.7 39.9 1.0
OD1 F:ASP96 2.7 53.6 1.0
OG G:SER174 2.7 48.2 1.0
CB G:SER174 3.3 42.3 1.0
C F:ASP96 3.4 38.9 1.0
C G:THR168 3.4 40.6 1.0
CG G:ASP172 3.5 42.0 1.0
C G:PHE170 3.5 42.8 1.0
CG F:ASP96 3.8 51.9 1.0
CB G:THR168 3.9 41.9 1.0
OD2 G:ASP172 3.9 43.3 1.0
N G:PHE170 4.0 35.4 1.0
CA G:THR168 4.0 36.7 1.0
CA F:ASP96 4.1 35.9 1.0
N G:SER174 4.2 43.8 1.0
C G:SER169 4.2 39.2 1.0
CA G:PHE170 4.2 35.8 1.0
N G:THR168 4.2 37.1 1.0
N G:ASP172 4.3 39.4 1.0
CA G:SER174 4.3 41.9 1.0
N G:SER169 4.4 37.6 1.0
CB F:ASP96 4.4 38.4 1.0
N F:LEU97 4.4 36.5 1.0
O G:SER169 4.5 39.0 1.0
N G:VAL171 4.6 40.2 1.0
CA F:LEU97 4.7 35.7 1.0
CA G:SER169 4.7 36.9 1.0
CB G:ASP172 4.7 42.3 1.0
OD2 F:ASP96 4.8 58.9 1.0
CB G:PHE170 4.8 37.3 1.0
CA G:VAL171 4.9 40.3 1.0
N G:ALA173 5.0 43.9 1.0
CG2 G:THR168 5.0 37.6 1.0
CA G:ASP172 5.0 40.4 1.0

Calcium binding site 4 out of 4 in 6wyd

Go back to Calcium Binding Sites List in 6wyd
Calcium binding site 4 out of 4 in the Crystal Structure of Myeloperoxidase Subform C (Mpo) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid


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) Complex with Compound-12 (Aka; 7-Benzyl-1H-[1,2,3]Triazolo[4,5-B]Pyrid within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca611

b:39.1
occ:1.00
 O H:ASP96 2.1 40.2 1.0
O I:PHE170 2.3 38.0 1.0
OG1 I:THR168 2.4 36.8 1.0
O I:THR168 2.4 40.1 1.0
OD1 I:ASP172 2.5 37.6 1.0
OG I:SER174 2.6 44.5 1.0
OD1 H:ASP96 2.7 53.0 1.0
C H:ASP96 3.3 41.4 1.0
C I:THR168 3.3 40.4 1.0
CB I:SER174 3.5 38.5 1.0
C I:PHE170 3.5 37.8 1.0
CG I:ASP172 3.5 38.4 1.0
CB I:THR168 3.7 36.5 1.0
CG H:ASP96 3.7 50.2 1.0
CA I:THR168 4.0 36.0 1.0
N I:PHE170 4.0 34.4 1.0
CA H:ASP96 4.0 38.7 1.0
OD2 I:ASP172 4.1 42.8 1.0
C I:SER169 4.1 40.2 1.0
N I:ASP172 4.1 33.6 1.0
N I:SER174 4.2 35.9 1.0
N I:THR168 4.2 36.8 1.0
CA I:PHE170 4.3 34.1 1.0
O I:SER169 4.3 41.8 1.0
CB H:ASP96 4.3 40.7 1.0
N I:SER169 4.3 35.9 1.0
N H:LEU97 4.4 36.9 1.0
CA I:SER174 4.5 35.5 1.0
N I:VAL171 4.6 32.5 1.0
CG2 I:THR168 4.6 28.9 1.0
CA I:SER169 4.6 34.9 1.0
OD2 H:ASP96 4.7 49.2 1.0
CA H:LEU97 4.7 36.0 1.0
CB I:ASP172 4.7 35.2 1.0
O I:HOH714 4.8 36.7 1.0
CA I:VAL171 4.8 32.6 1.0
CA I:ASP172 4.8 34.2 1.0
CB I:PHE170 4.8 35.5 1.0
N I:ALA173 4.9 37.2 1.0
C I:VAL171 5.0 36.6 1.0

Reference:

S.A.Shaw, B.P.Vokits, A.K.Dilger, A.Viet, C.G.Clark, L.M.Abell, G.A.Locke, G.Duke, L.M.Kopcho, A.Dongre, J.Gao, A.Krishnakumar, S.Jusuf, J.Khan, S.A.Spronk, M.D.Basso, L.Zhao, G.H.Cantor, J.M.Onorato, R.R.Wexler, F.Duclos, E.K.Kick. Discovery and Structure Activity Relationships of 7-Benzyl Triazolopyridines As Stable, Selective, and Reversible Inhibitors of Myeloperoxidase. Bioorg.Med.Chem. V. 28 15723 2020.
ISSN: ESSN 1464-3391
PubMed: 33007547
DOI: 10.1016/J.BMC.2020.115723
Page generated: Sat Dec 12 07:53:08 2020

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