Atomistry » Calcium » PDB 6wm1-6x68 » 6wyd
Atomistry »
  Calcium »
    PDB 6wm1-6x68 »
      6wyd »

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

Go back to Calcium Binding Sites List in 6wyd
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: Tue Jul 16 17:35:54 2024

Last articles

Cl in 6COG
Cl in 6CST
Cl in 6CTW
Cl in 6CTZ
Cl in 6CTT
Cl in 6CSP
Cl in 6CU9
Cl in 6CTX
Cl in 6CTU
Cl in 6CTP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy