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Iron 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:

Chlorine (Cl) 8 atoms
Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6wyd

Go back to Iron Binding Sites List in 6wyd
Iron 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 Iron with other atoms in the Fe 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:Fe606

b:38.9
occ:1.00
 FE B:HEC606 0.0 38.9 1.0
NB B:HEC606 1.9 38.7 1.0
NC B:HEC606 2.0 38.8 1.0
NA B:HEC606 2.0 39.1 1.0
NE2 B:HIS336 2.0 29.9 1.0
ND B:HEC606 2.0 38.9 1.0
C1B B:HEC606 2.9 39.1 1.0
C4B B:HEC606 3.0 39.0 1.0
CD2 B:HIS336 3.0 30.8 1.0
C4C B:HEC606 3.0 39.1 1.0
C1C B:HEC606 3.0 38.8 1.0
C4A B:HEC606 3.0 39.1 1.0
CE1 B:HIS336 3.0 30.2 1.0
C4D B:HEC606 3.0 39.2 1.0
C1D B:HEC606 3.0 39.3 1.0
C1A B:HEC606 3.1 39.2 1.0
CHB B:HEC606 3.4 39.5 1.0
CHC B:HEC606 3.4 39.5 1.0
CHD B:HEC606 3.4 39.7 1.0
CHA B:HEC606 3.5 39.7 1.0
N16 B:7GD611 3.6 44.5 1.0
N15 B:7GD611 4.0 46.5 1.0
CG B:HIS336 4.1 30.5 1.0
ND1 B:HIS336 4.2 31.6 1.0
C2B B:HEC606 4.2 39.2 1.0
C3B B:HEC606 4.2 39.4 1.0
C3A B:HEC606 4.2 39.7 1.0
C3C B:HEC606 4.2 39.4 1.0
C2C B:HEC606 4.2 39.4 1.0
C2A B:HEC606 4.3 39.7 1.0
C3D B:HEC606 4.3 39.7 1.0
C2D B:HEC606 4.3 39.6 1.0
C10 B:7GD611 4.4 44.1 1.0
CD2 B:LEU417 4.7 44.1 1.0
NE2 A:GLN91 4.9 19.6 1.0
N13 B:7GD611 4.9 44.1 1.0

Iron binding site 2 out of 4 in 6wyd

Go back to Iron Binding Sites List in 6wyd
Iron 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 Iron with other atoms in the Fe 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:Fe610

b:40.0
occ:1.00
 FE E:HEC610 0.0 40.0 1.0
NC E:HEC610 1.9 39.9 1.0
NA E:HEC610 2.0 40.2 1.0
NB E:HEC610 2.0 39.8 1.0
ND E:HEC610 2.0 40.1 1.0
NE2 E:HIS336 2.3 43.9 1.0
C4B E:HEC610 3.0 40.0 1.0
C1C E:HEC610 3.0 39.8 1.0
C4C E:HEC610 3.0 40.1 1.0
C1B E:HEC610 3.0 40.2 1.0
C1D E:HEC610 3.0 40.5 1.0
C4D E:HEC610 3.0 40.4 1.0
C1A E:HEC610 3.0 40.3 1.0
C4A E:HEC610 3.0 40.2 1.0
CD2 E:HIS336 3.3 44.1 1.0
CE1 E:HIS336 3.3 43.6 1.0
CHC E:HEC610 3.4 40.5 1.0
CHD E:HEC610 3.4 40.9 1.0
CHB E:HEC610 3.4 40.6 1.0
CHA E:HEC610 3.4 40.8 1.0
N16 E:7GD611 3.7 43.8 1.0
N15 E:7GD611 4.1 44.8 1.0
C3B E:HEC610 4.2 40.5 1.0
C2B E:HEC610 4.2 40.3 1.0
C2C E:HEC610 4.2 40.4 1.0
C3C E:HEC610 4.2 40.5 1.0
C2A E:HEC610 4.2 40.8 1.0
C3A E:HEC610 4.3 40.7 1.0
C3D E:HEC610 4.3 40.9 1.0
C2D E:HEC610 4.3 40.9 1.0
CG E:HIS336 4.4 42.7 1.0
C10 E:7GD611 4.5 46.6 1.0
ND1 E:HIS336 4.5 44.3 1.0
NE2 D:GLN91 4.7 35.8 1.0
CD2 E:LEU417 4.8 39.7 1.0
CG D:GLN91 5.0 33.4 1.0

Iron binding site 3 out of 4 in 6wyd

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Iron 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 Iron with other atoms in the Fe 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:Fe605

b:40.3
occ:1.00
 FE G:HEC605 0.0 40.3 1.0
NC G:HEC605 1.9 40.2 1.0
NA G:HEC605 1.9 40.5 1.0
NB G:HEC605 2.0 40.1 1.0
ND G:HEC605 2.0 40.4 1.0
NE2 G:HIS336 2.2 38.1 1.0
C1C G:HEC605 2.9 40.2 1.0
C4C G:HEC605 3.0 40.5 1.0
C4B G:HEC605 3.0 40.5 1.0
C1B G:HEC605 3.0 40.5 1.0
C4A G:HEC605 3.0 40.5 1.0
C1D G:HEC605 3.0 40.7 1.0
C4D G:HEC605 3.0 40.6 1.0
C1A G:HEC605 3.0 40.6 1.0
CD2 G:HIS336 3.1 38.4 1.0
CE1 G:HIS336 3.2 37.6 1.0
CHC G:HEC605 3.3 40.9 1.0
CHD G:HEC605 3.4 41.2 1.0
CHB G:HEC605 3.4 40.9 1.0
CHA G:HEC605 3.4 41.0 1.0
N16 G:7GD610 3.6 46.6 1.0
N15 G:7GD610 3.9 49.3 1.0
C2C G:HEC605 4.1 40.7 1.0
C3C G:HEC605 4.2 40.8 1.0
C2B G:HEC605 4.2 40.7 1.0
C3A G:HEC605 4.2 41.0 1.0
C2A G:HEC605 4.2 41.0 1.0
CG G:HIS336 4.2 37.1 1.0
C3B G:HEC605 4.3 40.9 1.0
ND1 G:HIS336 4.3 38.3 1.0
C2D G:HEC605 4.3 41.1 1.0
C3D G:HEC605 4.3 41.1 1.0
C10 G:7GD610 4.5 44.0 1.0
CD2 G:LEU417 4.7 42.0 1.0
NE2 F:GLN91 4.8 38.0 1.0
N13 G:7GD610 4.9 44.2 1.0
CG F:GLN91 4.9 40.4 1.0

Iron binding site 4 out of 4 in 6wyd

Go back to Iron Binding Sites List in 6wyd
Iron 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 Iron with other atoms in the Fe 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:Fe610

b:44.6
occ:1.00
 FE I:HEC610 0.0 44.6 1.0
NA I:HEC610 2.0 44.8 1.0
NC I:HEC610 2.0 44.5 1.0
NB I:HEC610 2.0 44.4 1.0
ND I:HEC610 2.0 44.7 1.0
NE2 I:HIS336 2.1 37.2 1.0
C4B I:HEC610 3.0 44.7 1.0
C1B I:HEC610 3.0 44.8 1.0
C4A I:HEC610 3.0 44.8 1.0
C4D I:HEC610 3.0 45.0 1.0
C1C I:HEC610 3.0 44.5 1.0
C4C I:HEC610 3.0 44.8 1.0
C1D I:HEC610 3.0 45.0 1.0
CD2 I:HIS336 3.1 38.2 1.0
C1A I:HEC610 3.1 45.0 1.0
CE1 I:HIS336 3.1 37.3 1.0
CHB I:HEC610 3.4 45.2 1.0
CHC I:HEC610 3.4 45.2 1.0
CHD I:HEC610 3.4 45.5 1.0
CHA I:HEC610 3.4 45.4 1.0
N16 H:7GD201 3.7 42.9 1.0
N15 H:7GD201 4.0 47.6 1.0
CG I:HIS336 4.2 38.6 1.0
ND1 I:HIS336 4.2 39.0 1.0
C3B I:HEC610 4.2 45.2 1.0
C2B I:HEC610 4.2 45.0 1.0
C3A I:HEC610 4.2 45.3 1.0
C2C I:HEC610 4.2 45.1 1.0
C3C I:HEC610 4.3 45.1 1.0
C2A I:HEC610 4.3 45.4 1.0
C3D I:HEC610 4.3 45.5 1.0
C2D I:HEC610 4.3 45.5 1.0
C10 H:7GD201 4.5 44.8 1.0
CD2 I:LEU417 4.6 43.1 1.0
NE2 H:GLN91 4.8 35.0 1.0
N13 H:7GD201 5.0 47.9 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: Wed Aug 7 14:29:02 2024

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