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Iron in PDB 8fgq: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine, PDB code: 8fgq was solved by H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.78 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.569, 151.48, 108.348, 90, 91.08, 90
R / Rfree (%) 19.3 / 24.6

Other elements in 8fgq:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine also contains other interesting chemical elements:

Gadolinium (Gd) 4 atoms
Chlorine (Cl) 4 atoms
Fluorine (F) 8 atoms
Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine (pdb code 8fgq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine, PDB code: 8fgq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8fgq

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Iron binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:38.0
occ:1.00
 FE A:HEM501 0.0 38.0 1.0
NC A:HEM501 2.1 48.9 1.0
ND A:HEM501 2.1 48.5 1.0
NA A:HEM501 2.1 46.0 1.0
NB A:HEM501 2.1 49.4 1.0
SG A:CYS184 2.2 28.3 1.0
C4D A:HEM501 3.1 51.1 1.0
C1C A:HEM501 3.1 48.0 1.0
C4B A:HEM501 3.1 51.9 1.0
C4C A:HEM501 3.1 54.7 1.0
C1D A:HEM501 3.1 57.3 1.0
C1A A:HEM501 3.1 44.5 1.0
C1B A:HEM501 3.1 51.0 1.0
C4A A:HEM501 3.1 49.5 1.0
CB A:CYS184 3.3 27.3 1.0
CHA A:HEM501 3.4 45.2 1.0
CHC A:HEM501 3.4 46.6 1.0
CHD A:HEM501 3.5 57.2 1.0
CHB A:HEM501 3.5 49.2 1.0
C05 A:V80503 4.0 53.1 1.0
CA A:CYS184 4.0 28.6 1.0
C04 A:V80503 4.0 44.3 1.0
C06 A:V80503 4.2 54.0 1.0
N03 A:V80503 4.3 45.3 1.0
C3D A:HEM501 4.3 59.5 1.0
C3B A:HEM501 4.3 55.1 1.0
C2C A:HEM501 4.3 52.8 1.0
C2B A:HEM501 4.3 53.1 1.0
C3C A:HEM501 4.3 56.1 1.0
C2D A:HEM501 4.3 58.7 1.0
C2A A:HEM501 4.3 49.9 1.0
C3A A:HEM501 4.4 51.3 1.0
C07 A:V80503 4.5 38.6 1.0
N01 A:V80503 4.5 50.6 1.0
C02 A:V80503 4.5 44.6 1.0
NE1 A:TRP178 4.6 55.7 1.0
C A:CYS184 4.8 28.8 1.0
N A:GLY186 4.9 38.5 1.0
C08 A:V80503 4.9 62.1 1.0

Iron binding site 2 out of 4 in 8fgq

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Iron binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.4
occ:1.00
 FE B:HEM501 0.0 20.4 1.0
NC B:HEM501 2.0 25.8 1.0
ND B:HEM501 2.0 24.1 1.0
NB B:HEM501 2.1 24.3 1.0
NA B:HEM501 2.2 19.0 1.0
SG B:CYS184 2.4 16.6 1.0
C4C B:HEM501 3.0 14.5 1.0
C1D B:HEM501 3.0 18.9 1.0
C1B B:HEM501 3.0 25.6 1.0
C1C B:HEM501 3.1 24.9 1.0
C4B B:HEM501 3.1 25.8 1.0
C4D B:HEM501 3.1 24.0 1.0
C4A B:HEM501 3.1 26.7 1.0
C1A B:HEM501 3.2 16.4 1.0
CHD B:HEM501 3.3 16.0 1.0
CHB B:HEM501 3.4 25.7 1.0
CB B:CYS184 3.5 15.4 1.0
CHC B:HEM501 3.5 19.9 1.0
CHA B:HEM501 3.5 21.8 1.0
C05 B:V80503 4.1 15.2 1.0
CA B:CYS184 4.1 19.8 1.0
C04 B:V80503 4.1 17.3 1.0
C3C B:HEM501 4.2 19.4 1.0
C2D B:HEM501 4.2 19.9 1.0
C06 B:V80503 4.2 28.4 1.0
C2B B:HEM501 4.3 28.9 1.0
C3D B:HEM501 4.3 31.8 1.0
C2C B:HEM501 4.3 21.6 1.0
C3B B:HEM501 4.3 22.6 1.0
N03 B:V80503 4.3 18.3 1.0
NE1 B:TRP178 4.3 21.2 1.0
C3A B:HEM501 4.4 26.1 1.0
C2A B:HEM501 4.4 29.5 1.0
N01 B:V80503 4.4 27.9 1.0
C02 B:V80503 4.4 20.5 1.0
C07 B:V80503 4.7 16.0 1.0
N B:GLY186 4.8 24.8 1.0
C B:CYS184 4.9 19.2 1.0
C08 B:V80503 4.9 24.3 1.0
N B:VAL185 5.0 20.6 1.0

Iron binding site 3 out of 4 in 8fgq

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Iron binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:30.0
occ:1.00
 FE C:HEM501 0.0 30.0 1.0
ND C:HEM501 2.1 37.8 1.0
NC C:HEM501 2.1 43.0 1.0
NB C:HEM501 2.1 38.1 1.0
NA C:HEM501 2.1 37.1 1.0
SG C:CYS184 2.3 28.1 1.0
C4D C:HEM501 3.1 42.1 1.0
C1D C:HEM501 3.1 41.3 1.0
C1C C:HEM501 3.1 42.1 1.0
C4C C:HEM501 3.1 36.7 1.0
C4B C:HEM501 3.1 39.8 1.0
C1B C:HEM501 3.1 44.2 1.0
C4A C:HEM501 3.1 37.5 1.0
C1A C:HEM501 3.1 40.8 1.0
CB C:CYS184 3.3 30.9 1.0
CHC C:HEM501 3.4 34.6 1.0
CHD C:HEM501 3.4 34.6 1.0
CHA C:HEM501 3.5 40.6 1.0
CHB C:HEM501 3.5 37.3 1.0
CA C:CYS184 4.1 26.8 1.0
C05 C:V80503 4.1 49.1 1.0
C04 C:V80503 4.1 51.2 1.0
N03 C:V80503 4.3 48.9 1.0
C06 C:V80503 4.3 52.8 1.0
C2B C:HEM501 4.3 44.6 1.0
C3B C:HEM501 4.3 44.5 1.0
C3D C:HEM501 4.3 40.8 1.0
C2D C:HEM501 4.3 33.8 1.0
C2C C:HEM501 4.3 45.1 1.0
C3C C:HEM501 4.3 41.8 1.0
C3A C:HEM501 4.3 46.3 1.0
C2A C:HEM501 4.4 47.1 1.0
NE1 C:TRP178 4.4 31.0 1.0
N01 C:V80503 4.5 49.8 1.0
C02 C:V80503 4.5 53.6 1.0
C07 C:V80503 4.6 53.9 1.0
N C:GLY186 4.8 30.7 1.0
C C:CYS184 4.8 20.3 1.0
CD1 C:TRP178 5.0 31.6 1.0
C08 C:V80503 5.0 61.3 1.0

Iron binding site 4 out of 4 in 8fgq

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Iron binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:20.9
occ:1.00
 FE D:HEM501 0.0 20.9 1.0
ND D:HEM501 2.1 19.3 1.0
NA D:HEM501 2.1 25.9 1.0
NC D:HEM501 2.1 19.4 1.0
NB D:HEM501 2.1 23.3 1.0
SG D:CYS184 2.3 17.2 1.0
C4A D:HEM501 3.0 25.1 1.0
C1D D:HEM501 3.0 21.1 1.0
C1B D:HEM501 3.1 22.9 1.0
C4C D:HEM501 3.1 19.3 1.0
C4D D:HEM501 3.1 23.1 1.0
C1A D:HEM501 3.1 24.1 1.0
C1C D:HEM501 3.1 21.4 1.0
C4B D:HEM501 3.1 19.5 1.0
CB D:CYS184 3.4 21.1 1.0
CHB D:HEM501 3.4 17.6 1.0
CHD D:HEM501 3.4 21.1 1.0
CHA D:HEM501 3.5 16.8 1.0
CHC D:HEM501 3.5 24.6 1.0
C05 D:V80503 3.9 24.7 1.0
C04 D:V80503 4.0 25.5 1.0
CA D:CYS184 4.1 17.1 1.0
C06 D:V80503 4.2 32.4 1.0
N03 D:V80503 4.3 22.6 1.0
C2D D:HEM501 4.3 25.7 1.0
C3A D:HEM501 4.3 26.6 1.0
C3D D:HEM501 4.3 30.3 1.0
C2B D:HEM501 4.3 24.7 1.0
C3C D:HEM501 4.3 23.2 1.0
C2A D:HEM501 4.3 28.1 1.0
C3B D:HEM501 4.3 26.4 1.0
C2C D:HEM501 4.3 24.6 1.0
NE1 D:TRP178 4.4 23.6 1.0
C07 D:V80503 4.5 25.4 1.0
C02 D:V80503 4.5 21.2 1.0
N01 D:V80503 4.5 22.7 1.0
N D:GLY186 4.8 20.1 1.0
C D:CYS184 4.8 16.3 1.0
N D:VAL185 4.9 21.9 1.0
C08 D:V80503 4.9 28.5 1.0
CD1 D:TRP178 5.0 15.7 1.0

Reference:

D.Vasu, H.T.Do, H.Li, C.D.Hardy, A.Awasthi, T.L.Poulos, R.B.Silverman. Potent, Selective, and Membrane Permeable 2-Amino-4-Substituted Pyridine-Based Neuronal Nitric Oxide Synthase Inhibitors. J.Med.Chem. V. 66 9934 2023.
ISSN: ISSN 0022-2623
PubMed: 37433128
DOI: 10.1021/ACS.JMEDCHEM.3C00782
Page generated: Sat Aug 10 03:52:01 2024

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