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

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

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

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-2-Amine, PDB code: 8fgn 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) 75.79 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.33, 151.58, 107.85, 90, 91.09, 90
R / Rfree (%) 18.6 / 23.6

Other elements in 8fgn:

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

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

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-2-Amine (pdb code 8fgn). 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 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-2-Amine, PDB code: 8fgn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8fgn

Go back to Iron Binding Sites List in 8fgn
Iron binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-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 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:44.8
occ:1.00
 FE A:HEM501 0.0 44.8 1.0
ND A:HEM501 2.0 55.5 1.0
NC A:HEM501 2.1 58.6 1.0
NA A:HEM501 2.1 52.6 1.0
NB A:HEM501 2.1 48.6 1.0
SG A:CYS184 2.3 34.9 1.0
C4D A:HEM501 3.0 55.5 1.0
C1A A:HEM501 3.1 49.5 1.0
C4B A:HEM501 3.1 54.0 1.0
C1C A:HEM501 3.1 53.9 1.0
C1D A:HEM501 3.1 64.2 1.0
C4C A:HEM501 3.1 63.8 1.0
C1B A:HEM501 3.1 53.2 1.0
C4A A:HEM501 3.1 55.6 1.0
CHA A:HEM501 3.4 49.4 1.0
CHC A:HEM501 3.4 53.9 1.0
CHD A:HEM501 3.5 64.5 1.0
CB A:CYS184 3.5 42.3 1.0
CHB A:HEM501 3.5 51.3 1.0
C04 A:XVO503 3.7 58.3 1.0
C03 A:XVO503 3.9 57.7 1.0
C05 A:XVO503 4.0 64.3 1.0
CA A:CYS184 4.1 37.3 1.0
C3D A:HEM501 4.3 63.8 1.0
C3B A:HEM501 4.3 52.7 1.0
C2D A:HEM501 4.3 65.7 1.0
C2B A:HEM501 4.3 51.8 1.0
C2A A:HEM501 4.3 59.3 1.0
C3A A:HEM501 4.3 60.9 1.0
C2C A:HEM501 4.3 58.0 1.0
C3C A:HEM501 4.3 60.2 1.0
C02 A:XVO503 4.3 58.3 1.0
C06 A:XVO503 4.4 59.1 1.0
NE1 A:TRP178 4.5 50.4 1.0
N01 A:XVO503 4.5 58.3 1.0
N A:GLY186 4.9 47.2 1.0
C A:CYS184 4.9 40.7 1.0

Iron binding site 2 out of 4 in 8fgn

Go back to Iron Binding Sites List in 8fgn
Iron binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-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 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:26.6
occ:1.00
 FE B:HEM501 0.0 26.6 1.0
ND B:HEM501 2.0 26.2 1.0
NB B:HEM501 2.1 37.6 1.0
NA B:HEM501 2.1 20.4 1.0
NC B:HEM501 2.1 26.8 1.0
SG B:CYS184 2.3 25.2 1.0
C1D B:HEM501 3.0 26.3 1.0
C1B B:HEM501 3.0 26.8 1.0
C4D B:HEM501 3.1 35.3 1.0
C1A B:HEM501 3.1 23.9 1.0
C4C B:HEM501 3.1 28.8 1.0
C4A B:HEM501 3.1 26.4 1.0
C4B B:HEM501 3.1 34.7 1.0
C1C B:HEM501 3.1 30.3 1.0
CB B:CYS184 3.4 21.5 1.0
CHB B:HEM501 3.4 24.4 1.0
CHD B:HEM501 3.4 27.0 1.0
CHA B:HEM501 3.4 24.1 1.0
CHC B:HEM501 3.5 27.1 1.0
C04 B:XVO503 3.9 38.3 1.0
CA B:CYS184 4.0 26.6 1.0
C05 B:XVO503 4.1 36.8 1.0
C03 B:XVO503 4.2 40.7 1.0
C2D B:HEM501 4.2 24.9 1.0
C3D B:HEM501 4.3 34.0 1.0
C2B B:HEM501 4.3 31.3 1.0
C3B B:HEM501 4.3 29.8 1.0
C2A B:HEM501 4.3 35.6 1.0
C3A B:HEM501 4.3 28.9 1.0
C3C B:HEM501 4.3 33.4 1.0
C2C B:HEM501 4.4 36.8 1.0
NE1 B:TRP178 4.4 26.3 1.0
C06 B:XVO503 4.5 43.3 1.0
C02 B:XVO503 4.6 32.4 1.0
N01 B:XVO503 4.8 35.6 1.0
C B:CYS184 4.8 25.9 1.0
N B:GLY186 4.8 29.5 1.0
N B:VAL185 4.9 23.6 1.0

Iron binding site 3 out of 4 in 8fgn

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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 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-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 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:38.1
occ:1.00
 FE C:HEM501 0.0 38.1 1.0
ND C:HEM501 2.1 43.0 1.0
NC C:HEM501 2.1 46.1 1.0
NB C:HEM501 2.1 45.0 1.0
NA C:HEM501 2.1 46.1 1.0
SG C:CYS184 2.3 35.0 1.0
C4D C:HEM501 3.1 42.7 1.0
C1C C:HEM501 3.1 51.6 1.0
C4B C:HEM501 3.1 49.2 1.0
C1A C:HEM501 3.1 38.7 1.0
C4C C:HEM501 3.1 45.8 1.0
C1D C:HEM501 3.1 45.2 1.0
C1B C:HEM501 3.1 46.4 1.0
C4A C:HEM501 3.1 43.0 1.0
CB C:CYS184 3.3 35.8 1.0
CHC C:HEM501 3.4 43.2 1.0
CHA C:HEM501 3.4 36.2 1.0
CHD C:HEM501 3.5 47.2 1.0
CHB C:HEM501 3.5 40.0 1.0
C04 C:XVO503 3.9 56.1 1.0
CA C:CYS184 4.0 32.0 1.0
C03 C:XVO503 4.1 55.5 1.0
C05 C:XVO503 4.2 58.7 1.0
C3D C:HEM501 4.3 44.2 1.0
C3B C:HEM501 4.3 49.6 1.0
C2C C:HEM501 4.3 52.4 1.0
C2B C:HEM501 4.3 43.4 1.0
C2D C:HEM501 4.3 38.2 1.0
C3C C:HEM501 4.3 45.0 1.0
C2A C:HEM501 4.3 51.9 1.0
C3A C:HEM501 4.3 52.8 1.0
NE1 C:TRP178 4.4 41.5 1.0
C02 C:XVO503 4.5 50.1 1.0
C06 C:XVO503 4.6 54.7 1.0
N01 C:XVO503 4.8 54.3 1.0
C C:CYS184 4.8 29.2 1.0
N C:GLY186 4.8 31.1 1.0
N C:VAL185 5.0 31.9 1.0
CD1 C:TRP178 5.0 37.3 1.0

Iron binding site 4 out of 4 in 8fgn

Go back to Iron Binding Sites List in 8fgn
Iron binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-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 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:28.3
occ:1.00
 FE D:HEM501 0.0 28.3 1.0
ND D:HEM501 2.0 35.4 1.0
NA D:HEM501 2.1 34.4 1.0
NB D:HEM501 2.1 29.7 1.0
NC D:HEM501 2.1 28.7 1.0
SG D:CYS184 2.2 22.8 1.0
C1D D:HEM501 3.0 34.1 1.0
C4A D:HEM501 3.0 38.4 1.0
C4D D:HEM501 3.1 39.9 1.0
C1B D:HEM501 3.1 35.7 1.0
C1A D:HEM501 3.1 34.7 1.0
C4C D:HEM501 3.1 30.9 1.0
C4B D:HEM501 3.2 29.2 1.0
C1C D:HEM501 3.2 30.8 1.0
CB D:CYS184 3.2 25.0 1.0
CHD D:HEM501 3.4 27.6 1.0
CHB D:HEM501 3.4 26.4 1.0
CHA D:HEM501 3.4 32.4 1.0
CHC D:HEM501 3.6 36.0 1.0
C05 D:XVO503 4.0 40.3 1.0
CA D:CYS184 4.0 22.7 1.0
C04 D:XVO503 4.0 41.0 1.0
C06 D:XVO503 4.2 43.4 1.0
C2D D:HEM501 4.2 38.8 1.0
C3D D:HEM501 4.2 40.9 1.0
C3A D:HEM501 4.3 45.7 1.0
C2A D:HEM501 4.3 39.2 1.0
C2B D:HEM501 4.3 30.6 1.0
C03 D:XVO503 4.3 28.8 1.0
C3B D:HEM501 4.4 33.4 1.0
C3C D:HEM501 4.4 36.7 1.0
C2C D:HEM501 4.4 35.7 1.0
NE1 D:TRP178 4.5 32.6 1.0
N01 D:XVO503 4.5 32.6 1.0
C02 D:XVO503 4.6 32.8 1.0
C D:CYS184 4.8 23.1 1.0
N D:GLY186 4.8 23.9 1.0
C07 D:XVO503 4.8 48.2 1.0
N D:VAL185 4.9 28.2 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 03:48:31 2024

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