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Iron in PDB 8fgm: Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine

Enzymatic activity of Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine

All present enzymatic activity of Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine, PDB code: 8fgm 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) 35.97 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 118.09, 52.079, 164.549, 90, 90, 90
R / Rfree (%) 20.7 / 26.9

Other elements in 8fgm:

The structure of Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Fluorine (F) 16 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine (pdb code 8fgm). 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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine, PDB code: 8fgm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8fgm

Go back to Iron Binding Sites List in 8fgm
Iron binding site 1 out of 4 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:27.2
occ:1.00
 FE A:HEM801 0.0 27.2 1.0
ND A:HEM801 2.0 20.2 1.0
NC A:HEM801 2.0 27.8 1.0
NB A:HEM801 2.1 22.6 1.0
NA A:HEM801 2.1 26.2 1.0
SG A:CYS420 2.3 28.8 1.0
C4D A:HEM801 3.0 31.3 1.0
C1C A:HEM801 3.0 24.2 1.0
C1D A:HEM801 3.0 27.3 1.0
C4B A:HEM801 3.0 32.6 1.0
C1A A:HEM801 3.1 27.9 1.0
C4C A:HEM801 3.1 21.7 1.0
C1B A:HEM801 3.1 31.7 1.0
C4A A:HEM801 3.1 21.2 1.0
CB A:CYS420 3.3 30.2 1.0
CHC A:HEM801 3.4 33.6 1.0
CHA A:HEM801 3.4 25.6 1.0
CHD A:HEM801 3.5 22.2 1.0
CHB A:HEM801 3.5 27.8 1.0
C04 A:XVA803 4.1 22.7 1.0
CA A:CYS420 4.1 30.8 1.0
C3D A:HEM801 4.2 29.7 1.0
C03 A:XVA803 4.2 20.8 1.0
C2D A:HEM801 4.2 21.1 1.0
C2C A:HEM801 4.3 23.8 1.0
C3B A:HEM801 4.3 35.0 1.0
C2A A:HEM801 4.3 30.8 1.0
C3C A:HEM801 4.3 26.1 1.0
NE1 A:TRP414 4.3 25.2 1.0
C2B A:HEM801 4.3 29.2 1.0
C3A A:HEM801 4.3 27.5 1.0
C07 A:XVA803 4.4 33.4 1.0
C05 A:XVA803 4.4 34.4 1.0
C02 A:XVA803 4.6 28.1 1.0
C06 A:XVA803 4.8 43.6 1.0
C A:CYS420 4.9 22.6 1.0
N01 A:XVA803 4.9 32.6 1.0
N A:GLY422 4.9 23.0 1.0

Iron binding site 2 out of 4 in 8fgm

Go back to Iron Binding Sites List in 8fgm
Iron binding site 2 out of 4 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:30.4
occ:1.00
 FE B:HEM802 0.0 30.4 1.0
NB B:HEM802 2.0 28.4 1.0
ND B:HEM802 2.0 30.6 1.0
NC B:HEM802 2.1 23.9 1.0
NA B:HEM802 2.1 35.9 1.0
SG B:CYS420 2.3 27.2 1.0
C1B B:HEM802 3.1 32.7 1.0
C4B B:HEM802 3.1 33.3 1.0
C4D B:HEM802 3.1 38.8 1.0
C1D B:HEM802 3.1 31.4 1.0
C1C B:HEM802 3.1 25.0 1.0
C4C B:HEM802 3.1 28.0 1.0
C4A B:HEM802 3.1 33.4 1.0
C1A B:HEM802 3.1 36.7 1.0
CB B:CYS420 3.2 21.4 1.0
CHC B:HEM802 3.4 22.7 1.0
CHA B:HEM802 3.4 39.6 1.0
CHB B:HEM802 3.4 33.4 1.0
CHD B:HEM802 3.5 26.2 1.0
CA B:CYS420 4.0 22.7 1.0
C04 B:XVA803 4.2 34.5 1.0
C03 B:XVA803 4.2 24.6 1.0
C2B B:HEM802 4.3 28.3 1.0
C3B B:HEM802 4.3 32.3 1.0
C3D B:HEM802 4.3 33.7 1.0
C2D B:HEM802 4.3 28.5 1.0
C2C B:HEM802 4.3 35.0 1.0
C3C B:HEM802 4.3 30.8 1.0
C3A B:HEM802 4.3 44.6 1.0
C2A B:HEM802 4.3 44.9 1.0
C07 B:XVA803 4.5 43.3 1.0
NE1 B:TRP414 4.5 24.9 1.0
C05 B:XVA803 4.6 40.5 1.0
C02 B:XVA803 4.7 33.1 1.0
C B:CYS420 4.8 19.4 1.0
N B:GLY422 4.9 26.4 1.0

Iron binding site 3 out of 4 in 8fgm

Go back to Iron Binding Sites List in 8fgm
Iron binding site 3 out of 4 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe801

b:32.5
occ:1.00
 FE C:HEM801 0.0 32.5 1.0
ND C:HEM801 2.0 22.9 1.0
NB C:HEM801 2.1 28.6 1.0
NC C:HEM801 2.1 26.8 1.0
NA C:HEM801 2.1 35.7 1.0
SG C:CYS420 2.4 26.1 1.0
C4D C:HEM801 3.0 32.0 1.0
C1D C:HEM801 3.1 29.0 1.0
C4B C:HEM801 3.1 30.2 1.0
C1B C:HEM801 3.1 37.9 1.0
C1C C:HEM801 3.1 23.8 1.0
C4C C:HEM801 3.1 27.2 1.0
C1A C:HEM801 3.1 32.4 1.0
C4A C:HEM801 3.2 38.3 1.0
CB C:CYS420 3.2 29.0 1.0
CHC C:HEM801 3.4 32.5 1.0
CHA C:HEM801 3.4 29.4 1.0
CHD C:HEM801 3.4 21.7 1.0
CHB C:HEM801 3.5 38.7 1.0
CA C:CYS420 4.0 29.2 1.0
C04 C:XVA803 4.2 29.3 1.0
C03 C:XVA803 4.2 22.6 1.0
C3D C:HEM801 4.2 29.9 1.0
C2D C:HEM801 4.3 32.7 1.0
C3B C:HEM801 4.3 31.9 1.0
C2B C:HEM801 4.3 28.4 1.0
C2C C:HEM801 4.3 27.2 1.0
C3C C:HEM801 4.3 31.3 1.0
C2A C:HEM801 4.4 38.1 1.0
C3A C:HEM801 4.4 41.6 1.0
C07 C:XVA803 4.4 38.6 1.0
NE1 C:TRP414 4.5 22.0 1.0
C05 C:XVA803 4.6 38.5 1.0
C02 C:XVA803 4.7 34.1 1.0
C C:CYS420 4.8 21.3 1.0
N C:VAL421 4.9 27.1 1.0
N C:GLY422 4.9 24.9 1.0

Iron binding site 4 out of 4 in 8fgm

Go back to Iron Binding Sites List in 8fgm
Iron binding site 4 out of 4 in the Structure of Human Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-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 Neuronal Nitric Oxide Synthase R354A/G357D Mutant Heme Domain in Complex with 4-(Difluoromethyl)-6-(5-(2- (Dimethylamino)Ethyl)-2,3-Difluorophenethyl)Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe801

b:28.8
occ:1.00
 FE D:HEM801 0.0 28.8 1.0
ND D:HEM801 2.0 25.9 1.0
NB D:HEM801 2.0 24.4 1.0
NA D:HEM801 2.0 30.4 1.0
NC D:HEM801 2.1 28.0 1.0
SG D:CYS420 2.3 30.7 1.0
C4D D:HEM801 3.0 33.4 1.0
C1A D:HEM801 3.0 28.7 1.0
C1D D:HEM801 3.0 33.9 1.0
C4B D:HEM801 3.1 35.8 1.0
C1B D:HEM801 3.1 34.4 1.0
C4A D:HEM801 3.1 30.4 1.0
C4C D:HEM801 3.1 29.3 1.0
C1C D:HEM801 3.1 27.8 1.0
CB D:CYS420 3.3 24.4 1.0
CHA D:HEM801 3.4 27.9 1.0
CHD D:HEM801 3.4 27.5 1.0
CHC D:HEM801 3.5 30.7 1.0
CHB D:HEM801 3.5 23.6 1.0
C04 D:XVA803 4.1 26.2 1.0
CA D:CYS420 4.1 30.7 1.0
C03 D:XVA803 4.1 21.0 1.0
C3D D:HEM801 4.2 32.2 1.0
C2D D:HEM801 4.2 26.2 1.0
C2A D:HEM801 4.3 38.2 1.0
C2B D:HEM801 4.3 30.7 1.0
C3B D:HEM801 4.3 34.1 1.0
C3A D:HEM801 4.3 37.8 1.0
C3C D:HEM801 4.3 37.4 1.0
C2C D:HEM801 4.3 33.5 1.0
C07 D:XVA803 4.4 29.9 1.0
C05 D:XVA803 4.4 32.6 1.0
NE1 D:TRP414 4.5 26.1 1.0
C02 D:XVA803 4.5 28.3 1.0
C06 D:XVA803 4.8 46.9 1.0
N01 D:XVA803 4.8 32.9 1.0
N D:GLY422 4.8 28.1 1.0
C D:CYS420 4.9 27.4 1.0
N D:VAL421 5.0 27.5 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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