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Iron in PDB 6nh3: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3 was solved by G.Chreifi, H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.87 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.469, 153.089, 109.150, 90.00, 90.80, 90.00
R / Rfree (%) 20.6 / 25.7

Other elements in 6nh3:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Zinc (Zn) 6 atoms
Gadolinium (Gd) 4 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine (pdb code 6nh3). 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6nh3

Go back to Iron Binding Sites List in 6nh3
Iron binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:44.1
occ:1.00
FE A:HEM501 0.0 44.1 1.0
ND A:HEM501 2.0 48.7 1.0
NC A:HEM501 2.1 48.1 1.0
NA A:HEM501 2.1 39.9 1.0
NB A:HEM501 2.1 34.3 1.0
SG A:CYS184 2.4 39.5 1.0
C1D A:HEM501 3.0 50.2 1.0
C4C A:HEM501 3.0 50.8 1.0
C4D A:HEM501 3.0 40.1 1.0
C1B A:HEM501 3.1 42.0 1.0
C4A A:HEM501 3.1 41.9 1.0
C1C A:HEM501 3.1 45.3 1.0
C1A A:HEM501 3.1 33.9 1.0
C4B A:HEM501 3.1 40.7 1.0
CHD A:HEM501 3.4 52.8 1.0
CB A:CYS184 3.4 40.3 1.0
CHB A:HEM501 3.4 39.7 1.0
CHA A:HEM501 3.5 39.5 1.0
CHC A:HEM501 3.5 41.8 1.0
C04 A:KL4502 4.0 43.9 1.0
CA A:CYS184 4.1 35.3 1.0
C05 A:KL4502 4.1 48.7 1.0
C2D A:HEM501 4.2 43.6 1.0
C3D A:HEM501 4.2 46.2 1.0
C03 A:KL4502 4.3 38.8 1.0
C3C A:HEM501 4.3 51.9 1.0
C2B A:HEM501 4.3 42.2 1.0
C2C A:HEM501 4.3 53.2 1.0
C07 A:KL4502 4.3 47.1 1.0
C3B A:HEM501 4.3 41.5 1.0
C3A A:HEM501 4.3 39.7 1.0
C2A A:HEM501 4.4 44.4 1.0
NE1 A:TRP178 4.4 41.9 1.0
C06 A:KL4502 4.5 45.8 1.0
C02 A:KL4502 4.6 40.3 1.0
N01 A:KL4502 4.7 46.2 1.0
C A:CYS184 4.8 31.7 1.0
N A:GLY186 4.9 35.3 1.0
N A:VAL185 5.0 31.7 1.0
CD1 A:TRP178 5.0 39.3 1.0

Iron binding site 2 out of 4 in 6nh3

Go back to Iron Binding Sites List in 6nh3
Iron binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:27.9
occ:1.00
FE B:HEM802 0.0 27.9 1.0
NA B:HEM802 2.1 27.9 1.0
ND B:HEM802 2.1 32.8 1.0
NB B:HEM802 2.1 29.1 1.0
NC B:HEM802 2.1 24.6 1.0
SG B:CYS184 2.3 26.8 1.0
C1B B:HEM802 3.0 24.9 1.0
C4A B:HEM802 3.0 35.4 1.0
C1D B:HEM802 3.1 33.3 1.0
C4D B:HEM802 3.1 32.9 1.0
C4C B:HEM802 3.1 32.2 1.0
C4B B:HEM802 3.1 29.5 1.0
C1A B:HEM802 3.1 30.4 1.0
C1C B:HEM802 3.1 31.0 1.0
CHB B:HEM802 3.3 23.6 1.0
CHD B:HEM802 3.4 28.8 1.0
CB B:CYS184 3.4 28.4 1.0
CHA B:HEM802 3.5 24.2 1.0
CHC B:HEM802 3.5 26.4 1.0
C04 B:KL4803 4.0 29.4 1.0
CA B:CYS184 4.1 30.6 1.0
C05 B:KL4803 4.2 33.1 1.0
C03 B:KL4803 4.2 28.9 1.0
C2B B:HEM802 4.3 33.0 1.0
C2D B:HEM802 4.3 37.6 1.0
C3B B:HEM802 4.3 27.8 1.0
C3D B:HEM802 4.3 24.8 1.0
C3A B:HEM802 4.3 26.0 1.0
C3C B:HEM802 4.3 35.8 1.0
NE1 B:TRP178 4.3 34.1 1.0
C2A B:HEM802 4.3 28.7 1.0
C2C B:HEM802 4.4 30.7 1.0
C07 B:KL4803 4.5 28.4 1.0
C06 B:KL4803 4.5 37.0 1.0
C02 B:KL4803 4.6 32.2 1.0
N01 B:KL4803 4.7 29.3 1.0
N B:GLY186 4.8 29.9 1.0
C B:CYS184 4.9 26.5 1.0
N B:VAL185 5.0 25.0 1.0

Iron binding site 3 out of 4 in 6nh3

Go back to Iron Binding Sites List in 6nh3
Iron binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:39.6
occ:1.00
FE C:HEM501 0.0 39.6 1.0
NC C:HEM501 2.0 47.6 1.0
NA C:HEM501 2.1 44.3 1.0
ND C:HEM501 2.1 45.4 1.0
NB C:HEM501 2.1 38.4 1.0
SG C:CYS184 2.3 38.7 1.0
C4C C:HEM501 3.0 48.8 1.0
C1C C:HEM501 3.0 42.5 1.0
C4A C:HEM501 3.1 43.2 1.0
C1D C:HEM501 3.1 44.3 1.0
C1A C:HEM501 3.1 45.2 1.0
C4B C:HEM501 3.1 36.6 1.0
C1B C:HEM501 3.1 39.2 1.0
C4D C:HEM501 3.1 45.6 1.0
CB C:CYS184 3.2 44.4 1.0
CHD C:HEM501 3.4 47.4 1.0
CHC C:HEM501 3.4 37.8 1.0
CHB C:HEM501 3.5 34.5 1.0
CHA C:HEM501 3.5 43.2 1.0
CA C:CYS184 4.0 37.8 1.0
C04 C:KL4502 4.2 40.8 1.0
C3C C:HEM501 4.2 45.0 1.0
C05 C:KL4502 4.2 45.9 1.0
C2C C:HEM501 4.2 42.8 1.0
C03 C:KL4502 4.3 43.0 1.0
C3A C:HEM501 4.3 37.4 1.0
C2A C:HEM501 4.3 49.5 1.0
C2D C:HEM501 4.3 38.7 1.0
C2B C:HEM501 4.3 40.9 1.0
C3B C:HEM501 4.3 40.6 1.0
NE1 C:TRP178 4.3 38.0 1.0
C3D C:HEM501 4.3 46.5 1.0
C06 C:KL4502 4.5 46.6 1.0
C02 C:KL4502 4.5 44.9 1.0
N01 C:KL4502 4.6 47.1 1.0
C07 C:KL4502 4.6 44.7 1.0
N C:GLY186 4.7 35.8 1.0
C C:CYS184 4.8 31.0 1.0
N C:VAL185 5.0 30.8 1.0
CD1 C:TRP178 5.0 35.2 1.0

Iron binding site 4 out of 4 in 6nh3

Go back to Iron Binding Sites List in 6nh3
Iron binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:25.3
occ:1.00
FE D:HEM501 0.0 25.3 1.0
ND D:HEM501 2.0 27.8 1.0
NC D:HEM501 2.1 23.6 1.0
NA D:HEM501 2.1 26.4 1.0
NB D:HEM501 2.1 21.4 1.0
SG D:CYS184 2.2 25.5 1.0
C1D D:HEM501 3.0 26.6 1.0
C4D D:HEM501 3.1 27.1 1.0
C4A D:HEM501 3.1 25.8 1.0
C1B D:HEM501 3.1 26.8 1.0
C4C D:HEM501 3.1 28.3 1.0
C1C D:HEM501 3.1 25.1 1.0
C1A D:HEM501 3.1 25.6 1.0
C4B D:HEM501 3.2 23.4 1.0
CB D:CYS184 3.3 23.8 1.0
CHD D:HEM501 3.4 23.6 1.0
CHB D:HEM501 3.4 22.6 1.0
CHA D:HEM501 3.5 30.4 1.0
CHC D:HEM501 3.5 21.3 1.0
CA D:CYS184 4.0 21.8 1.0
C04 D:KL4502 4.0 32.1 1.0
C05 D:KL4502 4.2 32.3 1.0
C03 D:KL4502 4.3 29.6 1.0
C3D D:HEM501 4.3 28.6 1.0
C2D D:HEM501 4.3 26.3 1.0
C3A D:HEM501 4.3 27.9 1.0
C2B D:HEM501 4.3 32.0 1.0
C3C D:HEM501 4.3 26.5 1.0
NE1 D:TRP178 4.3 27.6 1.0
C2C D:HEM501 4.3 29.1 1.0
C2A D:HEM501 4.3 27.7 1.0
C3B D:HEM501 4.4 28.8 1.0
C07 D:KL4502 4.4 25.2 1.0
C06 D:KL4502 4.5 35.3 1.0
C02 D:KL4502 4.6 33.9 1.0
N01 D:KL4502 4.7 33.6 1.0
N D:GLY186 4.7 20.8 1.0
C D:CYS184 4.8 24.6 1.0
N D:VAL185 4.9 26.4 1.0

Reference:

H.T.Do, H.Li, G.Chreifi, T.L.Poulos, R.B.Silverman. Optimization of Blood-Brain Barrier Permeability with Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibitors Having A 2-Aminopyridine Scaffold. J. Med. Chem. V. 62 2690 2019.
ISSN: ISSN 1520-4804
PubMed: 30802056
DOI: 10.1021/ACS.JMEDCHEM.8B02032
Page generated: Sun Dec 13 16:45:47 2020

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