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Iron in PDB 4d2y: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine

Enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine

All present enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine, PDB code: 4d2y 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) 43.840 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.852, 110.465, 164.192, 90.00, 90.00, 90.00
R / Rfree (%) 17.05 / 20.83

Other elements in 4d2y:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine (pdb code 4d2y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine, PDB code: 4d2y:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4d2y

Go back to Iron Binding Sites List in 4d2y
Iron binding site 1 out of 2 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe750

b:30.1
occ:1.00
 FE A:HEM750 0.0 30.1 1.0
NC A:HEM750 2.0 24.9 1.0
NA A:HEM750 2.1 33.2 1.0
NB A:HEM750 2.1 33.2 1.0
ND A:HEM750 2.1 35.3 1.0
N01 A:L5Z800 2.3 31.8 1.0
SG A:CYS415 2.4 28.7 1.0
C1C A:HEM750 3.0 23.9 1.0
C1A A:HEM750 3.0 26.2 1.0
C4D A:HEM750 3.0 33.6 1.0
C4C A:HEM750 3.1 26.4 1.0
C4B A:HEM750 3.1 37.5 1.0
C4A A:HEM750 3.1 31.5 1.0
C1B A:HEM750 3.1 30.8 1.0
C1D A:HEM750 3.1 32.7 1.0
C02 A:L5Z800 3.2 35.2 1.0
C05 A:L5Z800 3.3 40.0 1.0
CHA A:HEM750 3.4 26.6 1.0
CB A:CYS415 3.4 26.0 1.0
CHC A:HEM750 3.4 28.3 1.0
CHB A:HEM750 3.5 27.9 1.0
CHD A:HEM750 3.5 26.3 1.0
CA A:CYS415 4.2 28.0 1.0
C2C A:HEM750 4.3 25.8 1.0
C2A A:HEM750 4.3 35.4 1.0
C3C A:HEM750 4.3 28.1 1.0
N03 A:L5Z800 4.3 38.0 1.0
C3A A:HEM750 4.3 36.6 1.0
C3D A:HEM750 4.3 37.8 1.0
C2B A:HEM750 4.3 33.5 1.0
C3B A:HEM750 4.3 39.1 1.0
C2D A:HEM750 4.3 31.5 1.0
C04 A:L5Z800 4.4 38.2 1.0
NE1 A:TRP409 4.5 33.7 1.0
N A:GLY417 4.9 28.3 1.0
C A:CYS415 4.9 25.1 1.0
O A:HOH2090 5.0 40.9 1.0

Iron binding site 2 out of 2 in 4d2y

Go back to Iron Binding Sites List in 4d2y
Iron binding site 2 out of 2 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2-(1H-Imidazol- 1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe750

b:28.9
occ:1.00
 FE B:HEM750 0.0 28.9 1.0
ND B:HEM750 2.0 25.0 1.0
NB B:HEM750 2.0 32.9 1.0
NC B:HEM750 2.0 24.3 1.0
NA B:HEM750 2.1 25.4 1.0
N01 B:L5Z800 2.3 31.0 1.0
SG B:CYS415 2.5 28.4 1.0
C1C B:HEM750 3.0 19.9 1.0
C4D B:HEM750 3.0 26.6 1.0
C4B B:HEM750 3.0 33.6 1.0
C1A B:HEM750 3.0 24.2 1.0
C4C B:HEM750 3.1 26.3 1.0
C1D B:HEM750 3.1 29.4 1.0
C1B B:HEM750 3.1 33.6 1.0
C4A B:HEM750 3.1 27.2 1.0
C02 B:L5Z800 3.2 27.9 1.0
C05 B:L5Z800 3.2 33.5 1.0
CHC B:HEM750 3.3 29.8 1.0
CHA B:HEM750 3.3 26.3 1.0
CB B:CYS415 3.4 26.4 1.0
CHD B:HEM750 3.5 28.7 1.0
CHB B:HEM750 3.5 28.8 1.0
C2C B:HEM750 4.2 24.4 1.0
CA B:CYS415 4.2 21.5 1.0
C3D B:HEM750 4.3 25.4 1.0
C3C B:HEM750 4.3 22.8 1.0
C3B B:HEM750 4.3 34.4 1.0
C2A B:HEM750 4.3 31.4 1.0
C2B B:HEM750 4.3 34.5 1.0
N03 B:L5Z800 4.3 34.0 1.0
C3A B:HEM750 4.3 31.1 1.0
C2D B:HEM750 4.3 28.1 1.0
C04 B:L5Z800 4.4 37.8 1.0
NE1 B:TRP409 4.5 24.4 1.0
N B:GLY417 4.9 34.2 1.0
C B:CYS415 4.9 25.7 1.0
O B:HOH2135 5.0 40.5 1.0

Reference:

P.Mukherjee, H.Li, I.F.Sevrioukova, G.Chreifi, P.Martasek, L.J.Roman, T.L.Poulos, R.B.Silverman. Novel 2,4-Disubstituted Pyrimidines As Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. J.Med.Chem. 2014.
ISSN: ESSN 1520-4804
PubMed: 25489882
DOI: 10.1021/JM501719E
Page generated: Tue Aug 5 09:42:20 2025

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