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Gadolinium in PDB 8fgs: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine

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

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-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-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine, PDB code: 8fgs 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) 38.75 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.52, 153.104, 108.745, 90, 90.7, 90
R / Rfree (%) 18.4 / 21.8

Other elements in 8fgs:

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

Chlorine (Cl) 4 atoms
Fluorine (F) 8 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms

Gadolinium Binding Sites:

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

Gadolinium binding site 1 out of 4 in 8fgs

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:68.0
occ:0.65
 O3 A:BTB504 2.6 47.1 1.0
N A:BTB504 2.7 79.0 1.0
O A:HOH615 2.7 53.3 1.0
O4 A:BTB504 2.7 82.5 1.0
O A:HOH635 2.7 61.4 1.0
O8 A:BTB504 2.7 72.5 1.0
O A:HOH725 2.8 82.0 1.0
O6 A:BTB504 2.9 88.0 1.0
C2 A:BTB504 3.1 76.1 1.0
C4 A:BTB504 3.1 77.6 1.0
C3 A:BTB504 3.2 58.2 1.0
C6 A:BTB504 3.5 83.6 1.0
C7 A:BTB504 3.5 79.2 1.0
C5 A:BTB504 3.6 79.3 1.0
C8 A:BTB504 3.7 75.2 1.0
OD2 A:ASP384 4.5 71.7 1.0
C1 A:BTB504 4.6 85.8 1.0
OD1 A:ASP384 4.8 73.8 1.0

Gadolinium binding site 2 out of 4 in 8fgs

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd511

b:39.0
occ:1.00
 O B:THR319 2.4 35.6 1.0
N B:BTB504 2.6 44.0 1.0
OE1 B:GLU321 2.7 61.2 1.0
O4 B:BTB504 2.7 58.2 1.0
O B:HOH797 2.7 63.7 1.0
O3 B:BTB504 2.7 53.4 1.0
O8 B:BTB504 2.7 58.7 1.0
C6 B:BTB504 2.7 48.1 1.0
O6 B:BTB504 2.7 59.1 1.0
O C:HOH602 2.8 41.7 1.0
C5 B:BTB504 3.2 47.9 1.0
C8 B:BTB504 3.3 52.1 1.0
C2 B:BTB504 3.4 63.7 1.0
C7 B:BTB504 3.5 48.7 1.0
C3 B:BTB504 3.5 64.2 1.0
C4 B:BTB504 3.5 62.5 1.0
CD B:GLU321 3.6 55.5 1.0
C B:THR319 3.6 52.0 1.0
OE2 B:GLU321 3.8 61.2 1.0
CA B:THR319 4.4 39.9 1.0
N B:GLU321 4.5 42.5 1.0
OD1 C:ASP378 4.5 56.8 1.0
O B:HOH810 4.5 66.3 1.0
OD2 C:ASP378 4.6 58.3 1.0
N B:LEU320 4.6 42.5 1.0
CB B:THR319 4.6 46.1 1.0
CA B:LEU320 4.6 39.3 1.0
O B:HOH628 4.7 46.0 1.0
C1 B:BTB504 4.8 76.5 1.0
CG B:GLU321 5.0 50.4 1.0
CG C:ASP378 5.0 58.0 1.0

Gadolinium binding site 3 out of 4 in 8fgs

Go back to Gadolinium Binding Sites List in 8fgs
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd512

b:67.6
occ:0.68
 O3 C:BTB504 2.4 22.5 1.0
O C:HOH604 2.7 68.7 1.0
O4 C:BTB504 2.7 87.3 1.0
O C:HOH648 2.7 56.9 1.0
O8 C:BTB504 2.7 77.0 1.0
O6 C:BTB504 2.8 86.1 1.0
O B:HOH657 2.8 62.8 1.0
O C:HOH755 2.8 68.5 1.0
N C:BTB504 2.8 75.2 1.0
C4 C:BTB504 3.1 79.3 1.0
C8 C:BTB504 3.2 78.5 1.0
C2 C:BTB504 3.2 72.1 1.0
C3 C:BTB504 3.3 45.6 1.0
C6 C:BTB504 3.5 78.3 1.0
C7 C:BTB504 3.5 79.3 1.0
C5 C:BTB504 3.7 71.1 1.0
OD2 B:ASP378 4.3 87.2 1.0
OD2 C:ASP384 4.5 72.6 1.0
C1 C:BTB504 4.7 74.0 1.0
OD1 B:ASP378 4.7 86.6 1.0
OD1 C:ASP384 4.8 78.0 1.0
CG B:ASP378 4.9 77.9 1.0

Gadolinium binding site 4 out of 4 in 8fgs

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Diethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd508

b:42.0
occ:1.00
 O D:THR319 2.4 31.5 1.0
C6 D:BTB504 2.6 42.0 1.0
O4 D:BTB504 2.7 65.1 1.0
O6 D:BTB504 2.7 46.1 1.0
OE1 D:GLU321 2.7 67.9 1.0
O D:HOH800 2.7 58.5 1.0
O3 D:BTB504 2.7 57.2 1.0
O8 D:BTB504 2.8 60.8 1.0
N D:BTB504 2.8 72.2 1.0
C8 D:BTB504 3.2 68.3 1.0
C5 D:BTB504 3.3 52.3 1.0
C2 D:BTB504 3.5 77.2 1.0
CD D:GLU321 3.6 62.8 1.0
C7 D:BTB504 3.6 69.8 1.0
C D:THR319 3.6 49.5 1.0
C3 D:BTB504 3.7 65.9 1.0
C4 D:BTB504 3.7 71.2 1.0
OE2 D:GLU321 3.7 72.2 1.0
CA D:THR319 4.4 32.1 1.0
N D:LEU320 4.5 47.0 1.0
N D:GLU321 4.5 44.9 1.0
CA D:LEU320 4.6 41.6 1.0
CB D:THR319 4.6 41.1 1.0
CG D:GLU321 4.9 55.0 1.0
C1 D:BTB504 5.0 84.8 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 22:46:08 2024

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