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Gadolinium in PDB 8fgo: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)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-(Dimethylamino)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-(Dimethylamino)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-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine, PDB code: 8fgo 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) 40.05 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.889, 153.487, 109.036, 90, 90.79, 90
R / Rfree (%) 18.8 / 22.7

Other elements in 8fgo:

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

Iron (Fe) 4 atoms
Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms
Fluorine (F) 8 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-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine (pdb code 8fgo). 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-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine, PDB code: 8fgo:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 8fgo

Go back to Gadolinium Binding Sites List in 8fgo
Gadolinium 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)-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-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:69.2
occ:0.67
 C4 A:BTB504 2.6 75.5 1.0
O3 A:BTB504 2.6 29.4 1.0
N A:BTB504 2.7 74.1 1.0
O4 A:BTB504 2.7 84.8 1.0
O A:HOH724 2.7 82.8 1.0
O8 A:BTB504 2.8 71.5 1.0
O A:HOH744 2.8 58.9 1.0
C2 A:BTB504 2.8 70.4 1.0
O6 A:BTB504 3.0 86.4 1.0
O A:HOH733 3.0 74.7 1.0
C3 A:BTB504 3.1 44.4 1.0
C6 A:BTB504 3.5 83.6 1.0
C5 A:BTB504 3.5 77.6 1.0
C8 A:BTB504 3.7 67.8 1.0
C7 A:BTB504 3.7 72.5 1.0
C1 A:BTB504 4.3 73.8 1.0
OD2 A:ASP384 4.6 63.7 1.0
OD1 A:ASP384 4.7 61.2 1.0

Gadolinium binding site 2 out of 4 in 8fgo

Go back to Gadolinium Binding Sites List in 8fgo
Gadolinium 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)-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-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:38.0
occ:1.00
 O B:THR319 2.5 30.9 1.0
O3 B:BTB504 2.6 46.9 1.0
O B:HOH816 2.7 43.8 1.0
OE1 B:GLU321 2.7 43.7 1.0
O4 B:BTB504 2.7 53.4 1.0
N B:BTB504 2.7 42.7 1.0
O8 B:BTB504 2.7 50.5 1.0
O C:HOH609 2.7 37.0 1.0
O6 B:BTB504 2.8 57.8 1.0
C6 B:BTB504 2.8 43.0 1.0
C8 B:BTB504 3.2 47.6 1.0
C5 B:BTB504 3.3 48.8 1.0
C2 B:BTB504 3.3 58.3 1.0
C3 B:BTB504 3.4 53.7 1.0
C7 B:BTB504 3.5 47.6 1.0
C4 B:BTB504 3.6 56.0 1.0
CD B:GLU321 3.6 50.0 1.0
C B:THR319 3.6 46.4 1.0
OE2 B:GLU321 3.8 51.8 1.0
O B:HOH850 4.4 49.7 1.0
CA B:THR319 4.4 38.2 1.0
N B:GLU321 4.5 33.9 1.0
OD2 C:ASP378 4.5 44.5 1.0
OD1 C:ASP378 4.5 41.9 1.0
N B:LEU320 4.6 40.4 1.0
CA B:LEU320 4.6 37.0 1.0
CB B:THR319 4.7 39.8 1.0
C1 B:BTB504 4.8 72.3 1.0
O B:HOH646 4.8 40.2 1.0
CG B:GLU321 5.0 40.3 1.0
CG C:ASP378 5.0 52.1 1.0

Gadolinium binding site 3 out of 4 in 8fgo

Go back to Gadolinium Binding Sites List in 8fgo
Gadolinium 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)-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-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd510

b:52.3
occ:0.66
 O3 C:BTB504 2.3 14.7 1.0
O4 C:BTB504 2.7 54.0 1.0
O B:HOH732 2.7 45.6 1.0
O8 C:BTB504 2.8 60.8 1.0
N C:BTB504 2.9 63.4 1.0
O6 C:BTB504 2.9 78.9 1.0
O C:HOH776 3.1 56.1 1.0
C3 C:BTB504 3.3 40.9 1.0
C2 C:BTB504 3.3 62.0 1.0
C8 C:BTB504 3.3 63.9 1.0
C4 C:BTB504 3.5 61.6 1.0
C6 C:BTB504 3.6 68.9 1.0
C7 C:BTB504 3.6 65.0 1.0
C5 C:BTB504 3.8 63.8 1.0
OD2 B:ASP378 4.2 82.9 1.0
OD2 C:ASP384 4.5 72.0 1.0
OD1 C:ASP384 4.7 67.5 1.0
OD1 B:ASP378 4.8 78.0 1.0
C1 C:BTB504 4.8 65.1 1.0
CG B:ASP378 4.9 67.9 1.0

Gadolinium binding site 4 out of 4 in 8fgo

Go back to Gadolinium Binding Sites List in 8fgo
Gadolinium 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)-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-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd508

b:41.8
occ:1.00
 O D:THR319 2.4 33.4 1.0
O D:HOH813 2.6 54.8 1.0
O4 D:BTB504 2.6 58.4 1.0
O6 D:BTB504 2.6 41.2 1.0
O3 D:BTB504 2.7 52.5 1.0
OE1 D:GLU321 2.7 58.3 1.0
C6 D:BTB504 2.7 42.2 1.0
N D:BTB504 2.8 66.1 1.0
O8 D:BTB504 2.9 54.0 1.0
C5 D:BTB504 3.4 55.3 1.0
C2 D:BTB504 3.5 71.0 1.0
CD D:GLU321 3.5 49.0 1.0
C8 D:BTB504 3.6 58.5 1.0
OE2 D:GLU321 3.6 61.0 1.0
C D:THR319 3.6 52.3 1.0
C4 D:BTB504 3.6 64.6 1.0
C3 D:BTB504 3.6 59.9 1.0
C7 D:BTB504 3.8 64.5 1.0
O D:HOH871 4.2 46.5 1.0
CA D:THR319 4.4 35.1 1.0
N D:LEU320 4.6 38.6 1.0
O D:HOH657 4.6 44.3 1.0
N D:GLU321 4.6 37.2 1.0
CA D:LEU320 4.6 34.1 1.0
CB D:THR319 4.6 45.8 1.0
CG D:GLU321 4.9 41.7 1.0
C1 D:BTB504 5.0 73.4 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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