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Gadolinium in PDB 8fgn: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-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) Pyridin-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) Pyridin-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) Pyridin-2-Amine, PDB code: 8fgn 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) 75.79 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.33, 151.58, 107.85, 90, 91.09, 90
R / Rfree (%) 18.6 / 23.6

Other elements in 8fgn:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl) Pyridin-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) Pyridin-2-Amine (pdb code 8fgn). 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) Pyridin-2-Amine, PDB code: 8fgn:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 8fgn

Go back to Gadolinium Binding Sites List in 8fgn
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) Pyridin-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) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:86.4
occ:1.00
 O6 A:BTB504 2.7 92.3 1.0
O A:HOH615 2.7 55.1 1.0
O4 A:BTB504 2.8 104.5 1.0
O3 A:BTB504 2.8 49.4 1.0
O A:HOH681 2.8 66.9 1.0
N A:BTB504 2.9 83.9 1.0
C4 A:BTB504 3.0 94.0 1.0
O8 A:BTB504 3.1 79.8 1.0
C2 A:BTB504 3.2 83.1 1.0
C3 A:BTB504 3.4 63.3 1.0
C7 A:BTB504 3.7 80.8 1.0
C6 A:BTB504 3.8 85.8 1.0
C5 A:BTB504 3.8 80.7 1.0
C8 A:BTB504 4.0 76.6 1.0
OD1 A:ASP384 4.5 70.9 1.0
OD2 A:ASP384 4.6 76.0 1.0
C1 A:BTB504 4.7 81.7 1.0
CG A:ASP384 5.0 65.0 1.0

Gadolinium binding site 2 out of 4 in 8fgn

Go back to Gadolinium Binding Sites List in 8fgn
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) Pyridin-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) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd507

b:44.4
occ:1.00
 O4 B:BTB504 2.6 57.5 1.0
O B:HOH670 2.6 52.4 1.0
O B:THR319 2.6 51.7 1.0
N B:BTB504 2.7 43.4 1.0
O3 B:BTB504 2.7 63.9 1.0
OE1 B:GLU321 2.7 55.5 1.0
O8 B:BTB504 2.7 54.3 1.0
O C:HOH633 2.7 51.6 1.0
O6 B:BTB504 2.8 46.9 1.0
C6 B:BTB504 2.9 35.0 1.0
C5 B:BTB504 3.3 31.9 1.0
C8 B:BTB504 3.3 50.4 1.0
C2 B:BTB504 3.3 65.7 1.0
C3 B:BTB504 3.4 67.0 1.0
C7 B:BTB504 3.5 42.1 1.0
C4 B:BTB504 3.6 61.5 1.0
C B:THR319 3.6 44.1 1.0
CD B:GLU321 3.6 58.0 1.0
OE2 B:GLU321 3.8 59.6 1.0
CA B:THR319 4.4 39.5 1.0
OD1 C:ASP378 4.4 51.2 1.0
N B:LEU320 4.5 50.6 1.0
OD2 C:ASP378 4.5 49.2 1.0
CA B:LEU320 4.6 38.4 1.0
CB B:THR319 4.6 35.3 1.0
N B:GLU321 4.7 44.8 1.0
C1 B:BTB504 4.8 72.0 1.0
CG C:ASP378 4.9 50.3 1.0

Gadolinium binding site 3 out of 4 in 8fgn

Go back to Gadolinium Binding Sites List in 8fgn
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) Pyridin-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) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd510

b:80.8
occ:1.00
 O3 C:BTB504 2.6 29.3 1.0
O4 C:BTB504 2.7 68.7 1.0
O C:HOH671 2.8 61.5 1.0
O8 C:BTB504 2.8 54.5 1.0
O C:HOH711 2.8 63.5 1.0
O C:HOH702 2.9 55.2 1.0
N C:BTB504 2.9 69.8 1.0
O6 C:BTB504 3.1 71.8 1.0
C2 C:BTB504 3.3 70.7 1.0
O C:HOH709 3.4 63.9 1.0
C6 C:BTB504 3.4 69.4 1.0
C3 C:BTB504 3.4 43.7 1.0
C4 C:BTB504 3.5 77.4 1.0
C5 C:BTB504 3.8 63.1 1.0
C8 C:BTB504 3.8 56.1 1.0
C7 C:BTB504 3.8 64.3 1.0
OD1 C:ASP384 4.3 72.9 1.0
OD2 C:ASP384 4.5 74.8 1.0
C1 C:BTB504 4.9 73.9 1.0
CG C:ASP384 4.9 60.5 1.0

Gadolinium binding site 4 out of 4 in 8fgn

Go back to Gadolinium Binding Sites List in 8fgn
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) Pyridin-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) Pyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd507

b:45.4
occ:1.00
 O D:THR319 2.6 30.6 1.0
O D:HOH686 2.6 60.8 1.0
OE1 D:GLU321 2.6 58.0 1.0
O4 D:BTB504 2.6 53.0 1.0
N D:BTB504 2.7 69.8 1.0
O3 D:BTB504 2.7 80.3 1.0
C4 D:BTB504 2.9 67.3 1.0
O6 D:BTB504 3.0 43.5 1.0
O8 D:BTB504 3.0 63.2 1.0
C2 D:BTB504 3.1 81.0 1.0
C5 D:BTB504 3.2 47.2 1.0
C3 D:BTB504 3.4 85.6 1.0
CD D:GLU321 3.5 51.1 1.0
C6 D:BTB504 3.6 50.5 1.0
OE2 D:GLU321 3.6 56.9 1.0
C D:THR319 3.7 55.4 1.0
C8 D:BTB504 3.8 63.2 1.0
C7 D:BTB504 3.8 66.3 1.0
CA D:THR319 4.4 45.7 1.0
N D:GLU321 4.6 34.7 1.0
CB D:THR319 4.6 44.9 1.0
C1 D:BTB504 4.6 84.3 1.0
CA D:LEU320 4.7 40.5 1.0
N D:LEU320 4.7 56.3 1.0
CG D:GLU321 4.9 39.5 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 22:46:08 2024

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