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

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

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine, PDB code: 8fgq 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) 75.78 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.569, 151.48, 108.348, 90, 91.08, 90
R / Rfree (%) 19.3 / 24.6

Other elements in 8fgq:

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

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

Gadolinium Binding Sites:

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

Gadolinium binding site 1 out of 4 in 8fgq

Go back to Gadolinium Binding Sites List in 8fgq
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd509

b:81.2
occ:1.00
 N A:BTB504 2.7 81.5 1.0
O A:HOH621 2.8 53.9 1.0
O4 A:BTB504 2.8 90.5 1.0
O3 A:BTB504 2.8 52.3 1.0
O6 A:BTB504 2.8 88.9 1.0
O A:HOH703 2.8 74.5 1.0
O A:HOH698 2.8 54.0 1.0
C4 A:BTB504 3.0 85.4 1.0
O8 A:BTB504 3.1 68.8 1.0
C2 A:BTB504 3.1 78.7 1.0
C6 A:BTB504 3.2 87.7 1.0
C3 A:BTB504 3.4 64.5 1.0
C5 A:BTB504 3.5 85.0 1.0
C7 A:BTB504 3.8 74.9 1.0
C8 A:BTB504 3.9 69.0 1.0
OD1 A:ASP384 4.5 63.0 1.0
OD2 A:ASP384 4.6 64.8 1.0
C1 A:BTB504 4.6 78.6 1.0
CG A:ASP384 5.0 54.1 1.0

Gadolinium binding site 2 out of 4 in 8fgq

Go back to Gadolinium Binding Sites List in 8fgq
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:38.1
occ:1.00
 O4 B:BTB504 2.5 38.4 1.0
O B:THR319 2.6 38.2 1.0
O B:HOH713 2.6 59.2 1.0
O3 B:BTB504 2.7 50.8 1.0
O C:HOH605 2.7 48.7 1.0
O8 B:BTB504 2.7 48.0 1.0
OE1 B:GLU321 2.7 42.7 1.0
O6 B:BTB504 2.7 39.6 1.0
N B:BTB504 2.7 42.0 1.0
C6 B:BTB504 2.9 33.3 1.0
C5 B:BTB504 3.3 24.2 1.0
C2 B:BTB504 3.4 56.9 1.0
C8 B:BTB504 3.4 43.6 1.0
C3 B:BTB504 3.4 57.3 1.0
C4 B:BTB504 3.5 50.7 1.0
C7 B:BTB504 3.6 38.0 1.0
C B:THR319 3.7 39.9 1.0
CD B:GLU321 3.8 47.8 1.0
OE2 B:GLU321 4.1 55.6 1.0
OD2 C:ASP378 4.3 50.3 1.0
OD1 C:ASP378 4.4 45.9 1.0
CA B:THR319 4.5 35.8 1.0
CA B:LEU320 4.6 33.2 1.0
N B:GLU321 4.6 34.1 1.0
N B:LEU320 4.6 43.9 1.0
CB B:THR319 4.7 31.8 1.0
CG C:ASP378 4.8 45.1 1.0
C1 B:BTB504 4.8 64.7 1.0
O B:HOH747 4.9 48.8 1.0

Gadolinium binding site 3 out of 4 in 8fgq

Go back to Gadolinium Binding Sites List in 8fgq
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd510

b:74.2
occ:1.00
 O3 C:BTB504 2.7 25.5 1.0
O4 C:BTB504 2.7 44.5 1.0
O C:HOH719 2.8 58.2 1.0
O8 C:BTB504 2.8 53.8 1.0
O C:HOH735 2.8 53.0 1.0
N C:BTB504 2.9 60.4 1.0
O6 C:BTB504 3.1 68.2 1.0
C2 C:BTB504 3.2 57.2 1.0
C3 C:BTB504 3.2 30.5 1.0
C6 C:BTB504 3.4 63.4 1.0
C4 C:BTB504 3.4 57.5 1.0
O C:HOH732 3.4 64.9 1.0
O B:HOH777 3.6 51.5 1.0
C8 C:BTB504 3.6 52.0 1.0
C5 C:BTB504 3.7 59.6 1.0
C7 C:BTB504 3.8 59.4 1.0
OD1 C:ASP384 4.5 65.1 1.0
OD2 C:ASP384 4.7 68.2 1.0
C1 C:BTB504 4.7 65.1 1.0

Gadolinium binding site 4 out of 4 in 8fgq

Go back to Gadolinium Binding Sites List in 8fgq
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-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 4-(5-(2-(Dimethylamino)Ethyl)-2,3-Difluorophenethyl)-6- Methylpyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd507

b:40.0
occ:1.00
 O D:THR319 2.6 24.2 1.0
OE1 D:GLU321 2.6 48.9 1.0
O4 D:BTB504 2.6 48.6 1.0
O D:HOH759 2.7 50.2 1.0
O3 D:BTB504 2.7 55.4 1.0
N D:BTB504 2.8 57.1 1.0
O6 D:BTB504 2.9 35.0 1.0
O8 D:BTB504 3.0 57.1 1.0
C6 D:BTB504 3.1 36.8 1.0
C2 D:BTB504 3.4 69.7 1.0
C5 D:BTB504 3.5 45.5 1.0
C3 D:BTB504 3.5 64.9 1.0
CD D:GLU321 3.5 46.8 1.0
C8 D:BTB504 3.5 57.7 1.0
C4 D:BTB504 3.6 63.8 1.0
OE2 D:GLU321 3.6 60.5 1.0
C D:THR319 3.7 48.6 1.0
C7 D:BTB504 3.7 54.3 1.0
CA D:THR319 4.4 38.9 1.0
CB D:THR319 4.5 35.4 1.0
N D:GLU321 4.6 34.7 1.0
N D:LEU320 4.7 45.1 1.0
CA D:LEU320 4.8 32.4 1.0
CG D:GLU321 4.9 33.8 1.0
C1 D:BTB504 4.9 76.4 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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