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Gadolinium in PDB 7tsn: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine, PDB code: 7tsn 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) 49.02 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.784, 151.035, 107.412, 90, 90.66, 90
R / Rfree (%) 21.4 / 26.2

Other elements in 7tsn:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Iron (Fe) 4 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine (pdb code 7tsn). 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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine, PDB code: 7tsn:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 7tsn

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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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:92.3
occ:0.74
 N A:BTB504 2.4 72.6 1.0
O4 A:BTB504 2.6 69.3 1.0
O A:HOH677 2.6 66.2 1.0
O3 A:BTB504 2.7 44.1 1.0
C2 A:BTB504 2.7 66.1 1.0
C4 A:BTB504 2.7 64.7 1.0
O8 A:BTB504 2.8 80.1 1.0
O6 A:BTB504 3.0 83.3 1.0
C3 A:BTB504 3.0 52.7 1.0
O A:HOH616 3.1 74.2 1.0
C5 A:BTB504 3.2 74.3 1.0
C6 A:BTB504 3.4 80.2 1.0
C7 A:BTB504 3.5 74.7 1.0
C8 A:BTB504 3.5 77.2 1.0
OD2 A:ASP384 4.0 70.5 1.0
C1 A:BTB504 4.2 72.7 1.0
OD1 A:ASP384 4.7 69.3 1.0
CG A:ASP384 4.7 60.5 1.0
O1 A:BTB504 5.0 76.0 1.0

Gadolinium binding site 2 out of 4 in 7tsn

Go back to Gadolinium Binding Sites List in 7tsn
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:45.9
occ:1.00
 O4 B:BTB504 2.5 52.7 1.0
O B:THR319 2.6 49.5 1.0
O B:HOH737 2.6 47.3 1.0
O C:HOH607 2.7 46.4 1.0
OE1 B:GLU321 2.7 47.5 1.0
N B:BTB504 2.7 39.2 1.0
O8 B:BTB504 2.7 44.3 1.0
O3 B:BTB504 3.0 51.6 1.0
O6 B:BTB504 3.0 56.5 1.0
C6 B:BTB504 3.1 43.4 1.0
C8 B:BTB504 3.2 42.8 1.0
C5 B:BTB504 3.3 35.0 1.0
C2 B:BTB504 3.4 61.0 1.0
C4 B:BTB504 3.4 59.7 1.0
C7 B:BTB504 3.6 41.0 1.0
CD B:GLU321 3.6 45.2 1.0
C3 B:BTB504 3.6 65.3 1.0
C B:THR319 3.6 46.4 1.0
OE2 B:GLU321 3.7 43.2 1.0
OD1 C:ASP378 4.3 48.2 1.0
OD2 C:ASP378 4.4 53.0 1.0
CA B:THR319 4.4 41.4 1.0
N B:GLU321 4.5 39.9 1.0
N B:LEU320 4.6 45.1 1.0
CA B:LEU320 4.6 36.2 1.0
CB B:THR319 4.6 40.7 1.0
CG C:ASP378 4.8 45.2 1.0
C1 B:BTB504 4.8 68.8 1.0
O B:HOH620 4.9 47.4 1.0
CG B:GLU321 5.0 40.0 1.0

Gadolinium binding site 3 out of 4 in 7tsn

Go back to Gadolinium Binding Sites List in 7tsn
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd512

b:73.8
occ:0.76
 O3 C:BTB504 2.5 25.1 1.0
O4 C:BTB504 2.7 66.8 1.0
O C:HOH652 2.7 63.6 1.0
O6 C:BTB504 2.7 72.7 1.0
O B:HOH707 2.7 60.6 1.0
N C:BTB504 2.8 63.5 1.0
O8 C:BTB504 3.0 61.8 1.0
C3 C:BTB504 3.2 31.1 1.0
C2 C:BTB504 3.2 62.7 1.0
C4 C:BTB504 3.2 68.5 1.0
O C:HOH715 3.2 53.2 1.0
C6 C:BTB504 3.5 65.5 1.0
C7 C:BTB504 3.7 67.9 1.0
C5 C:BTB504 3.7 58.5 1.0
C8 C:BTB504 3.9 64.2 1.0
OD1 B:ASP378 4.0 79.6 1.0
OD2 C:ASP384 4.2 73.5 1.0
OD1 C:ASP384 4.4 78.4 1.0
C1 C:BTB504 4.7 66.0 1.0
CG C:ASP384 4.7 62.4 1.0

Gadolinium binding site 4 out of 4 in 7tsn

Go back to Gadolinium Binding Sites List in 7tsn
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-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-(3-(3,3-Difluoroazetidin-1-Yl)Prop-1-Yn-1-Yl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd508

b:49.7
occ:1.00
 O D:THR319 2.6 29.7 1.0
O D:HOH756 2.6 54.5 1.0
O4 D:BTB504 2.6 59.2 1.0
OE1 D:GLU321 2.7 65.4 1.0
O3 D:BTB504 2.7 65.5 1.0
O8 D:BTB504 2.7 56.5 1.0
O6 D:BTB504 2.8 36.0 1.0
N D:BTB504 2.8 62.8 1.0
C6 D:BTB504 2.9 35.9 1.0
C5 D:BTB504 3.4 45.8 1.0
C2 D:BTB504 3.5 76.8 1.0
C8 D:BTB504 3.5 52.2 1.0
C3 D:BTB504 3.6 73.4 1.0
C4 D:BTB504 3.7 65.9 1.0
CD D:GLU321 3.7 54.1 1.0
C D:THR319 3.7 49.0 1.0
C7 D:BTB504 3.7 54.1 1.0
OE2 D:GLU321 4.0 53.9 1.0
CA D:THR319 4.4 46.5 1.0
CB D:THR319 4.6 47.5 1.0
N D:GLU321 4.6 38.3 1.0
N D:LEU320 4.7 46.1 1.0
CA D:LEU320 4.7 41.8 1.0
O D:HOH663 4.8 61.6 1.0
CG D:GLU321 5.0 48.4 1.0
C1 D:BTB504 5.0 80.7 1.0

Reference:

D.Vasu, H.Li, C.D.Hardy, T.L.Poulos, R.B.Silverman. 2-Aminopyridines with A Shortened Amino Sidechain As Potent, Selective, and Highly Permeable Human Neuronal Nitric Oxide Synthase Inhibitors. Bioorg.Med.Chem. V. 69 16878 2022.
ISSN: ESSN 1464-3391
PubMed: 35772285
DOI: 10.1016/J.BMC.2022.116878
Page generated: Sat Aug 10 22:24:49 2024

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