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Gadolinium in PDB 8fgr: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-Aminoethyl)-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-Aminoethyl)-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-Aminoethyl)-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-Aminoethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine, PDB code: 8fgr 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) 48.60 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.783, 150.897, 107.428, 90, 90.6, 90
R / Rfree (%) 20.8 / 26.3

Other elements in 8fgr:

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

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

Gadolinium binding site 1 out of 4 in 8fgr

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

b:126.7
occ:0.76
 O4 A:BTB503 2.7 90.1 1.0
O3 A:BTB503 2.7 55.4 1.0
O6 A:BTB503 2.8 86.7 1.0
O8 A:BTB503 2.8 83.0 1.0
O A:HOH690 2.8 58.1 1.0
O A:HOH604 2.8 64.3 1.0
N A:BTB503 3.0 83.0 1.0
O A:HOH614 3.1 69.3 1.0
C4 A:BTB503 3.4 85.7 1.0
C2 A:BTB503 3.4 76.9 1.0
C3 A:BTB503 3.5 58.5 1.0
C6 A:BTB503 3.8 83.0 1.0
C5 A:BTB503 3.8 82.2 1.0
C7 A:BTB503 3.9 84.6 1.0
C8 A:BTB503 3.9 82.4 1.0
OD2 A:ASP384 4.2 81.3 1.0
OD1 A:ASP384 4.8 63.6 1.0
C1 A:BTB503 4.9 71.8 1.0
CG A:ASP384 4.9 66.6 1.0

Gadolinium binding site 2 out of 4 in 8fgr

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

b:45.4
occ:1.00
 O B:THR319 2.5 54.8 1.0
C6 B:BTB504 2.6 37.1 1.0
O B:HOH752 2.6 56.0 1.0
O4 B:BTB504 2.6 46.8 1.0
N B:BTB504 2.7 38.0 1.0
OE1 B:GLU321 2.7 53.5 1.0
O3 B:BTB504 2.7 49.0 1.0
O C:HOH601 2.7 46.5 1.0
O6 B:BTB504 2.7 58.8 1.0
O8 B:BTB504 2.9 66.5 1.0
C5 B:BTB504 3.1 31.6 1.0
C8 B:BTB504 3.3 53.2 1.0
C2 B:BTB504 3.4 56.0 1.0
C3 B:BTB504 3.5 55.4 1.0
C4 B:BTB504 3.5 50.7 1.0
C7 B:BTB504 3.5 48.5 1.0
CD B:GLU321 3.5 46.7 1.0
C B:THR319 3.6 46.7 1.0
OE2 B:GLU321 3.6 48.9 1.0
OD1 C:ASP378 4.1 72.8 1.0
OD2 C:ASP378 4.3 71.0 1.0
CA B:THR319 4.4 38.3 1.0
O B:HOH759 4.4 60.7 1.0
N B:LEU320 4.6 47.6 1.0
N B:GLU321 4.6 41.6 1.0
CB B:THR319 4.6 39.8 1.0
CA B:LEU320 4.6 34.4 1.0
CG C:ASP378 4.6 59.6 1.0
O B:HOH666 4.8 40.3 1.0
C1 B:BTB504 4.8 67.9 1.0
CG B:GLU321 5.0 45.0 1.0

Gadolinium binding site 3 out of 4 in 8fgr

Go back to Gadolinium Binding Sites List in 8fgr
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(5-(2-Aminoethyl)-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-Aminoethyl)-2,3-Difluorophenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd511

b:70.1
occ:0.54
 O3 C:BTB504 2.5 36.5 1.0
O4 C:BTB504 2.7 89.9 1.0
N C:BTB504 2.8 78.7 1.0
C4 C:BTB504 3.0 82.9 1.0
O8 C:BTB504 3.0 61.7 1.0
O6 C:BTB504 3.1 83.9 1.0
C2 C:BTB504 3.1 73.4 1.0
C3 C:BTB504 3.2 52.2 1.0
C6 C:BTB504 3.5 84.5 1.0
C7 C:BTB504 3.6 71.9 1.0
C5 C:BTB504 3.7 79.0 1.0
C8 C:BTB504 3.9 65.3 1.0
OD2 C:ASP384 4.2 86.8 1.0
C1 C:BTB504 4.7 67.5 1.0
OD1 C:ASP384 4.7 88.5 1.0
CG C:ASP384 4.9 74.1 1.0

Gadolinium binding site 4 out of 4 in 8fgr

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

b:47.6
occ:1.00
 O D:THR319 2.5 26.8 1.0
OE1 D:GLU321 2.6 56.9 1.0
O3 D:BTB504 2.7 67.1 1.0
O D:HOH743 2.7 61.5 1.0
O4 D:BTB504 2.7 71.2 1.0
O8 D:BTB504 2.8 81.2 1.0
O6 D:BTB504 2.8 33.9 1.0
C6 D:BTB504 2.8 38.5 1.0
N D:BTB504 2.8 71.8 1.0
C8 D:BTB504 3.3 72.2 1.0
C5 D:BTB504 3.3 50.5 1.0
CD D:GLU321 3.4 55.6 1.0
OE2 D:GLU321 3.5 62.2 1.0
C2 D:BTB504 3.5 79.2 1.0
C7 D:BTB504 3.6 72.4 1.0
C3 D:BTB504 3.6 75.5 1.0
C4 D:BTB504 3.6 69.7 1.0
C D:THR319 3.7 47.2 1.0
CA D:THR319 4.5 43.0 1.0
CA D:LEU320 4.6 42.0 1.0
N D:LEU320 4.6 43.9 1.0
N D:GLU321 4.7 40.8 1.0
CB D:THR319 4.7 44.0 1.0
O D:HOH695 4.7 44.9 1.0
CG D:GLU321 4.8 42.4 1.0
C1 D:BTB504 5.0 85.1 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: Thu Dec 28 06:32:28 2023

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