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Gadolinium in PDB 5uob: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile, PDB code: 5uob was solved by G.Chreifi, H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.534, 153.951, 109.828, 90.00, 90.57, 90.00
R / Rfree (%) 22.1 / 27.9

Other elements in 5uob:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Iron (Fe) 4 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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile (pdb code 5uob). 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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile, PDB code: 5uob:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 5uob

Go back to Gadolinium Binding Sites List in 5uob
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:0.2
occ:1.00
O3 A:BTB504 2.6 37.6 1.0
O6 A:BTB504 2.7 80.9 1.0
O A:HOH620 2.8 73.8 1.0
O A:HOH623 2.8 93.8 1.0
O4 A:BTB504 3.1 73.7 1.0
OD2 A:ASP384 3.4 69.6 1.0
N A:BTB504 3.5 85.3 1.0
C8 A:BTB504 3.8 87.2 1.0
C3 A:BTB504 3.9 81.1 1.0
C6 A:BTB504 4.0 85.5 1.0
C4 A:BTB504 4.0 77.7 1.0
C2 A:BTB504 4.0 82.2 1.0
C7 A:BTB504 4.1 86.1 1.0
O A:HOH625 4.1 79.4 1.0
CG A:ASP384 4.2 65.4 1.0
OD1 A:ASP384 4.2 68.0 1.0
C5 A:BTB504 4.4 86.3 1.0
O8 A:BTB504 4.5 86.8 1.0

Gadolinium binding site 2 out of 4 in 5uob

Go back to Gadolinium Binding Sites List in 5uob
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:62.8
occ:1.00
N B:BTB504 2.6 64.8 1.0
O B:HOH605 2.6 55.6 1.0
O6 B:BTB504 2.7 64.1 1.0
O3 B:BTB504 2.7 74.2 1.0
O B:THR319 2.7 60.5 1.0
O4 B:BTB504 2.7 69.2 1.0
OE1 B:GLU321 2.7 76.5 1.0
C8 B:BTB504 2.9 55.9 1.0
C6 B:BTB504 3.1 67.1 1.0
O8 B:BTB504 3.1 57.6 1.0
C7 B:BTB504 3.3 56.5 1.0
C2 B:BTB504 3.4 73.8 1.0
C5 B:BTB504 3.4 64.9 1.0
OE2 B:GLU321 3.4 75.2 1.0
CD B:GLU321 3.5 72.5 1.0
C3 B:BTB504 3.5 76.3 1.0
C4 B:BTB504 3.6 73.7 1.0
C B:THR319 3.6 53.8 1.0
CA B:THR319 4.3 49.6 1.0
OD2 C:ASP378 4.3 53.2 1.0
CB B:THR319 4.6 45.7 1.0
OD1 C:ASP378 4.6 58.7 1.0
N B:LEU320 4.6 59.2 1.0
CA B:LEU320 4.7 53.1 1.0
N B:GLU321 4.8 56.7 1.0
C1 B:BTB504 4.8 78.2 1.0
CG C:ASP378 4.9 53.2 1.0
CG B:GLU321 4.9 66.2 1.0

Gadolinium binding site 3 out of 4 in 5uob

Go back to Gadolinium Binding Sites List in 5uob
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd510

b:0.8
occ:1.00
O3 C:BTB504 2.7 95.3 1.0
O C:HOH627 2.8 0.6 1.0
O C:HOH628 2.8 94.2 1.0
N C:BTB504 2.9 0.6 1.0
O4 C:BTB504 2.9 0.6 1.0
O8 C:BTB504 3.2 0.7 1.0
C6 C:BTB504 3.3 0.8 1.0
O6 C:BTB504 3.5 0.3 1.0
C5 C:BTB504 3.6 0.6 1.0
C2 C:BTB504 3.6 0.3 1.0
C8 C:BTB504 3.6 0.7 1.0
C3 C:BTB504 3.6 99.3 1.0
C7 C:BTB504 3.8 0.3 1.0
C4 C:BTB504 3.8 0.4 1.0
OD2 C:ASP384 3.9 75.8 1.0
OD1 C:ASP384 4.5 75.7 1.0
CG C:ASP384 4.6 73.2 1.0

Gadolinium binding site 4 out of 4 in 5uob

Go back to Gadolinium Binding Sites List in 5uob
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile


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 (R)-3-[(2-Amino-4-Methylquinolin-7-Yl)Methoxy]-5-(2- (Methylamino)Propyl)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd508

b:59.5
occ:1.00
OE1 D:GLU321 2.7 64.8 1.0
O4 D:BTB504 2.7 90.2 1.0
O D:THR319 2.7 73.7 1.0
N D:BTB504 2.9 81.3 1.0
O3 D:BTB504 2.9 78.7 1.0
O6 D:BTB504 3.0 95.9 1.0
O8 D:BTB504 3.1 53.8 1.0
C8 D:BTB504 3.3 58.6 1.0
C7 D:BTB504 3.3 67.1 1.0
CD D:GLU321 3.5 66.1 1.0
OE2 D:GLU321 3.5 68.5 1.0
C D:THR319 3.6 66.0 1.0
C4 D:BTB504 3.6 90.5 1.0
C2 D:BTB504 3.6 88.1 1.0
C6 D:BTB504 3.7 92.8 1.0
C3 D:BTB504 3.8 84.5 1.0
C5 D:BTB504 3.8 88.9 1.0
CA D:THR319 4.3 57.1 1.0
N D:LEU320 4.4 68.2 1.0
CA D:LEU320 4.5 58.4 1.0
CB D:THR319 4.6 51.3 1.0
N D:GLU321 4.6 55.8 1.0
CG D:GLU321 4.9 60.4 1.0

Reference:

M.A.Cinelli, H.Li, G.Chreifi, T.L.Poulos, R.B.Silverman. Nitrile in the Hole: Discovery of A Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors. J. Med. Chem. V. 60 3958 2017.
ISSN: ISSN 1520-4804
PubMed: 28422508
DOI: 10.1021/ACS.JMEDCHEM.7B00259
Page generated: Sun Dec 13 19:00:12 2020

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