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Zinc 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:

Iron (Fe) 4 atoms
Gadolinium (Gd) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5uob

Go back to Zinc Binding Sites List in 5uob
Zinc binding site 1 out of 6 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 Zinc with other atoms in the Zn 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:Zn506

b:55.0
occ:1.00
 SG B:CYS99 2.2 53.3 1.0
SG A:CYS99 2.4 46.6 1.0
SG B:CYS94 2.4 48.4 1.0
SG A:CYS94 2.5 55.2 1.0
CB B:CYS99 3.3 48.5 1.0
CB A:CYS99 3.3 47.2 1.0
CB B:CYS94 3.3 50.0 1.0
CB A:CYS94 3.5 52.2 1.0
CA A:CYS99 3.6 60.1 1.0
CA B:CYS99 3.7 52.9 1.0
N A:LEU100 3.8 56.7 1.0
C A:CYS99 4.2 61.3 1.0
N B:GLY101 4.2 61.0 1.0
N A:GLY101 4.3 55.4 1.0
N B:LEU100 4.3 58.0 1.0
C B:CYS99 4.4 54.5 1.0
CA B:GLY101 4.6 57.0 1.0
CA B:CYS94 4.7 59.9 1.0
CA A:GLY101 4.7 57.2 1.0
N A:CYS99 4.9 55.0 1.0
CA A:CYS94 4.9 56.3 1.0
CA A:LEU100 4.9 53.2 1.0
C A:LEU100 4.9 54.8 1.0
N B:CYS99 4.9 50.1 1.0

Zinc binding site 2 out of 6 in 5uob

Go back to Zinc Binding Sites List in 5uob
Zinc binding site 2 out of 6 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 Zinc with other atoms in the Zn 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
A:Zn507

b:53.4
occ:0.91
 OD2 A:ASP369 2.0 48.8 1.0
O A:HOH618 2.1 41.0 1.0
O A:HOH615 2.1 44.1 1.0
NE2 B:HIS461 2.2 58.4 1.0
CG A:ASP369 2.9 50.8 1.0
CE1 B:HIS461 3.1 52.1 1.0
OD1 A:ASP369 3.1 46.7 1.0
CD2 B:HIS461 3.2 55.6 1.0
CB A:ARG365 3.6 50.1 1.0
CE2 B:PHE460 4.2 41.2 1.0
ND1 B:HIS461 4.2 49.8 1.0
CA A:ARG365 4.2 49.5 1.0
CB A:ASP369 4.3 52.4 1.0
CG B:HIS461 4.3 53.0 1.0
CB B:SER455 4.5 50.6 1.0
CD A:ARG365 4.6 61.4 1.0
CD2 B:PHE460 4.6 41.0 1.0
CG A:ARG365 4.6 54.7 1.0
O13 A:M4R503 4.6 70.2 1.0
C22 A:M4R503 4.6 73.3 1.0

Zinc binding site 3 out of 6 in 5uob

Go back to Zinc Binding Sites List in 5uob
Zinc binding site 3 out of 6 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 Zinc with other atoms in the Zn 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
A:Zn511

b:64.0
occ:0.96
 OD2 B:ASP369 2.0 51.8 1.0
O B:HOH622 2.1 39.6 1.0
O A:HOH617 2.1 38.6 1.0
NE2 A:HIS461 2.2 53.4 1.0
CG B:ASP369 3.0 53.0 1.0
CE1 A:HIS461 3.1 52.3 1.0
CD2 A:HIS461 3.2 43.4 1.0
OD1 B:ASP369 3.2 63.9 1.0
CG B:ARG365 3.8 54.5 1.0
ND1 A:HIS461 4.2 50.0 1.0
CG A:HIS461 4.3 43.4 1.0
CE2 A:PHE460 4.3 37.9 1.0
CB B:ASP369 4.4 45.8 1.0
C22 B:M4R503 4.4 67.5 1.0
CB B:ARG365 4.5 49.1 1.0
CA B:ARG365 4.5 47.4 1.0
CD2 A:PHE460 4.7 40.5 1.0
CB A:SER455 4.8 57.0 1.0
C12 B:M4R503 4.8 56.2 1.0
C23 B:M4R503 5.0 68.2 1.0
C09 B:M4R503 5.0 53.1 1.0
C27 B:M4R503 5.0 65.7 1.0

Zinc binding site 4 out of 6 in 5uob

Go back to Zinc Binding Sites List in 5uob
Zinc binding site 4 out of 6 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 Zinc with other atoms in the Zn 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
C:Zn506

b:50.5
occ:1.00
 SG C:CYS94 2.4 48.5 1.0
SG D:CYS99 2.4 38.7 1.0
SG C:CYS99 2.4 48.9 1.0
SG D:CYS94 2.5 48.6 1.0
CB D:CYS99 3.1 39.8 1.0
CB D:CYS94 3.2 49.3 1.0
CB C:CYS94 3.2 50.5 1.0
CB C:CYS99 3.4 46.7 1.0
CA D:CYS99 3.6 47.8 1.0
CA C:CYS99 3.8 50.5 1.0
N D:LEU100 4.0 50.6 1.0
N C:LEU100 4.2 52.8 1.0
N C:GLY101 4.2 61.6 1.0
N D:GLY101 4.2 54.7 1.0
C D:CYS99 4.3 50.3 1.0
C C:CYS99 4.4 55.0 1.0
CA C:GLY101 4.4 60.4 1.0
CA C:CYS94 4.6 52.3 1.0
CA D:GLY101 4.6 53.1 1.0
CA D:CYS94 4.7 56.1 1.0
N D:CYS99 4.9 44.6 1.0
C C:LEU100 5.0 60.9 1.0

Zinc binding site 5 out of 6 in 5uob

Go back to Zinc Binding Sites List in 5uob
Zinc binding site 5 out of 6 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 Zinc with other atoms in the Zn binding site number 5 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:Zn507

b:57.7
occ:0.90
 OD2 C:ASP369 2.0 55.0 1.0
O C:HOH621 2.1 30.8 1.0
NE2 D:HIS461 2.1 53.4 1.0
O C:HOH620 2.2 39.4 1.0
OD1 C:ASP369 2.2 53.5 1.0
CG C:ASP369 2.5 54.5 1.0
CE1 D:HIS461 3.0 51.9 1.0
CD2 D:HIS461 3.2 56.0 1.0
CG C:ARG365 3.6 44.4 1.0
CB C:ASP369 4.0 51.8 1.0
ND1 D:HIS461 4.2 51.8 1.0
C22 C:M4R503 4.3 74.8 1.0
CG D:HIS461 4.3 53.3 1.0
CB C:ARG365 4.4 36.0 1.0
CA C:ARG365 4.5 43.0 1.0
CE2 D:PHE460 4.5 40.7 1.0
CD2 D:PHE460 4.7 38.9 1.0
CD C:ARG365 4.7 53.2 1.0
O13 C:M4R503 4.8 74.3 1.0
CB D:SER455 4.8 44.7 1.0
C21 C:M4R503 4.9 76.1 1.0
CA C:ASP369 4.9 54.9 1.0
C23 C:M4R503 5.0 74.8 1.0
C27 C:M4R503 5.0 73.7 1.0

Zinc binding site 6 out of 6 in 5uob

Go back to Zinc Binding Sites List in 5uob
Zinc binding site 6 out of 6 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 Zinc with other atoms in the Zn binding site number 6 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:Zn511

b:55.7
occ:0.81
 OD2 D:ASP369 2.1 55.4 1.0
NE2 C:HIS461 2.1 60.1 1.0
O C:HOH623 2.1 35.1 1.0
O D:HOH614 2.1 44.2 1.0
OD1 D:ASP369 2.3 45.8 1.0
CG D:ASP369 2.5 51.5 1.0
CE1 C:HIS461 3.0 55.9 1.0
CD2 C:HIS461 3.2 56.5 1.0
CG D:ARG365 3.7 56.5 1.0
CB D:ASP369 4.1 42.0 1.0
ND1 C:HIS461 4.2 53.3 1.0
CG C:HIS461 4.3 50.5 1.0
C22 D:M4R503 4.3 68.3 1.0
CE2 C:PHE460 4.4 40.9 1.0
CB D:ARG365 4.5 46.9 1.0
CA D:ARG365 4.6 49.7 1.0
O13 D:M4R503 4.6 60.3 1.0
CD2 C:PHE460 4.7 38.4 1.0
C21 D:M4R503 4.8 61.6 1.0
CD D:ARG365 4.9 65.1 1.0
CB C:SER455 4.9 46.6 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: Mon Oct 28 11:22:33 2024

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