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Zinc in PDB 6nh2: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh2 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) 88.89 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.329, 153.769, 108.939, 90.00, 90.86, 90.00
R / Rfree (%) 17.3 / 22.2

Other elements in 6nh2:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Iron (Fe) 4 atoms
Gadolinium (Gd) 2 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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine (pdb code 6nh2). 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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6nh2

Go back to Zinc Binding Sites List in 6nh2
Zinc binding site 1 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine


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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:32.7
occ:1.00
 SG B:CYS94 2.4 33.1 1.0
SG A:CYS99 2.4 29.9 1.0
SG A:CYS94 2.4 33.9 1.0
SG B:CYS99 2.5 28.2 1.0
CB A:CYS99 3.2 23.0 1.0
CB B:CYS99 3.3 25.1 1.0
CB A:CYS94 3.3 32.6 1.0
CB B:CYS94 3.4 30.1 1.0
CA A:CYS99 3.7 32.2 1.0
CA B:CYS99 3.8 25.4 1.0
N A:GLY101 4.0 29.2 1.0
N A:LEU100 4.1 30.9 1.0
N B:GLY101 4.1 28.2 1.0
C A:CYS99 4.2 35.5 1.0
N B:LEU100 4.3 23.8 1.0
CA A:GLY101 4.3 26.7 1.0
C B:CYS99 4.4 30.4 1.0
CA B:GLY101 4.4 22.4 1.0
O B:HOH778 4.6 39.6 1.0
CA A:CYS94 4.7 37.5 1.0
CA B:CYS94 4.8 30.6 1.0
C A:LEU100 4.9 28.4 1.0
N A:CYS99 5.0 27.9 1.0

Zinc binding site 2 out of 6 in 6nh2

Go back to Zinc Binding Sites List in 6nh2
Zinc binding site 2 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine


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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:52.9
occ:0.64
 O A:HOH707 1.9 27.5 1.0
OD2 A:ASP369 2.0 50.5 1.0
OD1 A:ASP369 2.2 37.9 1.0
O A:HOH726 2.3 18.8 1.0
CG A:ASP369 2.5 38.9 1.0
NE2 B:HIS461 3.0 32.5 1.0
O A:HOH722 3.3 52.1 1.0
CD2 B:HIS461 3.5 35.4 1.0
O A:HOH615 3.7 33.6 1.0
CG A:ARG365 3.7 42.9 1.0
CB A:ASP369 4.0 30.3 1.0
CB A:ARG365 4.1 24.9 1.0
CA A:ARG365 4.2 19.0 1.0
CE1 B:HIS461 4.3 37.3 1.0
CE2 B:PHE460 4.3 22.2 1.0
CE1 A:HIS371 4.3 32.2 1.0
CD A:ARG365 4.3 51.8 1.0
O A:HOH730 4.5 49.3 1.0
CD2 B:PHE460 4.6 23.2 1.0
NE2 A:HIS371 4.6 32.5 1.0
CB B:SER455 4.7 26.4 1.0
O A:HOH699 4.7 26.9 1.0
O A:ARG365 4.7 20.3 1.0
CG B:HIS461 4.8 34.8 1.0
O4 A:H4B502 4.9 91.2 1.0
CA A:ASP369 4.9 26.2 1.0
C A:ARG365 4.9 29.4 1.0

Zinc binding site 3 out of 6 in 6nh2

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Zinc binding site 3 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine


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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:27.2
occ:0.72
 OD2 B:ASP369 2.0 37.7 1.0
NE2 A:HIS461 2.1 37.0 1.0
O B:HOH766 2.3 16.2 1.0
OD1 B:ASP369 2.3 38.1 1.0
O B:HOH755 2.3 11.7 1.0
CG B:ASP369 2.5 36.3 1.0
CE1 A:HIS461 3.1 32.6 1.0
CD2 A:HIS461 3.1 37.4 1.0
CG B:ARG365 3.9 29.1 1.0
O B:HOH679 4.0 33.6 1.0
CB B:ASP369 4.0 30.6 1.0
CE1 B:HIS371 4.1 38.9 1.0
ND1 A:HIS461 4.2 35.8 1.0
CG A:HIS461 4.3 29.6 1.0
O B:HOH661 4.3 42.8 1.0
NE2 B:HIS371 4.4 33.6 1.0
CE1 A:PHE460 4.5 21.9 1.0
CB B:ARG365 4.5 19.1 1.0
CA B:ARG365 4.6 24.1 1.0
CD1 A:PHE460 4.7 21.4 1.0
CB A:SER455 4.7 23.0 1.0
O B:HOH773 4.7 27.2 1.0
O A:HOH712 4.8 22.2 1.0
O B:ARG365 5.0 22.5 1.0

Zinc binding site 4 out of 6 in 6nh2

Go back to Zinc Binding Sites List in 6nh2
Zinc binding site 4 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine


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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn507

b:42.5
occ:0.61
 O C:HOH692 1.9 35.7 1.0
OD2 C:ASP369 2.1 36.5 1.0
O C:HOH718 2.2 20.5 1.0
O C:HOH724 2.5 43.3 1.0
CG C:ASP369 2.9 29.8 1.0
OD1 C:ASP369 3.0 28.4 1.0
CE1 D:HIS461 3.0 34.3 1.0
CG C:ARG365 3.4 45.4 1.0
ND1 D:HIS461 3.6 34.4 1.0
CD C:ARG365 3.9 58.7 1.0
O C:HOH700 3.9 37.0 1.0
CB C:ARG365 3.9 17.5 1.0
CE2 D:PHE460 4.0 27.2 1.0
NE2 D:HIS461 4.2 34.4 1.0
O C:HOH704 4.2 34.1 1.0
CA C:ARG365 4.3 25.4 1.0
CB C:ASP369 4.4 20.9 1.0
CD2 D:PHE460 4.5 22.1 1.0
O4 C:H4B503 4.5 80.9 1.0
CB D:SER455 4.7 29.2 1.0
CE1 C:HIS371 4.7 30.6 1.0
O C:HOH719 4.8 51.0 1.0
NE2 C:HIS371 4.9 32.0 1.0
C4 C:H4B503 4.9 77.9 1.0
O C:ARG365 5.0 27.7 1.0
CG D:HIS461 5.0 37.4 1.0
CZ D:PHE460 5.0 19.6 1.0

Zinc binding site 5 out of 6 in 6nh2

Go back to Zinc Binding Sites List in 6nh2
Zinc binding site 5 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine


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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn511

b:28.7
occ:0.81
 OD2 D:ASP369 2.1 38.9 1.0
NE2 C:HIS461 2.2 36.9 1.0
O D:HOH794 2.3 15.8 1.0
O D:HOH789 2.3 11.5 1.0
OD1 D:ASP369 2.3 35.8 1.0
CG D:ASP369 2.6 33.6 1.0
CE1 C:HIS461 3.1 30.6 1.0
CD2 C:HIS461 3.3 36.7 1.0
O D:HOH730 4.0 26.1 1.0
CG D:ARG365 4.0 19.1 1.0
CB D:ASP369 4.1 27.0 1.0
O D:HOH805 4.2 25.4 1.0
ND1 C:HIS461 4.2 33.6 1.0
O D:HOH677 4.3 38.1 1.0
CE1 D:HIS371 4.3 42.7 1.0
CG C:HIS461 4.4 34.0 1.0
CB D:ARG365 4.4 14.8 1.0
CA D:ARG365 4.4 16.1 1.0
CE1 C:PHE460 4.5 20.6 1.0
O D:HOH723 4.6 29.4 1.0
CB C:SER455 4.6 22.8 1.0
NE2 D:HIS371 4.7 42.4 1.0
CD1 C:PHE460 4.7 19.6 1.0

Zinc binding site 6 out of 6 in 6nh2

Go back to Zinc Binding Sites List in 6nh2
Zinc binding site 6 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (R)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine


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)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:27.1
occ:1.00
 SG D:CYS99 2.4 26.6 1.0
SG C:CYS99 2.4 26.2 1.0
SG D:CYS94 2.4 27.1 1.0
SG C:CYS94 2.4 28.5 1.0
CB C:CYS99 3.2 20.7 1.0
CB D:CYS99 3.3 22.0 1.0
CB D:CYS94 3.5 26.1 1.0
CB C:CYS94 3.6 30.2 1.0
CA C:CYS99 3.7 25.4 1.0
CA D:CYS99 3.8 22.9 1.0
N C:GLY101 3.9 27.0 1.0
N D:GLY101 4.0 21.4 1.0
N D:LEU100 4.1 26.6 1.0
N C:LEU100 4.1 30.8 1.0
C C:CYS99 4.3 29.8 1.0
CA D:GLY101 4.3 18.2 1.0
C D:CYS99 4.3 27.3 1.0
CA C:GLY101 4.3 22.0 1.0
CA D:CYS94 4.9 29.2 1.0
CA C:CYS94 4.9 28.4 1.0
C C:LEU100 4.9 30.1 1.0
C D:LEU100 4.9 27.2 1.0
N C:CYS99 5.0 20.9 1.0

Reference:

H.T.Do, H.Li, G.Chreifi, T.L.Poulos, R.B.Silverman. Optimization of Blood-Brain Barrier Permeability with Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibitors Having A 2-Aminopyridine Scaffold. J. Med. Chem. V. 62 2690 2019.
ISSN: ISSN 1520-4804
PubMed: 30802056
DOI: 10.1021/ACS.JMEDCHEM.8B02032
Page generated: Tue Oct 29 03:48:15 2024

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