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Zinc in PDB 6nh3: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3 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) 88.87 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.469, 153.089, 109.150, 90.00, 90.80, 90.00
R / Rfree (%) 20.6 / 25.7

Other elements in 6nh3:

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

Fluorine (F) 8 atoms
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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine (pdb code 6nh3). 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 (S)-6-(3-Fluoro-5-(2-(Pyrrolidin-2-Yl)Ethyl)Phenethyl)- 4-Methylpyridin-2-Amine, PDB code: 6nh3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6nh3

Go back to Zinc Binding Sites List in 6nh3
Zinc binding site 1 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-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:42.1
occ:1.00
 SG A:CYS99 2.3 38.8 1.0
SG A:CYS94 2.3 43.2 1.0
SG B:CYS99 2.4 38.8 1.0
SG B:CYS94 2.4 37.7 1.0
CB B:CYS99 3.2 34.4 1.0
CB A:CYS99 3.3 33.0 1.0
CB A:CYS94 3.3 43.1 1.0
CB B:CYS94 3.4 42.1 1.0
CA B:CYS99 3.6 35.9 1.0
CA A:CYS99 3.7 40.6 1.0
N B:GLY101 4.1 35.1 1.0
N B:LEU100 4.1 32.9 1.0
N A:LEU100 4.2 49.8 1.0
N A:GLY101 4.2 44.5 1.0
C B:CYS99 4.3 41.1 1.0
C A:CYS99 4.3 46.5 1.0
CA B:GLY101 4.5 37.9 1.0
CA A:GLY101 4.5 46.1 1.0
CA A:CYS94 4.7 47.3 1.0
CA B:CYS94 4.8 49.4 1.0
N B:CYS99 4.9 34.7 1.0
C A:LEU100 5.0 44.9 1.0
N A:CYS99 5.0 34.8 1.0

Zinc binding site 2 out of 6 in 6nh3

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Zinc binding site 2 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-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:Zn508

b:42.8
occ:0.68
 OD2 A:ASP369 2.0 45.8 1.0
O A:HOH677 2.0 30.2 1.0
O A:HOH673 2.1 28.1 1.0
NE2 B:HIS461 2.2 44.3 1.0
OD1 A:ASP369 2.3 42.4 1.0
CG A:ASP369 2.5 42.4 1.0
CD2 B:HIS461 3.1 41.6 1.0
CE1 B:HIS461 3.3 41.2 1.0
CG A:ARG365 3.9 52.9 1.0
CB A:ASP369 4.0 42.2 1.0
O A:HOH654 4.2 42.3 1.0
CB A:ARG365 4.3 37.2 1.0
CG B:HIS461 4.3 36.0 1.0
ND1 B:HIS461 4.3 37.3 1.0
CD A:ARG365 4.4 61.9 1.0
CE1 A:HIS371 4.4 45.9 1.0
CE2 B:PHE460 4.4 40.4 1.0
CA A:ARG365 4.5 33.3 1.0
O A:HOH631 4.5 39.2 1.0
CB B:SER455 4.6 37.6 1.0
CD2 B:PHE460 4.6 34.2 1.0
O A:HOH686 4.6 34.8 1.0
NE2 A:HIS371 4.9 49.3 1.0
CA A:ASP369 5.0 39.5 1.0

Zinc binding site 3 out of 6 in 6nh3

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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 (S)-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 (S)-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:37.3
occ:0.79
 OD2 B:ASP369 2.0 32.4 1.0
NE2 A:HIS461 2.2 44.6 1.0
O B:HOH1040 2.2 22.0 1.0
OD1 B:ASP369 2.3 35.7 1.0
O B:HOH1042 2.4 22.6 1.0
CG B:ASP369 2.5 35.3 1.0
CD2 A:HIS461 3.1 45.2 1.0
CE1 A:HIS461 3.2 40.1 1.0
O B:HOH923 3.8 35.2 1.0
CG B:ARG365 4.0 34.7 1.0
CB B:ASP369 4.0 30.1 1.0
ND1 A:HIS461 4.3 41.5 1.0
CG A:HIS461 4.3 40.3 1.0
CE1 B:HIS371 4.3 41.2 1.0
CE2 A:PHE460 4.3 32.6 1.0
CB B:ARG365 4.4 29.8 1.0
CA B:ARG365 4.4 25.9 1.0
O B:HOH1044 4.5 41.5 1.0
CD B:ARG365 4.6 34.6 1.0
O B:HOH984 4.6 36.0 1.0
CD2 A:PHE460 4.6 31.3 1.0
CB A:SER455 4.6 30.2 1.0
NE2 B:HIS371 4.7 41.3 1.0
O B:ARG365 5.0 28.3 1.0
CA B:ASP369 5.0 31.6 1.0

Zinc binding site 4 out of 6 in 6nh3

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Zinc binding site 4 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-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:Zn506

b:36.0
occ:1.00
 SG C:CYS94 2.2 34.2 1.0
SG C:CYS99 2.4 40.5 1.0
SG D:CYS99 2.5 33.8 1.0
SG D:CYS94 2.5 33.3 1.0
CB C:CYS99 2.5 42.0 1.0
CB D:CYS99 3.2 30.1 1.0
CB C:CYS94 3.3 35.0 1.0
CB D:CYS94 3.3 30.4 1.0
CA C:CYS99 3.5 43.1 1.0
CA D:CYS99 3.7 37.2 1.0
N C:GLY101 4.0 37.3 1.0
C C:CYS99 4.1 44.6 1.0
N D:GLY101 4.1 38.1 1.0
N C:LEU100 4.1 45.8 1.0
N D:LEU100 4.2 36.5 1.0
C D:CYS99 4.3 41.9 1.0
CA C:GLY101 4.3 40.3 1.0
CA D:GLY101 4.4 34.8 1.0
CA C:CYS94 4.6 38.9 1.0
N C:CYS99 4.7 31.8 1.0
CA D:CYS94 4.8 41.3 1.0
C C:LEU100 4.9 35.3 1.0
N D:CYS99 5.0 37.2 1.0

Zinc binding site 5 out of 6 in 6nh3

Go back to Zinc Binding Sites List in 6nh3
Zinc binding site 5 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-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:Zn510

b:35.7
occ:0.57
 O C:HOH694 2.0 25.0 1.0
OD2 C:ASP369 2.1 43.5 1.0
NE2 D:HIS461 2.2 37.5 1.0
O C:HOH692 2.2 25.4 1.0
OD1 C:ASP369 2.3 36.8 1.0
CG C:ASP369 2.6 42.2 1.0
CD2 D:HIS461 3.1 38.4 1.0
CE1 D:HIS461 3.2 32.1 1.0
CG C:ARG365 3.8 55.3 1.0
O C:HOH633 3.9 40.0 1.0
CB C:ASP369 4.1 40.7 1.0
CG D:HIS461 4.3 35.2 1.0
CE2 D:PHE460 4.3 29.7 1.0
ND1 D:HIS461 4.3 39.6 1.0
CB C:ARG365 4.3 32.7 1.0
CE1 C:HIS371 4.4 42.4 1.0
CD C:ARG365 4.4 66.5 1.0
CA C:ARG365 4.5 32.6 1.0
CD2 D:PHE460 4.5 26.4 1.0
NE2 C:HIS371 4.6 41.1 1.0
O C:HOH641 4.6 34.7 1.0
CB D:SER455 4.6 35.9 1.0

Zinc binding site 6 out of 6 in 6nh3

Go back to Zinc Binding Sites List in 6nh3
Zinc binding site 6 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with (S)-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 (S)-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:Zn512

b:41.9
occ:0.87
 OD2 D:ASP369 2.0 35.1 1.0
NE2 C:HIS461 2.1 47.2 1.0
O D:HOH754 2.2 23.6 1.0
OD1 D:ASP369 2.3 40.9 1.0
O D:HOH762 2.4 24.6 1.0
CG D:ASP369 2.5 31.7 1.0
CE1 C:HIS461 3.0 44.5 1.0
CD2 C:HIS461 3.2 47.1 1.0
CG D:ARG365 4.0 38.2 1.0
CB D:ASP369 4.0 28.4 1.0
O D:HOH703 4.1 46.2 1.0
ND1 C:HIS461 4.2 45.4 1.0
CE1 D:HIS371 4.3 49.3 1.0
CE1 C:PHE460 4.3 24.8 1.0
CG C:HIS461 4.3 43.6 1.0
O D:HOH722 4.4 51.2 1.0
CB D:ARG365 4.5 31.4 1.0
CA D:ARG365 4.5 32.4 1.0
O C:HOH699 4.5 53.9 1.0
CD1 C:PHE460 4.6 24.7 1.0
NE2 D:HIS371 4.6 49.1 1.0
O D:HOH773 4.6 33.6 1.0
CD D:ARG365 4.6 37.6 1.0
CB C:SER455 4.6 41.1 1.0
O D:HOH712 4.7 33.3 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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