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Gadolinium in PDB 6av6: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-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-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine, PDB code: 6av6 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) 39.13 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.643, 152.780, 108.882, 90.00, 90.78, 90.00
R / Rfree (%) 19.4 / 23.9

Other elements in 6av6:

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

Fluorine (F) 4 atoms
Zinc (Zn) 2 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 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine (pdb code 6av6). 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-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine, PDB code: 6av6:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 6av6

Go back to Gadolinium Binding Sites List in 6av6
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-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-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd508

b:0.8
occ:1.00
O3 A:BTB503 2.7 0.4 1.0
O8 A:BTB503 2.7 0.2 1.0
O4 A:BTB503 2.7 62.9 1.0
O A:HOH644 2.8 0.1 1.0
O6 A:BTB503 2.8 94.0 1.0
N A:BTB503 2.9 91.5 1.0
C3 A:BTB503 2.9 99.3 1.0
O A:HOH601 2.9 56.9 1.0
C2 A:BTB503 3.2 89.5 1.0
C4 A:BTB503 3.5 68.9 1.0
C5 A:BTB503 3.6 87.6 1.0
C6 A:BTB503 3.7 87.0 1.0
C8 A:BTB503 3.9 97.9 1.0
C7 A:BTB503 4.0 92.8 1.0
OD1 A:ASP384 4.6 80.5 1.0
OD2 A:ASP384 4.7 89.8 1.0
C1 A:BTB503 4.7 90.4 1.0

Gadolinium binding site 2 out of 4 in 6av6

Go back to Gadolinium Binding Sites List in 6av6
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-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-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:53.2
occ:1.00
O B:HOH674 2.6 63.0 1.0
O B:THR319 2.6 58.2 1.0
O3 B:BTB505 2.6 66.8 1.0
O4 B:BTB505 2.7 67.7 1.0
OE1 B:GLU321 2.7 67.2 1.0
O6 B:BTB505 2.7 72.6 1.0
N B:BTB505 2.7 55.5 1.0
O C:HOH603 2.8 44.5 1.0
O8 B:BTB505 2.8 64.6 1.0
C8 B:BTB505 2.8 40.3 1.0
C7 B:BTB505 3.3 46.9 1.0
C6 B:BTB505 3.4 64.6 1.0
C2 B:BTB505 3.4 72.5 1.0
C4 B:BTB505 3.5 73.1 1.0
C3 B:BTB505 3.6 71.6 1.0
CD B:GLU321 3.6 64.3 1.0
C5 B:BTB505 3.6 56.9 1.0
C B:THR319 3.7 62.2 1.0
OE2 B:GLU321 3.7 62.1 1.0
CA B:THR319 4.3 47.7 1.0
CB B:THR319 4.6 45.0 1.0
OD1 C:ASP378 4.6 70.7 1.0
N B:LEU320 4.6 56.4 1.0
CA B:LEU320 4.7 43.7 1.0
N B:GLU321 4.7 42.5 1.0
OD2 C:ASP378 4.7 63.6 1.0
C1 B:BTB505 4.9 87.0 1.0

Gadolinium binding site 3 out of 4 in 6av6

Go back to Gadolinium Binding Sites List in 6av6
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-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-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd508

b:0.7
occ:1.00
O3 B:BTB509 2.6 35.2 1.0
O B:HOH678 2.7 96.9 1.0
O6 B:BTB509 2.8 0.7 1.0
O B:HOH707 2.8 81.3 1.0
O4 B:BTB509 2.8 83.1 1.0
N B:BTB509 2.9 93.1 1.0
C6 B:BTB509 3.1 98.3 1.0
O8 B:BTB509 3.2 78.7 1.0
C3 B:BTB509 3.5 53.9 1.0
C8 B:BTB509 3.6 85.8 1.0
C2 B:BTB509 3.6 79.9 1.0
C5 B:BTB509 3.6 96.3 1.0
C4 B:BTB509 3.8 75.6 1.0
C7 B:BTB509 3.8 91.3 1.0
OD1 C:ASP384 4.2 85.3 1.0
OD2 C:ASP384 4.5 96.9 1.0
OD1 B:ASP378 4.8 0.1 1.0
CG C:ASP384 4.8 77.9 1.0

Gadolinium binding site 4 out of 4 in 6av6

Go back to Gadolinium Binding Sites List in 6av6
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-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-(3-Fluoro-5-(3-(Methylamino)Propyl)Phenethyl)-4- Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd506

b:57.8
occ:1.00
OE1 D:GLU321 2.6 80.4 1.0
O D:THR319 2.6 34.9 1.0
OE2 D:GLU321 2.6 82.8 1.0
O4 D:BTB504 2.7 66.8 1.0
O3 D:BTB504 2.7 69.7 1.0
C8 D:BTB504 2.8 42.0 1.0
O8 D:BTB504 2.8 44.8 1.0
CD D:GLU321 2.8 78.1 1.0
C7 D:BTB504 3.0 53.4 1.0
N D:BTB504 3.0 74.7 1.0
O6 D:BTB504 3.4 60.3 1.0
C4 D:BTB504 3.6 72.0 1.0
C2 D:BTB504 3.7 82.1 1.0
C D:THR319 3.7 71.6 1.0
C3 D:BTB504 3.8 74.6 1.0
C5 D:BTB504 4.2 76.3 1.0
CG D:GLU321 4.2 49.1 1.0
C6 D:BTB504 4.3 69.6 1.0
CA D:THR319 4.5 55.8 1.0
N D:GLU321 4.6 48.9 1.0
CB D:THR319 4.6 58.0 1.0
N D:LEU320 4.7 58.5 1.0
CA D:LEU320 4.8 51.3 1.0

Reference:

H.T.Do, H.Y.Wang, H.Li, G.Chreifi, T.L.Poulos, R.B.Silverman. Improvement of Cell Permeability of Human Neuronal Nitric Oxide Synthase Inhibitors Using Potent and Selective 2-Aminopyridine-Based Scaffolds with A Fluorobenzene Linker. J. Med. Chem. V. 60 9360 2017.
ISSN: ISSN 1520-4804
PubMed: 29091437
DOI: 10.1021/ACS.JMEDCHEM.7B01356
Page generated: Sun Dec 13 19:00:22 2020

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