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Gadolinium in PDB 7tsk: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine, PDB code: 7tsk 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) 36.40 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.745, 154.022, 109.19, 90, 90.49, 90
R / Rfree (%) 20.7 / 26.4

Other elements in 7tsk:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine (pdb code 7tsk). 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 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine, PDB code: 7tsk:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 7tsk

Go back to Gadolinium Binding Sites List in 7tsk
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-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 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:110.8
occ:0.91
 O4 A:BTB504 2.7 77.5 1.0
N A:BTB504 2.7 83.3 1.0
O A:HOH602 2.7 49.1 1.0
O3 A:BTB504 2.8 54.2 1.0
O8 A:BTB504 2.8 84.6 1.0
O A:HOH671 2.8 63.7 1.0
O6 A:BTB504 3.0 87.0 1.0
C2 A:BTB504 3.2 83.9 1.0
C3 A:BTB504 3.4 69.5 1.0
C4 A:BTB504 3.4 83.5 1.0
C8 A:BTB504 3.4 78.8 1.0
C6 A:BTB504 3.4 85.2 1.0
C5 A:BTB504 3.5 81.2 1.0
C7 A:BTB504 3.6 79.8 1.0
OD2 A:ASP384 4.0 75.7 1.0
OD1 A:ASP384 4.7 75.2 1.0
C1 A:BTB504 4.7 88.7 1.0
CG A:ASP384 4.8 72.1 1.0

Gadolinium binding site 2 out of 4 in 7tsk

Go back to Gadolinium Binding Sites List in 7tsk
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-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 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:48.3
occ:1.00
 O3 B:BTB504 2.5 39.9 1.0
O B:THR319 2.5 57.1 1.0
O8 B:BTB504 2.6 48.1 1.0
O4 B:BTB504 2.7 45.9 1.0
O C:HOH611 2.7 39.0 1.0
N B:BTB504 2.7 36.1 1.0
OE1 B:GLU321 2.7 56.9 1.0
O B:HOH700 2.7 80.2 1.0
O6 B:BTB504 2.9 46.7 1.0
C6 B:BTB504 3.1 31.1 1.0
C8 B:BTB504 3.2 41.6 1.0
C3 B:BTB504 3.3 52.6 1.0
C2 B:BTB504 3.3 53.2 1.0
C5 B:BTB504 3.4 28.6 1.0
C4 B:BTB504 3.5 56.6 1.0
C7 B:BTB504 3.5 34.8 1.0
CD B:GLU321 3.7 58.5 1.0
C B:THR319 3.7 58.6 1.0
OE2 B:GLU321 3.9 59.8 1.0
CA B:THR319 4.5 52.8 1.0
N B:GLU321 4.6 49.3 1.0
OD1 C:ASP378 4.6 52.6 1.0
CA B:LEU320 4.6 51.3 1.0
CB B:THR319 4.7 44.4 1.0
N B:LEU320 4.7 57.4 1.0
OD2 C:ASP378 4.7 49.4 1.0
C1 B:BTB504 4.8 62.4 1.0

Gadolinium binding site 3 out of 4 in 7tsk

Go back to Gadolinium Binding Sites List in 7tsk
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-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 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd509

b:76.5
occ:0.72
 O3 C:BTB504 2.4 29.2 1.0
O4 C:BTB504 2.7 66.7 1.0
O6 C:BTB504 2.7 81.6 1.0
O8 C:BTB504 2.8 64.7 1.0
O C:HOH716 2.8 80.5 1.0
O C:HOH704 2.8 54.4 1.0
N C:BTB504 2.8 71.6 1.0
C2 C:BTB504 3.2 66.2 1.0
C4 C:BTB504 3.2 67.3 1.0
C3 C:BTB504 3.2 43.9 1.0
C6 C:BTB504 3.6 71.4 1.0
C5 C:BTB504 3.7 65.5 1.0
C7 C:BTB504 3.8 71.1 1.0
C8 C:BTB504 3.8 68.7 1.0
OD2 C:ASP384 4.0 86.2 1.0
O C:HOH664 4.4 65.2 1.0
C1 C:BTB504 4.7 68.4 1.0
OD1 C:ASP384 4.8 85.6 1.0
CG C:ASP384 4.8 78.8 1.0

Gadolinium binding site 4 out of 4 in 7tsk

Go back to Gadolinium Binding Sites List in 7tsk
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-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 4-Methyl-6-(3-(Methylamino)Prop-1-Yn-1-Yl)Pyridin-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd508

b:51.9
occ:1.00
 O4 D:BTB504 2.5 53.5 1.0
O3 D:BTB504 2.6 44.8 1.0
O D:THR319 2.6 47.4 1.0
OE1 D:GLU321 2.6 60.0 1.0
O D:HOH753 2.7 65.6 1.0
O8 D:BTB504 2.7 59.8 1.0
N D:BTB504 2.7 58.7 1.0
O6 D:BTB504 3.0 44.5 1.0
C6 D:BTB504 3.2 43.2 1.0
C8 D:BTB504 3.2 56.5 1.0
OE2 D:GLU321 3.3 62.5 1.0
CD D:GLU321 3.3 54.5 1.0
C2 D:BTB504 3.4 67.3 1.0
C3 D:BTB504 3.4 57.9 1.0
C7 D:BTB504 3.5 56.2 1.0
C5 D:BTB504 3.5 50.8 1.0
C4 D:BTB504 3.5 65.5 1.0
C D:THR319 3.7 59.6 1.0
CA D:THR319 4.4 52.8 1.0
O D:HOH775 4.4 53.0 1.0
CB D:THR319 4.4 46.1 1.0
N D:GLU321 4.6 43.3 1.0
N D:LEU320 4.7 59.1 1.0
CG D:GLU321 4.8 49.4 1.0
CA D:LEU320 4.8 52.4 1.0
C1 D:BTB504 4.8 70.8 1.0

Reference:

D.Vasu, H.Li, C.D.Hardy, T.L.Poulos, R.B.Silverman. 2-Aminopyridines with A Shortened Amino Sidechain As Potent, Selective, and Highly Permeable Human Neuronal Nitric Oxide Synthase Inhibitors. Bioorg.Med.Chem. V. 69 16878 2022.
ISSN: ESSN 1464-3391
PubMed: 35772285
DOI: 10.1016/J.BMC.2022.116878
Page generated: Sat Aug 10 22:24:13 2024

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