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Gadolinium in PDB 5vvc: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile, PDB code: 5vvc 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) 88.56 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.330, 152.620, 108.740, 90.00, 90.57, 90.00
R / Rfree (%) 20.6 / 27.2

Other elements in 5vvc:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile also contains other interesting chemical elements:

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 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile (pdb code 5vvc). 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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile, PDB code: 5vvc:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 5vvc

Go back to Gadolinium Binding Sites List in 5vvc
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile


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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd510

b:0.9
occ:1.00
 O3 A:BTB504 2.7 92.4 1.0
O A:HOH615 2.7 47.8 1.0
O4 A:BTB504 2.8 91.2 1.0
O A:HOH643 2.8 98.5 1.0
O A:HOH674 2.8 91.0 1.0
N A:BTB504 3.0 93.4 1.0
O8 A:BTB504 3.1 95.4 1.0
C2 A:BTB504 3.4 93.2 1.0
C3 A:BTB504 3.5 93.7 1.0
C4 A:BTB504 3.5 92.2 1.0
C8 A:BTB504 3.6 94.8 1.0
O6 A:BTB504 3.8 89.5 1.0
C7 A:BTB504 3.8 94.0 1.0
C5 A:BTB504 3.9 92.8 1.0
C6 A:BTB504 4.4 91.0 1.0
OD2 A:ASP384 4.5 82.0 1.0
OD1 A:ASP384 4.5 86.1 1.0
O A:HOH659 4.6 49.7 1.0
C1 A:BTB504 4.9 94.1 1.0
CG A:ASP384 4.9 80.5 1.0

Gadolinium binding site 2 out of 4 in 5vvc

Go back to Gadolinium Binding Sites List in 5vvc
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile


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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd507

b:55.4
occ:1.00
 O C:HOH602 2.5 34.2 1.0
O3 B:BTB504 2.6 55.8 1.0
O B:HOH664 2.6 57.2 1.0
O6 B:BTB504 2.7 62.3 1.0
O4 B:BTB504 2.7 59.9 1.0
O B:THR319 2.7 70.7 1.0
OE1 B:GLU321 2.8 54.9 1.0
N B:BTB504 2.8 54.4 1.0
O8 B:BTB504 2.9 34.0 1.0
C8 B:BTB504 3.1 32.3 1.0
C6 B:BTB504 3.3 58.5 1.0
C7 B:BTB504 3.5 41.8 1.0
C2 B:BTB504 3.5 63.9 1.0
C5 B:BTB504 3.6 56.2 1.0
C3 B:BTB504 3.6 61.7 1.0
C4 B:BTB504 3.6 64.3 1.0
C B:THR319 3.7 61.1 1.0
CD B:GLU321 3.8 55.9 1.0
OE2 B:GLU321 4.0 55.3 1.0
CA B:THR319 4.4 56.2 1.0
OD1 C:ASP378 4.5 44.1 1.0
N B:LEU320 4.5 60.1 1.0
CA B:LEU320 4.6 53.9 1.0
CB B:THR319 4.6 47.7 1.0
OD2 C:ASP378 4.6 57.2 1.0
N B:GLU321 4.7 51.2 1.0
C1 B:BTB504 5.0 68.0 1.0

Gadolinium binding site 3 out of 4 in 5vvc

Go back to Gadolinium Binding Sites List in 5vvc
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile


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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd510

b:0.5
occ:1.00
 O3 B:BTB508 2.6 47.8 1.0
N B:BTB508 2.9 80.1 1.0
O4 B:BTB508 3.1 64.8 1.0
O8 B:BTB508 3.3 76.1 1.0
C6 B:BTB508 3.4 83.5 1.0
O6 B:BTB508 3.4 83.5 1.0
C5 B:BTB508 3.5 82.4 1.0
C8 B:BTB508 3.5 78.0 1.0
C3 B:BTB508 3.6 60.6 1.0
C2 B:BTB508 3.6 71.7 1.0
OD2 C:ASP384 3.7 78.9 1.0
C7 B:BTB508 3.8 80.2 1.0
C4 B:BTB508 3.9 67.5 1.0
OD1 C:ASP384 4.5 82.0 1.0
CG C:ASP384 4.5 77.2 1.0

Gadolinium binding site 4 out of 4 in 5vvc

Go back to Gadolinium Binding Sites List in 5vvc
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 4-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile


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-(2-(((2-Amino-4-Methylquinolin-7-Yl)Methyl)Amino) Ethyl)-2-Methylbenzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd506

b:53.5
occ:1.00
 O D:HOH606 2.5 30.3 1.0
O4 D:BTB504 2.6 60.5 1.0
OE1 D:GLU321 2.7 60.7 1.0
O6 D:BTB504 2.7 71.6 1.0
O D:HOH616 2.7 43.0 1.0
O3 D:BTB504 2.7 65.6 1.0
O D:THR319 2.8 43.6 1.0
O8 D:BTB504 2.8 50.7 1.0
N D:BTB504 2.9 71.0 1.0
C8 D:BTB504 3.2 51.9 1.0
C7 D:BTB504 3.3 58.6 1.0
OE2 D:GLU321 3.3 55.5 1.0
CD D:GLU321 3.4 56.6 1.0
C4 D:BTB504 3.4 67.5 1.0
C2 D:BTB504 3.5 72.5 1.0
C D:THR319 3.6 47.0 1.0
C3 D:BTB504 3.7 69.4 1.0
C6 D:BTB504 3.7 73.9 1.0
C5 D:BTB504 3.9 74.1 1.0
CA D:THR319 4.4 44.6 1.0
CB D:THR319 4.4 44.7 1.0
N D:LEU320 4.5 50.1 1.0
CA D:LEU320 4.6 48.2 1.0
N D:GLU321 4.7 47.0 1.0
CG D:GLU321 4.8 51.0 1.0
O D:HOH706 5.0 49.6 1.0
C1 D:BTB504 5.0 74.9 1.0

Reference:

A.V.Pensa, M.A.Cinelli, H.Li, G.Chreifi, P.Mukherjee, L.J.Roman, P.Martasek, T.L.Poulos, R.B.Silverman. Hydrophilic, Potent, and Selective 7-Substituted 2-Aminoquinolines As Improved Human Neuronal Nitric Oxide Synthase Inhibitors. J. Med. Chem. V. 60 7146 2017.
ISSN: ISSN 1520-4804
PubMed: 28776992
DOI: 10.1021/ACS.JMEDCHEM.7B00835
Page generated: Sat Aug 10 21:53:16 2024

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