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

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)Benzonitrile

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)Benzonitrile:
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)Benzonitrile, PDB code: 5vvd 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) 39.12 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.335, 153.135, 109.241, 90.00, 90.78, 90.00
R / Rfree (%) 20.6 / 26.9

Other elements in 5vvd:

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)Benzonitrile also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Gadolinium (Gd) 4 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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)Benzonitrile (pdb code 5vvd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron 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)Benzonitrile, PDB code: 5vvd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5vvd

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Iron 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)Benzonitrile


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:65.9
occ:1.00
 FE A:HEM501 0.0 65.9 1.0
NA A:HEM501 2.1 79.3 1.0
NC A:HEM501 2.1 83.5 1.0
ND A:HEM501 2.1 73.0 1.0
NB A:HEM501 2.1 82.2 1.0
SG A:CYS184 2.4 54.4 1.0
C1B A:HEM501 3.0 78.1 1.0
C4A A:HEM501 3.0 78.4 1.0
C1D A:HEM501 3.1 80.5 1.0
C4C A:HEM501 3.1 82.5 1.0
C1A A:HEM501 3.1 73.7 1.0
CB A:CYS184 3.1 58.7 1.0
C4B A:HEM501 3.1 79.5 1.0
C4D A:HEM501 3.1 78.2 1.0
C1C A:HEM501 3.2 74.6 1.0
CHB A:HEM501 3.4 78.7 1.0
CHD A:HEM501 3.4 83.1 1.0
CHA A:HEM501 3.5 74.6 1.0
CHC A:HEM501 3.5 69.4 1.0
C04 A:9OG503 3.8 75.3 1.0
C03 A:9OG503 3.9 65.2 1.0
C11 A:9OG503 3.9 82.0 1.0
CA A:CYS184 3.9 56.1 1.0
C2B A:HEM501 4.2 73.0 1.0
C3A A:HEM501 4.3 72.4 1.0
C05 A:9OG503 4.3 73.7 1.0
C3B A:HEM501 4.3 77.8 1.0
C2A A:HEM501 4.3 75.0 1.0
C2D A:HEM501 4.3 75.9 1.0
C3C A:HEM501 4.3 91.3 1.0
NE1 A:TRP178 4.4 59.9 1.0
C3D A:HEM501 4.4 78.8 1.0
C2C A:HEM501 4.4 84.2 1.0
C02 A:9OG503 4.5 68.6 1.0
C A:CYS184 4.6 53.9 1.0
N A:VAL185 4.7 53.5 1.0
C10 A:9OG503 4.8 75.2 1.0
C06 A:9OG503 4.8 68.6 1.0
N A:GLY186 4.8 59.8 1.0
N01 A:9OG503 4.9 68.4 1.0

Iron binding site 2 out of 4 in 5vvd

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Iron 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)Benzonitrile


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:45.0
occ:1.00
 FE B:HEM501 0.0 45.0 1.0
NA B:HEM501 2.1 64.6 1.0
NB B:HEM501 2.1 54.4 1.0
NC B:HEM501 2.1 57.4 1.0
ND B:HEM501 2.1 54.6 1.0
SG B:CYS184 2.2 35.7 1.0
C4A B:HEM501 3.0 46.5 1.0
C1B B:HEM501 3.0 54.5 1.0
C4C B:HEM501 3.1 57.5 1.0
C1D B:HEM501 3.1 54.5 1.0
C1A B:HEM501 3.1 59.4 1.0
C4D B:HEM501 3.1 68.7 1.0
C4B B:HEM501 3.2 59.0 1.0
C1C B:HEM501 3.2 57.9 1.0
CB B:CYS184 3.3 49.4 1.0
CHB B:HEM501 3.3 49.3 1.0
CHD B:HEM501 3.4 57.3 1.0
CHA B:HEM501 3.5 61.2 1.0
CHC B:HEM501 3.5 59.5 1.0
C04 B:9OG503 3.6 70.4 1.0
C11 B:9OG503 3.6 72.8 1.0
C03 B:9OG503 4.0 60.9 1.0
C05 B:9OG503 4.1 73.8 1.0
CA B:CYS184 4.1 53.1 1.0
C3A B:HEM501 4.3 52.7 1.0
C2B B:HEM501 4.3 59.2 1.0
C2A B:HEM501 4.3 61.8 1.0
C3C B:HEM501 4.3 65.8 1.0
C2D B:HEM501 4.3 56.0 1.0
C3B B:HEM501 4.3 56.2 1.0
C2C B:HEM501 4.4 59.8 1.0
C3D B:HEM501 4.4 64.6 1.0
C06 B:9OG503 4.4 70.5 1.0
NE1 B:TRP178 4.5 47.1 1.0
C02 B:9OG503 4.7 57.3 1.0
C10 B:9OG503 4.7 64.4 1.0
N B:GLY186 4.9 48.9 1.0
C B:CYS184 4.9 48.3 1.0
N01 B:9OG503 5.0 54.5 1.0

Iron binding site 3 out of 4 in 5vvd

Go back to Iron Binding Sites List in 5vvd
Iron 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)Benzonitrile


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:53.2
occ:1.00
 FE C:HEM501 0.0 53.2 1.0
ND C:HEM501 2.0 72.1 1.0
NC C:HEM501 2.0 70.7 1.0
NA C:HEM501 2.0 66.1 1.0
NB C:HEM501 2.2 69.7 1.0
SG C:CYS184 2.3 48.9 1.0
C4C C:HEM501 3.0 71.3 1.0
C1D C:HEM501 3.0 72.2 1.0
C4D C:HEM501 3.0 62.2 1.0
C1A C:HEM501 3.0 61.3 1.0
C1C C:HEM501 3.1 71.4 1.0
C4A C:HEM501 3.1 62.7 1.0
CB C:CYS184 3.2 41.5 1.0
C1B C:HEM501 3.2 64.7 1.0
C4B C:HEM501 3.2 62.4 1.0
CHD C:HEM501 3.3 75.8 1.0
CHA C:HEM501 3.4 49.4 1.0
CHC C:HEM501 3.5 66.4 1.0
CHB C:HEM501 3.5 65.8 1.0
C04 C:9OG503 3.7 69.7 1.0
C11 C:9OG503 3.9 66.6 1.0
C03 C:9OG503 3.9 66.0 1.0
CA C:CYS184 4.0 36.2 1.0
C3D C:HEM501 4.2 61.8 1.0
C2D C:HEM501 4.2 60.5 1.0
C3C C:HEM501 4.2 73.4 1.0
C05 C:9OG503 4.2 71.4 1.0
C2A C:HEM501 4.3 63.6 1.0
C2C C:HEM501 4.3 76.1 1.0
C3A C:HEM501 4.3 59.3 1.0
NE1 C:TRP178 4.3 50.7 1.0
C2B C:HEM501 4.4 64.2 1.0
C3B C:HEM501 4.4 58.0 1.0
C02 C:9OG503 4.5 67.1 1.0
C06 C:9OG503 4.8 76.3 1.0
C C:CYS184 4.8 47.0 1.0
C10 C:9OG503 4.8 66.2 1.0
N C:GLY186 4.8 52.0 1.0
CD1 C:TRP178 4.9 47.8 1.0
N01 C:9OG503 4.9 68.7 1.0
N C:VAL185 4.9 45.5 1.0

Iron binding site 4 out of 4 in 5vvd

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Iron 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)Benzonitrile


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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)Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:39.9
occ:1.00
 FE D:HEM502 0.0 39.9 1.0
NA D:HEM502 2.0 63.6 1.0
ND D:HEM502 2.1 46.3 1.0
NB D:HEM502 2.1 51.7 1.0
NC D:HEM502 2.1 54.9 1.0
SG D:CYS184 2.3 31.7 1.0
C4A D:HEM502 3.0 61.1 1.0
C1B D:HEM502 3.0 54.2 1.0
C1D D:HEM502 3.0 52.0 1.0
C4C D:HEM502 3.1 44.5 1.0
C4D D:HEM502 3.1 57.8 1.0
C1A D:HEM502 3.1 58.1 1.0
C1C D:HEM502 3.2 54.2 1.0
C4B D:HEM502 3.2 50.4 1.0
CB D:CYS184 3.2 34.4 1.0
CHB D:HEM502 3.3 50.2 1.0
CHD D:HEM502 3.4 40.4 1.0
CHA D:HEM502 3.5 58.0 1.0
CHC D:HEM502 3.6 54.7 1.0
C04 D:9OG504 3.7 66.6 1.0
C11 D:9OG504 3.9 68.9 1.0
C03 D:9OG504 3.9 53.0 1.0
CA D:CYS184 4.1 41.9 1.0
C05 D:9OG504 4.1 70.4 1.0
C3A D:HEM502 4.2 68.5 1.0
C2D D:HEM502 4.3 49.7 1.0
C2B D:HEM502 4.3 55.2 1.0
C2A D:HEM502 4.3 66.1 1.0
C3D D:HEM502 4.3 45.6 1.0
C3C D:HEM502 4.3 58.2 1.0
C3B D:HEM502 4.4 55.4 1.0
C2C D:HEM502 4.4 50.9 1.0
NE1 D:TRP178 4.4 42.4 1.0
C02 D:9OG504 4.5 54.1 1.0
C06 D:9OG504 4.6 66.8 1.0
C10 D:9OG504 4.7 69.1 1.0
C D:CYS184 4.8 42.0 1.0
N D:VAL185 4.8 48.8 1.0
N01 D:9OG504 4.8 59.2 1.0
N D:GLY186 4.9 43.2 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: Tue Aug 6 11:01:49 2024

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