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Iron in PDB 3dqt: Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine

Enzymatic activity of Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine

All present enzymatic activity of Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine, PDB code: 3dqt was solved by J.Igarashi, H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.78 / 2.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.250, 106.490, 156.420, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.8

Other elements in 3dqt:

The structure of Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine (pdb code 3dqt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine, PDB code: 3dqt:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3dqt

Go back to Iron Binding Sites List in 3dqt
Iron binding site 1 out of 2 in the Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:32.1
occ:1.00
 FE A:HEM700 0.0 32.1 1.0
NA A:HEM700 2.0 32.2 1.0
NB A:HEM700 2.0 30.4 1.0
NC A:HEM700 2.0 32.5 1.0
ND A:HEM700 2.0 29.0 1.0
SG A:CYS186 2.4 33.6 1.0
C1A A:HEM700 3.0 35.8 1.0
C1D A:HEM700 3.0 29.9 1.0
C1B A:HEM700 3.0 31.6 1.0
C4A A:HEM700 3.0 36.4 1.0
C4C A:HEM700 3.0 35.7 1.0
C4B A:HEM700 3.1 33.6 1.0
C4D A:HEM700 3.1 33.0 1.0
C1C A:HEM700 3.1 36.0 1.0
CB A:CYS186 3.3 39.4 1.0
CHD A:HEM700 3.4 32.9 1.0
CHB A:HEM700 3.4 32.6 1.0
CHA A:HEM700 3.4 33.7 1.0
CHC A:HEM700 3.5 36.8 1.0
C4 A:JI7800 4.0 36.1 1.0
CA A:CYS186 4.0 39.5 1.0
C5 A:JI7800 4.1 37.0 1.0
C3 A:JI7800 4.2 33.4 1.0
C2A A:HEM700 4.2 40.0 1.0
C2D A:HEM700 4.3 34.0 1.0
C2B A:HEM700 4.3 32.4 1.0
C3C A:HEM700 4.3 36.7 1.0
C3A A:HEM700 4.3 37.0 1.0
C3D A:HEM700 4.3 35.9 1.0
C3B A:HEM700 4.3 33.7 1.0
C2C A:HEM700 4.3 34.2 1.0
C6 A:JI7800 4.3 40.8 1.0
NE1 A:TRP180 4.5 27.7 1.0
C2 A:JI7800 4.5 41.5 1.0
C8 A:JI7800 4.5 30.0 1.0
N1 A:JI7800 4.5 40.8 1.0
C A:CYS186 4.8 40.8 1.0
N A:GLY188 4.9 31.9 1.0

Iron binding site 2 out of 2 in 3dqt

Go back to Iron Binding Sites List in 3dqt
Iron binding site 2 out of 2 in the Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Endothelial Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Trans-4'-[(6"-Amino-4"-Methylpyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}-N2-(3'-Chlorobenzyl)Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe700

b:36.4
occ:1.00
 FE B:HEM700 0.0 36.4 1.0
NB B:HEM700 2.0 30.8 1.0
ND B:HEM700 2.0 33.5 1.0
NC B:HEM700 2.0 29.2 1.0
NA B:HEM700 2.0 34.3 1.0
SG B:CYS186 2.3 38.5 1.0
C1B B:HEM700 3.0 33.9 1.0
C1D B:HEM700 3.0 35.5 1.0
C4C B:HEM700 3.0 30.1 1.0
C4B B:HEM700 3.1 34.7 1.0
C1C B:HEM700 3.1 29.9 1.0
C4A B:HEM700 3.1 34.9 1.0
C4D B:HEM700 3.1 37.2 1.0
C1A B:HEM700 3.1 37.6 1.0
CHD B:HEM700 3.4 33.0 1.0
CHB B:HEM700 3.4 37.0 1.0
CHC B:HEM700 3.4 30.4 1.0
CB B:CYS186 3.5 40.4 1.0
CHA B:HEM700 3.5 35.1 1.0
C4 B:JI7800 3.8 40.4 1.0
C3 B:JI7800 4.0 38.5 1.0
C5 B:JI7800 4.0 41.7 1.0
C8 B:JI7800 4.1 41.4 1.0
CA B:CYS186 4.2 40.5 1.0
C2B B:HEM700 4.2 33.6 1.0
C3C B:HEM700 4.3 32.0 1.0
C2D B:HEM700 4.3 35.8 1.0
C3B B:HEM700 4.3 34.0 1.0
C2C B:HEM700 4.3 31.9 1.0
C3D B:HEM700 4.3 37.4 1.0
C3A B:HEM700 4.3 36.7 1.0
C2A B:HEM700 4.4 38.9 1.0
NE1 B:TRP180 4.4 33.3 1.0
C2 B:JI7800 4.4 40.1 1.0
C6 B:JI7800 4.5 39.5 1.0
N1 B:JI7800 4.6 42.2 1.0
N B:GLY188 4.9 36.3 1.0
N B:VAL187 5.0 39.0 1.0
C B:CYS186 5.0 41.6 1.0

Reference:

J.Igarashi, H.Li, J.Jamal, H.Ji, J.Fang, G.R.Lawton, R.B.Silverman, T.L.Poulos. Crystal Structures of Constitutive Nitric Oxide Synthases in Complex with De Novo Designed Inhibitors. J.Med.Chem. V. 52 2060 2009.
ISSN: ISSN 0022-2623
PubMed: 19296678
DOI: 10.1021/JM900007A
Page generated: Sun Aug 4 09:09:44 2024

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