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Iron in PDB 4ups: Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide

Enzymatic activity of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide

All present enzymatic activity of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide:
1.14.13.39;

Protein crystallography data

The structure of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide, PDB code: 4ups 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) 39.33 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.776, 106.474, 157.187, 90.00, 90.00, 90.00
R / Rfree (%) 17.711 / 21.285

Other elements in 4ups:

The structure of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide (pdb code 4ups). 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 Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide, PDB code: 4ups:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4ups

Go back to Iron Binding Sites List in 4ups
Iron binding site 1 out of 2 in the Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:29.6
occ:1.00
 FE A:HEM500 0.0 29.6 1.0
ND A:HEM500 1.9 25.9 1.0
NA A:HEM500 2.0 29.0 1.0
NC A:HEM500 2.1 29.3 1.0
NB A:HEM500 2.1 26.8 1.0
SG A:CYS186 2.5 33.9 1.0
C1D A:HEM500 3.0 30.7 1.0
C4D A:HEM500 3.0 27.2 1.0
C4A A:HEM500 3.0 28.6 1.0
C1A A:HEM500 3.0 29.0 1.0
C4C A:HEM500 3.0 27.5 1.0
C4B A:HEM500 3.1 27.9 1.0
C1B A:HEM500 3.1 28.6 1.0
C1C A:HEM500 3.1 26.4 1.0
CHD A:HEM500 3.4 30.3 1.0
CHB A:HEM500 3.4 29.3 1.0
CHA A:HEM500 3.4 27.7 1.0
CB A:CYS186 3.5 29.1 1.0
CHC A:HEM500 3.5 28.3 1.0
S01 A:6E5800 3.8 36.2 1.0
C3A A:HEM500 4.2 27.9 1.0
C2A A:HEM500 4.2 28.6 1.0
CA A:CYS186 4.2 29.6 1.0
C2D A:HEM500 4.2 28.6 1.0
C3D A:HEM500 4.2 28.4 1.0
C12 A:6E5800 4.2 29.1 1.0
C3C A:HEM500 4.3 28.1 1.0
C2C A:HEM500 4.3 28.7 1.0
C2B A:HEM500 4.3 28.4 1.0
C3B A:HEM500 4.3 29.1 1.0
NE1 A:TRP180 4.4 30.5 1.0
C02 A:6E5800 4.6 31.4 1.0
C05 A:6E5800 4.6 30.7 1.0
N A:GLY188 4.8 30.5 1.0
C06 A:6E5800 4.8 31.5 1.0
CD1 A:TRP180 4.9 28.2 1.0
C13 A:6E5800 4.9 28.3 1.0
C A:CYS186 4.9 29.5 1.0

Iron binding site 2 out of 2 in 4ups

Go back to Iron Binding Sites List in 4ups
Iron binding site 2 out of 2 in the Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-Imino (Thiophen-2-Yl)Methyl]Amino}Benzyl)Oxy]Methyl}Pyrrolidin-3 -Yl]Oxy}Methyl)Phenyl]Thiophene-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:31.9
occ:1.00
 FE B:HEM500 0.0 31.9 1.0
ND B:HEM500 1.9 33.0 1.0
NA B:HEM500 2.0 33.4 1.0
NC B:HEM500 2.1 31.2 1.0
NB B:HEM500 2.1 31.8 1.0
SG B:CYS186 2.5 32.0 1.0
C4D B:HEM500 3.0 32.8 1.0
C1D B:HEM500 3.0 32.2 1.0
C1A B:HEM500 3.0 33.3 1.0
C4A B:HEM500 3.0 30.8 1.0
C4C B:HEM500 3.0 29.3 1.0
C1B B:HEM500 3.1 31.8 1.0
C4B B:HEM500 3.1 33.3 1.0
C1C B:HEM500 3.1 32.4 1.0
CHB B:HEM500 3.4 30.4 1.0
CHD B:HEM500 3.4 30.6 1.0
CHA B:HEM500 3.4 33.3 1.0
CHC B:HEM500 3.5 33.0 1.0
CB B:CYS186 3.5 31.7 1.0
S01 B:6E5800 3.9 37.5 1.0
C3A B:HEM500 4.2 31.4 1.0
CA B:CYS186 4.2 30.5 1.0
C2A B:HEM500 4.2 32.5 1.0
C3C B:HEM500 4.2 31.4 1.0
C12 B:6E5800 4.3 31.0 1.0
C2D B:HEM500 4.3 32.2 1.0
C2C B:HEM500 4.3 29.3 1.0
C3D B:HEM500 4.3 32.9 1.0
C2B B:HEM500 4.3 35.1 1.0
NE1 B:TRP180 4.3 33.1 1.0
C3B B:HEM500 4.4 35.2 1.0
C05 B:6E5800 4.6 33.3 1.0
C02 B:6E5800 4.7 34.5 1.0
N B:GLY188 4.8 30.8 1.0
C06 B:6E5800 4.8 30.0 1.0
CD1 B:TRP180 4.9 33.2 1.0
C B:CYS186 4.9 28.6 1.0
C13 B:6E5800 4.9 31.3 1.0
N B:VAL187 5.0 27.7 1.0

Reference:

Q.Jing, H.Li, L.J.Roman, P.Martasek, T.L.Poulos, R.B.Silverman. Combination of Chiral Linkers with Thiophenecarboximidamide Heads to Improve the Selectivity of Inhibitors of Neuronal Nitric Oxide Synthase. Bioorg.Med.Chem.Lett. V. 24 4504 2014.
ISSN: ISSN 0960-894X
PubMed: 25149509
DOI: 10.1016/J.BMCL.2014.07.079
Page generated: Mon Aug 5 13:33:36 2024

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