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Iron in PDB 4upo: Structure of Rat Neuronal 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 Rat Neuronal 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 Rat Neuronal 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 Rat Neuronal 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: 4upo 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) 38.03 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.157, 110.973, 164.735, 90.00, 90.00, 90.00
R / Rfree (%) 18.403 / 22.41

Other elements in 4upo:

The structure of Structure of Rat Neuronal 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:

Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Rat Neuronal 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 4upo). 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 Rat Neuronal 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: 4upo:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4upo

Go back to Iron Binding Sites List in 4upo
Iron binding site 1 out of 2 in the Structure of Rat Neuronal 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 Rat Neuronal 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:Fe750

b:30.2
occ:1.00
 FE A:HEM750 0.0 30.2 1.0
ND A:HEM750 1.9 30.3 1.0
NA A:HEM750 2.0 32.0 1.0
NC A:HEM750 2.1 30.5 1.0
NB A:HEM750 2.1 30.8 1.0
SG A:CYS415 2.4 30.5 1.0
C1D A:HEM750 3.0 30.1 1.0
C4D A:HEM750 3.0 30.9 1.0
C4A A:HEM750 3.0 31.4 1.0
C1A A:HEM750 3.0 30.7 1.0
C4C A:HEM750 3.0 31.1 1.0
C1B A:HEM750 3.1 31.4 1.0
C1C A:HEM750 3.1 32.5 1.0
C4B A:HEM750 3.1 31.1 1.0
CHB A:HEM750 3.4 31.1 1.0
CHD A:HEM750 3.4 28.9 1.0
CHA A:HEM750 3.5 30.6 1.0
CHC A:HEM750 3.5 33.0 1.0
CB A:CYS415 3.5 30.7 1.0
S01 A:6E5800 3.9 27.6 1.0
C3A A:HEM750 4.2 31.0 1.0
CA A:CYS415 4.2 28.7 1.0
C2A A:HEM750 4.2 31.9 1.0
C3C A:HEM750 4.2 30.7 1.0
C12 A:6E5800 4.2 20.1 1.0
C3D A:HEM750 4.3 30.2 1.0
C2D A:HEM750 4.3 29.6 1.0
C2C A:HEM750 4.3 33.2 1.0
C2B A:HEM750 4.3 31.9 1.0
C3B A:HEM750 4.3 33.0 1.0
NE1 A:TRP409 4.5 31.6 1.0
C02 A:6E5800 4.7 23.9 1.0
C05 A:6E5800 4.7 20.9 1.0
N A:GLY417 4.8 31.9 1.0
C13 A:6E5800 4.8 22.4 1.0
C A:CYS415 4.9 30.6 1.0
C06 A:6E5800 5.0 23.2 1.0

Iron binding site 2 out of 2 in 4upo

Go back to Iron Binding Sites List in 4upo
Iron binding site 2 out of 2 in the Structure of Rat Neuronal 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 Rat Neuronal 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:Fe750

b:28.4
occ:1.00
 FE B:HEM750 0.0 28.4 1.0
ND B:HEM750 1.9 28.1 1.0
NA B:HEM750 2.0 31.6 1.0
NC B:HEM750 2.0 29.3 1.0
NB B:HEM750 2.1 28.9 1.0
SG B:CYS415 2.4 28.3 1.0
C4D B:HEM750 3.0 29.3 1.0
C1D B:HEM750 3.0 28.9 1.0
C1A B:HEM750 3.0 28.6 1.0
C4A B:HEM750 3.0 29.1 1.0
C4C B:HEM750 3.0 28.4 1.0
C4B B:HEM750 3.0 27.8 1.0
C1C B:HEM750 3.1 27.0 1.0
C1B B:HEM750 3.1 29.6 1.0
CHD B:HEM750 3.4 28.6 1.0
CB B:CYS415 3.4 25.2 1.0
CHA B:HEM750 3.4 28.3 1.0
CHC B:HEM750 3.4 27.4 1.0
CHB B:HEM750 3.5 28.4 1.0
S01 B:6E5800 3.9 34.8 1.0
C2A B:HEM750 4.2 29.5 1.0
C3A B:HEM750 4.2 28.9 1.0
CA B:CYS415 4.2 26.4 1.0
C3C B:HEM750 4.2 27.8 1.0
C2C B:HEM750 4.2 27.4 1.0
C3D B:HEM750 4.3 29.3 1.0
C12 B:6E5800 4.3 26.0 1.0
C2D B:HEM750 4.3 28.8 1.0
C3B B:HEM750 4.3 29.9 1.0
C2B B:HEM750 4.3 28.7 1.0
NE1 B:TRP409 4.5 27.6 1.0
C05 B:6E5800 4.7 29.9 1.0
C02 B:6E5800 4.7 30.7 1.0
N B:GLY417 4.8 30.3 1.0
C06 B:6E5800 4.9 31.5 1.0
C13 B:6E5800 4.9 26.6 1.0
C B:CYS415 4.9 28.1 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 13:32:11 2024

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