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Iron in PDB 3dqr: Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine

Enzymatic activity of Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine

All present enzymatic activity of Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine, PDB code: 3dqr 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) 38.94 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.870, 110.700, 164.360, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.1

Other elements in 3dqr:

The structure of Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine (pdb code 3dqr). 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 Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine, PDB code: 3dqr:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3dqr

Go back to Iron Binding Sites List in 3dqr
Iron binding site 1 out of 2 in the Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}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 Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe750

b:27.3
occ:1.00
 FE A:HEM750 0.0 27.3 1.0
NC A:HEM750 2.0 26.0 1.0
ND A:HEM750 2.0 29.7 1.0
NB A:HEM750 2.0 29.6 1.0
NA A:HEM750 2.1 30.7 1.0
SG A:CYS415 2.3 30.2 1.0
C4C A:HEM750 3.0 26.5 1.0
C1C A:HEM750 3.0 26.8 1.0
C1D A:HEM750 3.0 28.7 1.0
C4D A:HEM750 3.1 29.2 1.0
C4B A:HEM750 3.1 29.6 1.0
C1B A:HEM750 3.1 31.3 1.0
C4A A:HEM750 3.1 30.2 1.0
C1A A:HEM750 3.1 30.6 1.0
CB A:CYS415 3.3 32.9 1.0
CHD A:HEM750 3.4 28.3 1.0
CHC A:HEM750 3.4 30.5 1.0
CHB A:HEM750 3.5 29.9 1.0
CHA A:HEM750 3.5 29.1 1.0
C4 A:JI2800 3.8 39.3 1.0
C5 A:JI2800 4.1 40.5 1.0
CA A:CYS415 4.1 29.9 1.0
C3 A:JI2800 4.1 41.9 1.0
C3C A:HEM750 4.2 27.3 1.0
C3D A:HEM750 4.3 30.7 1.0
C2C A:HEM750 4.3 27.1 1.0
C2D A:HEM750 4.3 28.6 1.0
C3B A:HEM750 4.3 32.4 1.0
C2B A:HEM750 4.3 32.2 1.0
C3A A:HEM750 4.4 32.4 1.0
C2A A:HEM750 4.4 32.8 1.0
NE1 A:TRP409 4.5 28.9 1.0
C6 A:JI2800 4.6 40.7 1.0
C2 A:JI2800 4.7 43.6 1.0
C A:CYS415 4.8 29.7 1.0
N1 A:JI2800 4.9 42.2 1.0
N A:GLY417 5.0 29.5 1.0

Iron binding site 2 out of 2 in 3dqr

Go back to Iron Binding Sites List in 3dqr
Iron binding site 2 out of 2 in the Structure of Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}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 Neuronal Nos D597N/M336V Mutant Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin- 2"-Yl)Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe750

b:24.6
occ:1.00
 FE B:HEM750 0.0 24.6 1.0
NA B:HEM750 2.0 28.9 1.0
NC B:HEM750 2.0 24.3 1.0
ND B:HEM750 2.0 23.9 1.0
NB B:HEM750 2.0 29.1 1.0
SG B:CYS415 2.3 29.4 1.0
C4C B:HEM750 3.0 22.6 1.0
C1A B:HEM750 3.0 30.5 1.0
C1D B:HEM750 3.0 23.6 1.0
C4D B:HEM750 3.0 25.3 1.0
C1C B:HEM750 3.0 25.2 1.0
C4A B:HEM750 3.0 31.2 1.0
C1B B:HEM750 3.1 31.3 1.0
C4B B:HEM750 3.1 31.0 1.0
CHD B:HEM750 3.3 24.3 1.0
CHA B:HEM750 3.4 28.5 1.0
CHC B:HEM750 3.4 28.0 1.0
CHB B:HEM750 3.5 31.7 1.0
CB B:CYS415 3.5 25.9 1.0
C4 B:JI2800 3.8 41.3 1.0
C5 B:JI2800 3.9 41.4 1.0
C3 B:JI2800 4.1 42.8 1.0
C3D B:HEM750 4.2 27.3 1.0
C2A B:HEM750 4.2 32.4 1.0
C3C B:HEM750 4.2 24.3 1.0
C2C B:HEM750 4.2 24.5 1.0
CA B:CYS415 4.2 26.1 1.0
C2D B:HEM750 4.3 25.4 1.0
C3A B:HEM750 4.3 31.2 1.0
C3B B:HEM750 4.4 32.8 1.0
C2B B:HEM750 4.4 33.1 1.0
C6 B:JI2800 4.4 40.6 1.0
NE1 B:TRP409 4.5 21.0 1.0
C2 B:JI2800 4.6 43.7 1.0
N1 B:JI2800 4.6 41.9 1.0
N B:GLY417 4.8 27.6 1.0
C B:CYS415 4.9 27.9 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 09:09:15 2024

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