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Iron in PDB 4d1p: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine, PDB code: 4d1p 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) 48.357 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.226, 110.378, 153.670, 90.00, 90.00, 90.00
R / Rfree (%) 15.66 / 18.65

Other elements in 4d1p:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine also contains other interesting chemical elements:

Gadolinium (Gd) 2 atoms
Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine (pdb code 4d1p). 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 Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine, PDB code: 4d1p:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4d1p

Go back to Iron Binding Sites List in 4d1p
Iron binding site 1 out of 2 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine


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 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:17.6
occ:1.00
 FE A:HEM500 0.0 17.6 1.0
ND A:HEM500 2.0 17.5 1.0
NC A:HEM500 2.1 16.3 1.0
NA A:HEM500 2.1 17.5 1.0
NB A:HEM500 2.1 18.8 1.0
SG A:CYS184 2.4 16.2 1.0
C4D A:HEM500 3.1 18.9 1.0
C1D A:HEM500 3.1 19.7 1.0
C1A A:HEM500 3.1 20.0 1.0
C4C A:HEM500 3.1 16.4 1.0
C1B A:HEM500 3.1 14.8 1.0
C1C A:HEM500 3.1 18.9 1.0
C4A A:HEM500 3.1 17.7 1.0
C4B A:HEM500 3.1 20.4 1.0
CB A:CYS184 3.4 14.7 1.0
CHA A:HEM500 3.4 17.5 1.0
CHD A:HEM500 3.4 19.2 1.0
CHB A:HEM500 3.5 16.6 1.0
CHC A:HEM500 3.5 18.3 1.0
C03 A:Q16800 4.0 18.0 1.0
CA A:CYS184 4.1 13.5 1.0
C04 A:Q16800 4.1 22.2 1.0
C3D A:HEM500 4.3 15.2 1.0
C2D A:HEM500 4.3 19.6 1.0
NE1 A:TRP178 4.3 16.7 1.0
C2A A:HEM500 4.3 18.3 1.0
C3C A:HEM500 4.3 17.2 1.0
C07 A:Q16800 4.3 27.7 1.0
C2B A:HEM500 4.3 19.5 1.0
C3A A:HEM500 4.3 20.5 1.0
C2C A:HEM500 4.3 20.1 1.0
C3B A:HEM500 4.4 20.1 1.0
C02 A:Q16800 4.5 27.7 1.0
C05 A:Q16800 4.7 26.9 1.0
N A:GLY186 4.8 18.7 1.0
C A:CYS184 4.8 19.6 1.0
N A:VAL185 5.0 14.8 1.0
CD1 A:TRP178 5.0 17.2 1.0

Iron binding site 2 out of 2 in 4d1p

Go back to Iron Binding Sites List in 4d1p
Iron binding site 2 out of 2 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine


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 6-((((3S, 5R)-5-(((6-Amino-4- Methylpyridin-2-Yl)Methoxy)Methyl)Pyrrolidin-3-Yl)Oxy) Methyl)-4-Methylpyridin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:15.4
occ:1.00
 FE B:HEM500 0.0 15.4 1.0
NA B:HEM500 2.1 16.0 1.0
NC B:HEM500 2.1 16.2 1.0
ND B:HEM500 2.1 13.6 1.0
NB B:HEM500 2.1 15.6 1.0
SG B:CYS184 2.4 14.2 1.0
C1D B:HEM500 3.1 15.3 1.0
C4C B:HEM500 3.1 16.1 1.0
C4A B:HEM500 3.1 18.9 1.0
C4D B:HEM500 3.1 15.5 1.0
C1A B:HEM500 3.1 15.3 1.0
C1B B:HEM500 3.1 15.7 1.0
C1C B:HEM500 3.1 15.8 1.0
C4B B:HEM500 3.1 17.1 1.0
CB B:CYS184 3.4 11.7 1.0
CHD B:HEM500 3.4 16.9 1.0
CHB B:HEM500 3.5 17.7 1.0
CHA B:HEM500 3.5 12.3 1.0
CHC B:HEM500 3.5 15.2 1.0
C03 B:Q16800 4.0 15.4 1.0
C04 B:Q16800 4.1 20.1 1.0
CA B:CYS184 4.1 10.8 1.0
C07 B:Q16800 4.2 20.4 1.0
C2D B:HEM500 4.3 14.2 1.0
C3A B:HEM500 4.3 16.0 1.0
C2A B:HEM500 4.3 17.4 1.0
C3D B:HEM500 4.3 17.5 1.0
C2B B:HEM500 4.3 13.4 1.0
C3C B:HEM500 4.3 15.2 1.0
C2C B:HEM500 4.3 15.1 1.0
C3B B:HEM500 4.3 14.0 1.0
NE1 B:TRP178 4.4 12.4 1.0
C02 B:Q16800 4.5 17.6 1.0
C05 B:Q16800 4.7 24.0 1.0
N B:GLY186 4.8 12.5 1.0
C B:CYS184 4.8 14.4 1.0
N B:VAL185 5.0 12.8 1.0

Reference:

H.Li, J.Jamal, C.Plaza, S.H.Pineda, G.Chreifi, Q.Jing, M.A.Cinelli, R.B.Silverman, T.L.Poulos. Structures of Human Constitutive Nitric Oxide Synthases Acta Crystallogr.,Sect.D V. 70 2667 2014.
ISSN: ISSN 0907-4449
PubMed: 25286850
DOI: 10.1107/S1399004714017064
Page generated: Mon Aug 5 01:02:24 2024

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