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Gadolinium 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:

Iron (Fe) 2 atoms
Zinc (Zn) 1 atom

Gadolinium Binding Sites:

The binding sites of Gadolinium 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 Gadolinium atom.
In total 2 binding sites of Gadolinium 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 Gadolinium binding site number: 1; 2;

Gadolinium binding site 1 out of 2 in 4d1p

Go back to Gadolinium Binding Sites List in 4d1p
Gadolinium 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 Gadolinium with other atoms in the Gd 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:Gd1490

b:49.5
occ:0.77
 O A:HOH2299 2.1 42.8 1.0
O1 A:BTB870 2.2 72.8 1.0
O3 A:BTB870 2.2 20.6 1.0
O A:HOH2300 2.6 60.3 1.0
O6 A:BTB870 2.6 84.2 1.0
O A:HOH2377 2.6 53.1 1.0
O A:HOH2375 2.7 53.9 1.0
C3 A:BTB870 2.8 32.2 1.0
O8 A:BTB870 2.9 51.5 1.0
O A:HOH2376 2.9 49.5 1.0
N A:BTB870 2.9 74.2 1.0
O A:HOH2381 3.0 58.0 1.0
C2 A:BTB870 3.0 81.2 1.0
C1 A:BTB870 3.0 62.2 1.0
O A:HOH2298 3.3 55.1 1.0
C6 A:BTB870 3.7 63.2 1.0
C5 A:BTB870 3.8 73.1 1.0
C8 A:BTB870 3.9 68.9 1.0
C7 A:BTB870 3.9 71.2 1.0
OD1 A:ASP384 4.4 37.5 1.0
OD2 A:ASP384 4.4 36.0 1.0
C4 A:BTB870 4.5 84.3 1.0
CG A:ASP384 4.9 41.5 1.0

Gadolinium binding site 2 out of 2 in 4d1p

Go back to Gadolinium Binding Sites List in 4d1p
Gadolinium 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 Gadolinium with other atoms in the Gd 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:Gd1490

b:21.2
occ:0.96
 O B:THR319 2.2 21.0 1.0
O1 B:BTB870 2.3 24.5 1.0
O B:HOH2269 2.3 21.8 1.0
O8 B:BTB870 2.4 24.2 1.0
O6 B:BTB870 2.4 22.8 1.0
O3 B:BTB870 2.4 24.3 1.0
O B:HOH2270 2.4 22.8 1.0
OE1 B:GLU321 2.5 22.7 1.0
N B:BTB870 2.7 22.6 1.0
C6 B:BTB870 3.2 26.1 1.0
C8 B:BTB870 3.3 30.7 1.0
C2 B:BTB870 3.3 24.7 1.0
C1 B:BTB870 3.4 28.7 1.0
C7 B:BTB870 3.4 21.9 1.0
C B:THR319 3.4 29.0 1.0
C3 B:BTB870 3.4 23.1 1.0
CD B:GLU321 3.5 34.4 1.0
C5 B:BTB870 3.5 19.7 1.0
OE2 B:GLU321 3.9 32.2 1.0
CA B:THR319 4.3 24.1 1.0
N B:LEU320 4.4 30.4 1.0
O B:HOH2371 4.4 35.0 1.0
N B:GLU321 4.5 21.4 1.0
CA B:LEU320 4.5 20.1 1.0
CB B:THR319 4.5 26.0 1.0
O B:HOH2268 4.7 30.2 1.0
O B:HOH2368 4.7 40.1 1.0
O B:HOH2275 4.8 37.2 1.0
C4 B:BTB870 4.8 27.6 1.0
CG B:GLU321 4.8 28.6 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: Fri Aug 8 08:32:26 2025

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