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Gadolinium in PDB 4d1o: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain with L-Arg Bound

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain with L-Arg Bound

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain with L-Arg Bound:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain with L-Arg Bound, PDB code: 4d1o 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) 48.392 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.395, 110.091, 153.322, 90.00, 90.00, 90.00
R / Rfree (%) 15.48 / 19.2

Other elements in 4d1o:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain with L-Arg Bound 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 with L-Arg Bound (pdb code 4d1o). 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 with L-Arg Bound, PDB code: 4d1o:
Jump to Gadolinium binding site number: 1; 2;

Gadolinium binding site 1 out of 2 in 4d1o

Go back to Gadolinium Binding Sites List in 4d1o
Gadolinium binding site 1 out of 2 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain with L-Arg Bound


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 with L-Arg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1482

b:53.0
occ:0.75
O A:HOH2298 2.1 48.0 1.0
O1 A:BTB870 2.3 70.7 1.0
O3 A:BTB870 2.4 23.4 1.0
O6 A:BTB870 2.5 85.6 1.0
O A:HOH2374 2.5 51.6 1.0
O A:HOH2373 2.5 52.5 1.0
C3 A:BTB870 2.7 30.2 1.0
O8 A:BTB870 2.7 60.9 1.0
O A:HOH2372 2.8 54.8 1.0
N A:BTB870 2.9 76.5 1.0
O A:HOH2379 2.9 53.7 1.0
C2 A:BTB870 3.0 82.9 1.0
C1 A:BTB870 3.0 66.7 1.0
O A:HOH2299 3.0 60.1 1.0
O A:HOH2297 3.3 55.3 1.0
C6 A:BTB870 3.6 64.8 1.0
C5 A:BTB870 3.7 75.1 1.0
C7 A:BTB870 3.9 68.6 1.0
C8 A:BTB870 3.9 70.6 1.0
OD2 A:ASP384 4.4 40.9 1.0
C4 A:BTB870 4.5 88.7 1.0
OD1 A:ASP384 4.5 39.0 1.0
CG A:ASP384 4.9 35.5 1.0

Gadolinium binding site 2 out of 2 in 4d1o

Go back to Gadolinium Binding Sites List in 4d1o
Gadolinium binding site 2 out of 2 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain with L-Arg Bound


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 with L-Arg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd1482

b:21.2
occ:0.91
O B:THR319 2.2 22.5 1.0
O1 B:BTB870 2.2 25.8 1.0
O8 B:BTB870 2.3 27.6 1.0
O6 B:BTB870 2.4 26.4 1.0
O B:HOH2284 2.4 23.3 1.0
O B:HOH2285 2.4 22.4 1.0
O3 B:BTB870 2.4 26.5 1.0
OE1 B:GLU321 2.5 28.0 1.0
N B:BTB870 2.7 21.9 1.0
C6 B:BTB870 3.2 23.4 1.0
C8 B:BTB870 3.3 25.7 1.0
C1 B:BTB870 3.4 25.6 1.0
C2 B:BTB870 3.4 32.2 1.0
C B:THR319 3.4 29.1 1.0
C7 B:BTB870 3.4 22.7 1.0
C3 B:BTB870 3.5 25.1 1.0
CD B:GLU321 3.5 48.3 1.0
C5 B:BTB870 3.5 23.2 1.0
OE2 B:GLU321 3.8 34.9 1.0
CA B:THR319 4.3 25.4 1.0
N B:LEU320 4.4 31.0 1.0
CA B:LEU320 4.5 23.3 1.0
CB B:THR319 4.5 32.5 1.0
N B:GLU321 4.5 22.1 1.0
O B:HOH2384 4.7 42.9 1.0
O B:HOH2287 4.7 29.5 1.0
CG B:GLU321 4.8 34.1 1.0
O B:HOH2289 4.8 43.4 1.0
C4 B:BTB870 4.9 34.3 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: Sun Dec 13 18:59:43 2020

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