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Gadolinium in PDB 6av7: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69, PDB code: 6av7 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) 39.03 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.445, 152.355, 108.655, 90.00, 90.79, 90.00
R / Rfree (%) 20.4 / 25.4

Other elements in 6av7:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69 also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 4 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69 (pdb code 6av7). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 4 binding sites of Gadolinium where determined in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69, PDB code: 6av7:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 6av7

Go back to Gadolinium Binding Sites List in 6av7
Gadolinium binding site 1 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69


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 HW69 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd509

b:0.2
occ:1.00
 O3 A:BTB504 2.7 0.2 1.0
O4 A:BTB504 2.7 52.6 1.0
O8 A:BTB504 2.8 0.9 1.0
N A:BTB504 2.8 92.3 1.0
C4 A:BTB504 3.2 58.3 1.0
C2 A:BTB504 3.2 88.8 1.0
C3 A:BTB504 3.3 0.7 1.0
C8 A:BTB504 3.4 92.7 1.0
O6 A:BTB504 3.4 81.9 1.0
C7 A:BTB504 3.6 90.7 1.0
C5 A:BTB504 3.7 91.5 1.0
C6 A:BTB504 4.1 85.9 1.0
OD2 A:ASP384 4.2 71.9 1.0
OD1 A:ASP384 4.5 93.5 1.0
C1 A:BTB504 4.7 98.2 1.0
CG A:ASP384 4.8 74.8 1.0

Gadolinium binding site 2 out of 4 in 6av7

Go back to Gadolinium Binding Sites List in 6av7
Gadolinium binding site 2 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69


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 HW69 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd507

b:54.7
occ:1.00
 O B:THR319 2.6 38.9 1.0
O3 B:BTB504 2.7 72.0 1.0
O4 B:BTB504 2.7 64.8 1.0
N B:BTB504 2.7 53.0 1.0
O B:HOH651 2.7 81.3 1.0
OE1 B:GLU321 2.7 58.0 1.0
O6 B:BTB504 2.7 69.0 1.0
O C:HOH608 2.7 44.1 1.0
O8 B:BTB504 2.8 74.4 1.0
C8 B:BTB504 2.8 47.8 1.0
C6 B:BTB504 3.2 59.4 1.0
C7 B:BTB504 3.3 45.0 1.0
C2 B:BTB504 3.4 75.2 1.0
C4 B:BTB504 3.4 74.4 1.0
C5 B:BTB504 3.5 49.2 1.0
C3 B:BTB504 3.6 74.0 1.0
CD B:GLU321 3.6 62.1 1.0
OE2 B:GLU321 3.7 69.5 1.0
C B:THR319 3.7 65.1 1.0
CA B:THR319 4.5 48.4 1.0
OD1 C:ASP378 4.6 57.5 1.0
CA B:LEU320 4.6 46.8 1.0
N B:GLU321 4.6 49.7 1.0
N B:LEU320 4.7 59.9 1.0
CB B:THR319 4.7 45.6 1.0
OD2 C:ASP378 4.7 61.9 1.0
C1 B:BTB504 4.8 90.2 1.0

Gadolinium binding site 3 out of 4 in 6av7

Go back to Gadolinium Binding Sites List in 6av7
Gadolinium binding site 3 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd510

b:0.7
occ:1.00
 O3 C:BTB504 2.5 35.8 1.0
O C:HOH650 2.8 0.3 1.0
O6 C:BTB504 2.8 0.1 1.0
O C:HOH671 2.8 0.2 1.0
N C:BTB504 2.9 0.3 1.0
C6 C:BTB504 3.1 0.6 1.0
O4 C:BTB504 3.3 67.4 1.0
O8 C:BTB504 3.4 82.0 1.0
C3 C:BTB504 3.5 58.6 1.0
C5 C:BTB504 3.5 0.4 1.0
C8 C:BTB504 3.6 85.8 1.0
C2 C:BTB504 3.6 83.8 1.0
C7 C:BTB504 3.8 93.1 1.0
C4 C:BTB504 4.1 70.3 1.0
OD1 C:ASP384 4.1 85.6 1.0
OD2 C:ASP384 4.6 98.9 1.0
CG C:ASP384 4.8 75.0 1.0

Gadolinium binding site 4 out of 4 in 6av7

Go back to Gadolinium Binding Sites List in 6av7
Gadolinium binding site 4 out of 4 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with HW69 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd506

b:54.8
occ:1.00
 O D:HOH602 2.2 39.8 1.0
O D:THR319 2.6 40.3 1.0
OE1 D:GLU321 2.6 81.1 1.0
O4 D:BTB504 2.7 54.9 1.0
O3 D:BTB504 2.7 66.8 1.0
O8 D:BTB504 2.8 74.8 1.0
O6 D:BTB504 2.8 66.2 1.0
OE2 D:GLU321 2.8 89.1 1.0
N D:BTB504 2.8 74.2 1.0
C8 D:BTB504 2.8 54.1 1.0
C7 D:BTB504 3.0 58.0 1.0
CD D:GLU321 3.0 79.4 1.0
C2 D:BTB504 3.5 87.9 1.0
C4 D:BTB504 3.5 79.0 1.0
C3 D:BTB504 3.6 88.4 1.0
C D:THR319 3.7 65.5 1.0
C6 D:BTB504 3.7 70.2 1.0
C5 D:BTB504 3.9 81.0 1.0
CA D:THR319 4.4 50.0 1.0
CG D:GLU321 4.5 50.4 1.0
CB D:THR319 4.6 52.9 1.0
N D:GLU321 4.6 58.6 1.0
CA D:LEU320 4.7 55.5 1.0
N D:LEU320 4.7 59.9 1.0
C1 D:BTB504 5.0 85.1 1.0

Reference:

H.T.Do, H.Y.Wang, H.Li, G.Chreifi, T.L.Poulos, R.B.Silverman. Improvement of Cell Permeability of Human Neuronal Nitric Oxide Synthase Inhibitors Using Potent and Selective 2-Aminopyridine-Based Scaffolds with A Fluorobenzene Linker. J. Med. Chem. V. 60 9360 2017.
ISSN: ISSN 1520-4804
PubMed: 29091437
DOI: 10.1021/ACS.JMEDCHEM.7B01356
Page generated: Sat Aug 10 21:57:47 2024

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