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Gadolinium in PDB 6cif: Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide

Enzymatic activity of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide

All present enzymatic activity of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide:
1.14.13.39;

Protein crystallography data

The structure of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide, PDB code: 6cif was solved by G.Chreifi, H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.07 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.789, 152.579, 108.690, 90.00, 90.81, 90.00
R / Rfree (%) 18.9 / 24.6

Other elements in 6cif:

The structure of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide also contains other interesting chemical elements:

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 the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide (pdb code 6cif). 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 the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide, PDB code: 6cif:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 6cif

Go back to Gadolinium Binding Sites List in 6cif
Gadolinium binding site 1 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd509

b:60.4
occ:0.63
 O A:HOH691 2.8 50.9 1.0
O A:HOH696 2.8 54.2 1.0
O A:HOH692 3.3 48.4 1.0
O A:HOH702 3.4 56.1 1.0
O C:GLN257 4.3 0.6 1.0
O A:LEU385 4.4 39.7 1.0
O A:ASP384 4.6 36.9 1.0
C A:ASP384 4.8 41.3 1.0
CA A:ASP384 4.9 39.3 1.0

Gadolinium binding site 2 out of 4 in 6cif

Go back to Gadolinium Binding Sites List in 6cif
Gadolinium binding site 2 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd508

b:48.8
occ:1.00
 O C:HOH611 2.5 34.1 1.0
O4 B:BTB504 2.6 51.6 1.0
O B:HOH602 2.6 68.2 1.0
O3 B:BTB504 2.7 63.2 1.0
OE1 B:GLU321 2.7 57.7 1.0
O6 B:BTB504 2.7 46.9 1.0
O B:THR319 2.7 38.0 1.0
N B:BTB504 2.9 65.1 1.0
O8 B:BTB504 3.1 68.4 1.0
C6 B:BTB504 3.1 34.2 1.0
C5 B:BTB504 3.3 45.8 1.0
C2 B:BTB504 3.5 75.8 1.0
C3 B:BTB504 3.6 71.0 1.0
C4 B:BTB504 3.6 69.0 1.0
C8 B:BTB504 3.6 65.9 1.0
C B:THR319 3.7 41.2 1.0
CD B:GLU321 3.7 64.7 1.0
C7 B:BTB504 3.8 61.7 1.0
O B:HOH603 3.9 58.6 1.0
OE2 B:GLU321 4.1 70.5 1.0
OD2 C:ASP378 4.1 61.5 1.0
CA B:THR319 4.4 40.1 1.0
OD1 C:ASP378 4.6 49.4 1.0
N B:LEU320 4.6 53.1 1.0
CA B:LEU320 4.6 47.1 1.0
CB B:THR319 4.6 40.6 1.0
N B:GLU321 4.6 38.1 1.0
CG C:ASP378 4.8 54.4 1.0

Gadolinium binding site 3 out of 4 in 6cif

Go back to Gadolinium Binding Sites List in 6cif
Gadolinium binding site 3 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd510

b:61.2
occ:0.75
 OD1 C:ASP384 2.7 89.7 1.0
O B:HOH761 2.7 61.7 1.0
O C:HOH710 2.8 57.6 1.0
O C:HOH690 2.8 40.0 1.0
O B:HOH755 3.2 59.8 1.0
CG C:ASP384 3.8 83.6 1.0
OD2 C:ASP384 4.4 90.0 1.0
O C:HOH705 4.7 61.5 1.0
C C:ASP384 4.7 47.1 1.0
O C:ASP384 4.8 46.2 1.0
O C:LEU385 4.8 46.5 1.0
CA C:ASP384 4.9 51.7 1.0
CB C:ASP384 5.0 64.6 1.0

Gadolinium binding site 4 out of 4 in 6cif

Go back to Gadolinium Binding Sites List in 6cif
Gadolinium binding site 4 out of 4 in the Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structure of the Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with N-(1-(Piperidin-4-Yl)Indolin-5-Yl)Thiophene-2- Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd507

b:43.2
occ:1.00
 O3 D:BTB504 2.6 44.3 1.0
O D:THR319 2.6 57.5 1.0
O D:HOH702 2.6 56.0 1.0
OE2 D:GLU321 2.7 63.6 1.0
O8 D:BTB504 2.7 62.4 1.0
O D:HOH698 2.7 43.5 1.0
N D:BTB504 2.8 56.3 1.0
O4 D:BTB504 2.9 62.4 1.0
O6 D:BTB504 3.0 51.7 1.0
OE1 D:GLU321 3.1 58.3 1.0
C5 D:BTB504 3.2 42.7 1.0
CD D:GLU321 3.3 54.4 1.0
C6 D:BTB504 3.4 43.3 1.0
C3 D:BTB504 3.4 60.7 1.0
C2 D:BTB504 3.5 68.4 1.0
C8 D:BTB504 3.6 58.9 1.0
C D:THR319 3.6 50.2 1.0
C7 D:BTB504 3.7 62.0 1.0
C4 D:BTB504 3.7 69.1 1.0
O D:HOH612 3.8 67.0 1.0
CA D:THR319 4.3 37.9 1.0
N D:LEU320 4.5 56.1 1.0
CB D:THR319 4.6 37.9 1.0
CA D:LEU320 4.6 40.1 1.0
N D:GLU321 4.7 34.2 1.0
CG D:GLU321 4.8 34.9 1.0
O D:HOH748 4.8 53.8 1.0
C1 D:BTB504 4.9 72.8 1.0

Reference:

H.Li, R.J.Evenson, G.Chreifi, R.B.Silverman, T.L.Poulos. Structural Basis For Isoform Selective Nitric Oxide Synthase Inhibition By Thiophene-2-Carboximidamides. Biochemistry V. 57 6319 2018.
ISSN: ISSN 1520-4995
PubMed: 30335983
DOI: 10.1021/ACS.BIOCHEM.8B00895
Page generated: Sat Aug 10 21:59:29 2024

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