Zinc in PDB 8ufu: Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine

Enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine

All present enzymatic activity of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine, PDB code: 8ufu 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) 38.74 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.673, 152.827, 109.162, 90, 90.82, 90
R / Rfree (%) 20.5 / 25.6

Other elements in 8ufu:

The structure of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms
Iron (Fe) 4 atoms
Gadolinium (Gd) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine (pdb code 8ufu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine, PDB code: 8ufu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8ufu

Go back to Zinc Binding Sites List in 8ufu
Zinc binding site 1 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:52.5
occ:1.00
 SG A:CYS94 2.3 63.2 1.0
SG A:CYS99 2.3 53.8 1.0
SG B:CYS99 2.4 52.2 1.0
SG B:CYS94 2.4 54.1 1.0
CB B:CYS99 3.2 54.8 1.0
CB A:CYS94 3.4 61.3 1.0
CB A:CYS99 3.4 51.4 1.0
CB B:CYS94 3.5 48.2 1.0
CA B:CYS99 3.7 47.5 1.0
CA A:CYS99 3.9 57.5 1.0
N A:GLY101 4.1 52.6 1.0
N B:GLY101 4.2 54.3 1.0
N A:LEU100 4.2 55.5 1.0
N B:LEU100 4.3 49.5 1.0
CA A:GLY101 4.4 51.1 1.0
C B:CYS99 4.4 56.2 1.0
C A:CYS99 4.5 62.6 1.0
CA B:GLY101 4.5 41.0 1.0
CA A:CYS94 4.8 66.1 1.0
CA B:CYS94 4.9 55.8 1.0
N B:CYS99 5.0 45.3 1.0
C A:LEU100 5.0 56.0 1.0

Zinc binding site 2 out of 6 in 8ufu

Go back to Zinc Binding Sites List in 8ufu
Zinc binding site 2 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:65.8
occ:1.00
 O A:HOH643 1.9 37.1 1.0
OD1 A:ASP369 2.1 77.1 1.0
OD2 A:ASP369 2.2 63.4 1.0
O A:HOH621 2.3 32.9 1.0
NE2 B:HIS461 2.3 70.6 1.0
CG A:ASP369 2.5 61.5 1.0
CD2 B:HIS461 3.1 64.3 1.0
CE1 B:HIS461 3.4 60.6 1.0
CG A:ARG365 3.4 77.1 1.0
CB A:ASP369 4.0 48.2 1.0
C22 A:WRI503 4.1 118.8 1.0
CG B:HIS461 4.3 56.5 1.0
CB A:ARG365 4.4 62.5 1.0
ND1 B:HIS461 4.4 60.5 1.0
CD A:ARG365 4.4 84.7 1.0
CE1 B:PHE460 4.5 43.3 1.0
CA A:ARG365 4.5 55.9 1.0
CE1 A:HIS371 4.5 60.2 1.0
C23 A:WRI503 4.6 124.2 1.0
CD1 B:PHE460 4.6 43.5 1.0
CB B:SER455 4.7 52.9 1.0
NE2 A:HIS371 4.7 65.9 1.0
CA A:ASP369 5.0 42.2 1.0

Zinc binding site 3 out of 6 in 8ufu

Go back to Zinc Binding Sites List in 8ufu
Zinc binding site 3 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn508

b:64.8
occ:1.00
 OD1 B:ASP369 2.1 80.2 1.0
OD2 B:ASP369 2.2 77.8 1.0
O B:HOH701 2.2 47.4 1.0
NE2 A:HIS461 2.3 60.9 1.0
O B:HOH691 2.4 37.0 1.0
CG B:ASP369 2.5 67.8 1.0
CE1 A:HIS461 3.2 54.9 1.0
CD2 A:HIS461 3.3 57.2 1.0
CG B:ARG365 3.5 53.2 1.0
CB B:ASP369 4.0 60.6 1.0
CB B:ARG365 4.3 45.0 1.0
C22 B:WRI503 4.3 109.0 1.0
ND1 A:HIS461 4.4 54.7 1.0
CA B:ARG365 4.4 41.0 1.0
CE1 A:PHE460 4.4 48.8 1.0
CG A:HIS461 4.5 47.9 1.0
CE1 B:HIS371 4.6 67.9 1.0
CD B:ARG365 4.6 74.9 1.0
NE2 B:HIS371 4.6 68.1 1.0
CB A:SER455 4.6 43.9 1.0
C23 B:WRI503 4.7 112.4 1.0
CD1 A:PHE460 4.7 42.9 1.0
O A:HOH636 4.9 45.4 1.0
CA B:ASP369 4.9 56.5 1.0
O B:ARG365 5.0 41.9 1.0

Zinc binding site 4 out of 6 in 8ufu

Go back to Zinc Binding Sites List in 8ufu
Zinc binding site 4 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn508

b:45.4
occ:1.00
 SG C:CYS94 2.3 49.0 1.0
SG C:CYS99 2.4 45.6 1.0
SG D:CYS99 2.5 46.5 1.0
SG D:CYS94 2.6 49.2 1.0
CB D:CYS99 3.2 44.4 1.0
CB C:CYS99 3.2 38.6 1.0
CB D:CYS94 3.4 46.4 1.0
CB C:CYS94 3.4 49.0 1.0
CA C:CYS99 3.7 49.0 1.0
CA D:CYS99 3.7 51.2 1.0
N D:GLY101 4.1 42.8 1.0
N D:LEU100 4.2 44.3 1.0
N C:LEU100 4.2 56.1 1.0
N C:GLY101 4.2 50.8 1.0
C D:CYS99 4.3 56.0 1.0
C C:CYS99 4.4 50.3 1.0
CA D:GLY101 4.4 47.0 1.0
CA C:GLY101 4.6 48.2 1.0
CA C:CYS94 4.8 50.1 1.0
CA D:CYS94 4.8 56.3 1.0
C D:LEU100 5.0 49.2 1.0
N C:CYS99 5.0 49.4 1.0

Zinc binding site 5 out of 6 in 8ufu

Go back to Zinc Binding Sites List in 8ufu
Zinc binding site 5 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn509

b:61.2
occ:1.00
 OD2 C:ASP369 2.1 71.2 1.0
O C:HOH661 2.1 37.2 1.0
NE2 D:HIS461 2.2 55.6 1.0
O C:HOH658 2.3 29.5 1.0
OD1 C:ASP369 2.4 57.9 1.0
CG C:ASP369 2.6 53.1 1.0
CD2 D:HIS461 3.2 52.4 1.0
CE1 D:HIS461 3.2 47.0 1.0
CG C:ARG365 3.5 69.3 1.0
CB C:ASP369 4.1 49.8 1.0
CD C:ARG365 4.1 84.4 1.0
CB C:ARG365 4.2 46.0 1.0
CE1 D:PHE460 4.3 35.7 1.0
ND1 D:HIS461 4.3 52.5 1.0
CG D:HIS461 4.4 56.8 1.0
CA C:ARG365 4.4 53.4 1.0
C22 C:WRI503 4.5 127.9 1.0
CE1 C:HIS371 4.6 59.3 1.0
CD1 D:PHE460 4.6 32.9 1.0
NE2 C:HIS371 4.8 54.3 1.0
CB D:SER455 4.8 51.0 1.0
O C:ARG365 4.8 39.8 1.0
O C:HOH641 4.8 40.5 1.0
C09 C:WRI503 5.0 83.7 1.0

Zinc binding site 6 out of 6 in 8ufu

Go back to Zinc Binding Sites List in 8ufu
Zinc binding site 6 out of 6 in the Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Endothelial Nitric Oxide Synthase Heme Domain in Complex with 7-(9-Amino-6,7,8,9-Tetrahydro-5H-Benzo[7]Annulen-2-Yl)- 4-Methylquinolin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn511

b:68.7
occ:1.00
 OD2 D:ASP369 2.0 88.0 1.0
OD1 D:ASP369 2.3 83.5 1.0
NE2 C:HIS461 2.3 76.7 1.0
CG D:ASP369 2.5 77.4 1.0
O D:HOH707 2.6 34.6 1.0
O D:HOH709 2.6 47.7 1.0
CE1 C:HIS461 3.2 72.4 1.0
CD2 C:HIS461 3.4 74.5 1.0
CG D:ARG365 3.8 47.4 1.0
CB D:ASP369 4.0 63.2 1.0
ND1 C:HIS461 4.4 73.0 1.0
C22 C:WRI510 4.4 110.7 1.0
CE1 D:HIS371 4.4 72.8 1.0
CE1 C:PHE460 4.5 45.4 1.0
CG C:HIS461 4.5 68.2 1.0
NE2 D:HIS371 4.6 75.0 1.0
CB D:ARG365 4.6 42.7 1.0
CA D:ARG365 4.6 47.1 1.0
CD1 C:PHE460 4.6 42.7 1.0
C23 C:WRI510 4.7 117.6 1.0
CB C:SER455 4.8 47.5 1.0
CD D:ARG365 4.9 60.1 1.0
CA D:ASP369 5.0 53.7 1.0

Reference:

H.Li, C.D.Hardy, C.T.Reidl, Q.Jing, F.Xue, M.Cinelli, R.B.Silverman, T.L.Poulos. Crystallographic and Computational Insights Into Isoform-Selective Dynamics in Nitric Oxide Synthase. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 38417024
DOI: 10.1021/ACS.BIOCHEM.3C00601
Page generated: Thu Oct 31 12:15:17 2024

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