Zinc in PDB 8qch: Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001

The structure of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001, PDB code: 8qch was solved by C.Zimberger, B.Canard, F.Ferron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	105.53 / 2.44
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	142.757, 142.983, 156.399, 90, 90, 90
R / Rfree (%)	21.4 / 24.3

The structure of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 (pdb code 8qch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001, PDB code: 8qch:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:51.9 occ:1.00 O A:HOH503 1.8 103.4 1.0 NE2 A:HIS26 2.0 38.0 1.0 NE2 A:HIS24 2.1 44.4 1.0 NE2 A:HIS208 2.2 43.6 1.0 OD1 A:ASP293 2.3 43.3 1.0 CE1 A:HIS26 3.0 38.1 1.0 CD2 A:HIS26 3.0 37.0 1.0 CD2 A:HIS24 3.1 42.6 1.0 CE1 A:HIS24 3.2 44.6 1.0 CD2 A:HIS208 3.2 42.2 1.0 CE1 A:HIS208 3.2 43.6 1.0 CG A:ASP293 3.3 43.3 1.0 C7 A:EIF401 3.7 55.0 1.0 OD2 A:ASP293 3.7 45.8 1.0 C10 A:EIF401 3.8 55.3 1.0 C8 A:EIF401 4.0 54.6 1.0 N1 A:EIF401 4.0 55.1 1.0 NE2 A:HIS232 4.0 41.4 1.0 N4 A:EIF401 4.1 55.2 1.0 ND1 A:HIS26 4.1 38.2 1.0 CG A:HIS26 4.1 36.8 1.0 O6 A:EIF401 4.2 55.6 1.0 CG A:HIS24 4.3 41.3 1.0 ND1 A:HIS24 4.3 43.7 1.0 CG A:HIS208 4.4 40.6 1.0 ND1 A:HIS208 4.4 43.0 1.0 N2 A:EIF401 4.4 54.7 1.0 C9 A:EIF401 4.4 54.9 1.0 C6 A:EIF401 4.5 54.9 1.0 N A:EIF401 4.5 54.6 1.0 CB A:ASP293 4.6 38.9 1.0 CD2 A:HIS232 4.8 40.4 1.0 CD A:ARG105 4.9 37.5 1.0 CA A:ASP293 4.9 38.0 1.0 OD2 A:ASP294 4.9 45.4 1.0 CE1 A:HIS232 5.0 42.2 1.0

Zinc binding site 2 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:56.5 occ:1.00 O B:HOH1108 1.8 82.7 1.0 NE2 B:HIS26 2.1 37.5 1.0 NE2 B:HIS24 2.1 46.4 1.0 OD1 B:ASP293 2.3 46.0 1.0 NE2 B:HIS208 2.3 44.4 1.0 CD2 B:HIS26 2.9 36.5 1.0 CE1 B:HIS24 3.1 46.0 1.0 CD2 B:HIS24 3.1 44.7 1.0 CE1 B:HIS26 3.2 36.9 1.0 CE1 B:HIS208 3.2 45.2 1.0 CD2 B:HIS208 3.3 43.7 1.0 CG B:ASP293 3.3 44.1 1.0 OD2 B:ASP293 3.7 44.2 1.0 C7 B:EIF1001 3.8 57.1 1.0 NE2 B:HIS232 3.9 44.1 1.0 C8 B:EIF1001 4.1 57.1 1.0 C10 B:EIF1001 4.1 57.7 1.0 N1 B:EIF1001 4.1 56.6 1.0 CG B:HIS26 4.1 35.8 1.0 CG B:HIS24 4.2 43.2 1.0 ND1 B:HIS24 4.2 45.2 1.0 ND1 B:HIS26 4.3 36.7 1.0 ND1 B:HIS208 4.4 45.2 1.0 CG B:HIS208 4.4 43.0 1.0 N4 B:EIF1001 4.4 57.4 1.0 C6 B:EIF1001 4.5 56.4 1.0 N2 B:EIF1001 4.5 57.4 1.0 O6 B:EIF1001 4.5 58.2 1.0 N B:EIF1001 4.5 56.5 1.0 CB B:ASP293 4.6 41.5 1.0 C9 B:EIF1001 4.6 57.3 1.0 CD2 B:HIS232 4.7 43.1 1.0 CE1 B:HIS232 4.8 44.1 1.0 CA B:ASP293 4.9 40.2 1.0 OD2 B:ASP294 5.0 45.3 1.0

Zinc binding site 3 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:53.2 occ:1.00 O C:HOH508 1.8 46.0 1.0 NE2 C:HIS26 2.1 36.3 1.0 NE2 C:HIS24 2.1 40.2 1.0 NE2 C:HIS208 2.1 40.6 1.0 OD1 C:ASP293 2.3 36.9 1.0 CE1 C:HIS24 3.1 40.3 1.0 CE1 C:HIS26 3.1 36.2 1.0 CE1 C:HIS208 3.1 40.9 1.0 CD2 C:HIS24 3.1 38.5 1.0 CD2 C:HIS26 3.1 35.4 1.0 CD2 C:HIS208 3.1 39.4 1.0 CG C:ASP293 3.4 35.8 1.0 C7 C:EIF401 3.8 52.7 1.0 OD2 C:ASP293 3.8 36.2 1.0 C10 C:EIF401 3.9 52.9 1.0 NE2 C:HIS232 3.9 37.4 1.0 C8 C:EIF401 4.0 52.7 1.0 N4 C:EIF401 4.1 52.9 1.0 ND1 C:HIS24 4.2 39.6 1.0 CG C:HIS24 4.2 37.3 1.0 N1 C:EIF401 4.2 52.4 1.0 CG C:HIS26 4.2 34.4 1.0 ND1 C:HIS26 4.2 35.9 1.0 CG C:HIS208 4.2 38.2 1.0 ND1 C:HIS208 4.2 40.5 1.0 N2 C:EIF401 4.3 52.9 1.0 O6 C:EIF401 4.3 53.1 1.0 C9 C:EIF401 4.4 52.9 1.0 N C:EIF401 4.6 52.1 1.0 C6 C:EIF401 4.6 52.3 1.0 CB C:ASP293 4.7 33.7 1.0 CD2 C:HIS232 4.8 35.9 1.0 CE1 C:HIS232 4.8 37.3 1.0 CA C:ASP293 5.0 33.6 1.0

Zinc binding site 4 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn404 b:50.9 occ:1.00 O D:HOH503 1.8 50.9 1.0 NE2 D:HIS24 2.0 41.7 1.0 NE2 D:HIS26 2.1 37.4 1.0 OD1 D:ASP293 2.2 45.6 1.0 NE2 D:HIS208 2.3 40.0 1.0 CD2 D:HIS26 3.0 36.5 1.0 CE1 D:HIS24 3.0 41.8 1.0 CD2 D:HIS24 3.1 40.2 1.0 CE1 D:HIS26 3.2 37.6 1.0 CG D:ASP293 3.2 42.3 1.0 CD2 D:HIS208 3.3 38.6 1.0 CE1 D:HIS208 3.3 40.0 1.0 OD2 D:ASP293 3.7 41.9 1.0 C7 D:EIF403 3.8 48.5 1.0 C10 D:EIF403 3.8 49.3 1.0 O6 D:EIF403 4.0 50.1 1.0 NE2 D:HIS232 4.0 36.0 1.0 N1 D:EIF403 4.1 48.0 1.0 C8 D:EIF403 4.2 48.1 1.0 ND1 D:HIS24 4.2 40.9 1.0 CG D:HIS24 4.2 39.0 1.0 N4 D:EIF403 4.2 48.8 1.0 CG D:HIS26 4.2 36.0 1.0 ND1 D:HIS26 4.3 37.7 1.0 CG D:HIS208 4.4 37.8 1.0 ND1 D:HIS208 4.5 39.6 1.0 CB D:ASP293 4.5 36.8 1.0 C9 D:EIF403 4.5 48.4 1.0 N2 D:EIF403 4.6 48.2 1.0 C6 D:EIF403 4.6 47.7 1.0 N D:EIF403 4.7 47.8 1.0 CE1 D:HIS232 4.8 36.2 1.0 CA D:ASP293 4.8 35.0 1.0 OD2 D:ASP294 4.9 41.2 1.0 O D:ASP293 4.9 34.9 1.0 CD2 D:HIS232 4.9 35.0 1.0

Zinc binding site 5 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn403 b:50.7 occ:1.00 O E:HOH508 1.9 60.8 1.0 NE2 E:HIS26 2.0 39.3 1.0 NE2 E:HIS24 2.2 43.1 1.0 NE2 E:HIS208 2.3 35.3 1.0 OD1 E:ASP293 2.3 43.2 1.0 CD2 E:HIS26 2.9 38.3 1.0 CE1 E:HIS26 3.0 39.2 1.0 CD2 E:HIS24 3.1 41.4 1.0 CE1 E:HIS208 3.2 36.1 1.0 CE1 E:HIS24 3.2 42.7 1.0 CD2 E:HIS208 3.2 34.5 1.0 CG E:ASP293 3.4 42.0 1.0 C7 E:EIF402 3.8 47.5 1.0 OD2 E:ASP293 3.8 43.6 1.0 C10 E:EIF402 3.9 47.8 1.0 NE2 E:HIS232 3.9 36.7 1.0 N1 E:EIF402 4.0 47.1 1.0 CG E:HIS26 4.1 37.6 1.0 O6 E:EIF402 4.1 47.9 1.0 ND1 E:HIS26 4.1 38.9 1.0 C8 E:EIF402 4.2 47.4 1.0 CG E:HIS24 4.3 39.8 1.0 N4 E:EIF402 4.3 48.0 1.0 ND1 E:HIS24 4.3 41.8 1.0 ND1 E:HIS208 4.4 36.6 1.0 CG E:HIS208 4.4 34.6 1.0 C6 E:EIF402 4.4 47.0 1.0 CB E:ASP293 4.6 37.3 1.0 N E:EIF402 4.6 46.7 1.0 C9 E:EIF402 4.6 47.9 1.0 N2 E:EIF402 4.6 47.9 1.0 CE1 E:HIS232 4.8 37.0 1.0 CD2 E:HIS232 4.8 36.0 1.0 CA E:ASP293 4.9 36.0 1.0 OD2 E:ASP294 4.9 43.0 1.0

Zinc binding site 6 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn402 b:53.5 occ:1.00 O F:HOH504 1.9 60.6 1.0 NE2 F:HIS208 1.9 39.0 1.0 NE2 F:HIS26 2.1 41.9 1.0 NE2 F:HIS24 2.1 41.8 1.0 OD1 F:ASP293 2.4 41.6 1.0 CE1 F:HIS208 2.8 39.5 1.0 CD2 F:HIS26 2.9 40.5 1.0 CD2 F:HIS208 3.1 38.2 1.0 CD2 F:HIS24 3.1 39.9 1.0 CE1 F:HIS24 3.1 41.8 1.0 CE1 F:HIS26 3.2 41.8 1.0 CG F:ASP293 3.4 41.6 1.0 C7 F:EIF401 3.9 50.8 1.0 OD2 F:ASP293 3.9 44.1 1.0 NE2 F:HIS232 4.0 37.5 1.0 ND1 F:HIS208 4.0 39.5 1.0 C10 F:EIF401 4.0 51.1 1.0 CG F:HIS208 4.1 38.1 1.0 CG F:HIS26 4.1 39.5 1.0 N1 F:EIF401 4.1 50.5 1.0 C8 F:EIF401 4.2 50.5 1.0 CG F:HIS24 4.2 38.7 1.0 ND1 F:HIS26 4.3 41.3 1.0 ND1 F:HIS24 4.3 41.0 1.0 O6 F:EIF401 4.3 51.6 1.0 N4 F:EIF401 4.3 51.1 1.0 C6 F:EIF401 4.5 50.2 1.0 N2 F:EIF401 4.6 50.9 1.0 C9 F:EIF401 4.6 51.1 1.0 CB F:ASP293 4.6 37.9 1.0 N F:EIF401 4.6 49.9 1.0 CD2 F:HIS232 4.8 36.5 1.0 CE1 F:HIS232 4.9 37.9 1.0 CA F:ASP293 4.9 36.5 1.0

Zinc binding site 7 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn403 b:53.5 occ:1.00 O G:HOH510 1.9 44.3 1.0 NE2 G:HIS24 2.1 41.8 1.0 NE2 G:HIS26 2.2 40.3 1.0 OD1 G:ASP293 2.3 39.5 1.0 NE2 G:HIS208 2.3 44.5 1.0 CD2 G:HIS26 2.9 39.0 1.0 CE1 G:HIS24 3.1 41.8 1.0 CD2 G:HIS24 3.1 40.5 1.0 CD2 G:HIS208 3.3 44.0 1.0 CE1 G:HIS208 3.3 44.7 1.0 CG G:ASP293 3.3 38.9 1.0 CE1 G:HIS26 3.4 40.8 1.0 OD2 G:ASP293 3.7 40.2 1.0 C7 G:EIF402 3.8 53.3 1.0 NE2 G:HIS232 3.9 42.9 1.0 C8 G:EIF402 4.0 53.3 1.0 C10 G:EIF402 4.1 53.8 1.0 N1 G:EIF402 4.1 52.9 1.0 CG G:HIS26 4.1 38.6 1.0 CG G:HIS24 4.2 39.6 1.0 ND1 G:HIS24 4.2 41.5 1.0 ND1 G:HIS26 4.4 40.5 1.0 N4 G:EIF402 4.4 53.9 1.0 N2 G:EIF402 4.4 53.7 1.0 O6 G:EIF402 4.4 54.3 1.0 CG G:HIS208 4.4 43.6 1.0 ND1 G:HIS208 4.5 44.6 1.0 C6 G:EIF402 4.5 52.8 1.0 N G:EIF402 4.5 53.1 1.0 CB G:ASP293 4.6 35.8 1.0 C9 G:EIF402 4.6 53.9 1.0 CE1 G:HIS232 4.6 42.8 1.0 CA G:ASP293 4.9 35.6 1.0 OD2 G:ASP294 4.9 45.1 1.0 O G:ASP293 4.9 36.6 1.0

Zinc binding site 8 out of 8 in the Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Adenosine Deaminase-Like Protein in Complex with Compound AT8001 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn402 b:59.3 occ:1.00 O H:HOH505 1.8 62.1 1.0 NE2 H:HIS24 2.1 42.0 1.0 NE2 H:HIS26 2.1 41.5 1.0 NE2 H:HIS208 2.2 40.2 1.0 OD1 H:ASP293 2.4 45.1 1.0 CE1 H:HIS24 3.0 42.2 1.0 CD2 H:HIS26 3.0 40.4 1.0 CD2 H:HIS24 3.2 40.2 1.0 CE1 H:HIS208 3.2 40.8 1.0 CE1 H:HIS26 3.2 41.2 1.0 CD2 H:HIS208 3.2 39.1 1.0 CG H:ASP293 3.4 44.4 1.0 C7 H:EIF401 3.7 58.0 1.0 OD2 H:ASP293 3.7 45.6 1.0 C10 H:EIF401 3.8 58.1 1.0 NE2 H:HIS232 4.0 40.9 1.0 N1 H:EIF401 4.0 57.7 1.0 O6 H:EIF401 4.1 58.2 1.0 C8 H:EIF401 4.1 57.9 1.0 ND1 H:HIS24 4.2 41.4 1.0 CG H:HIS26 4.2 39.8 1.0 N4 H:EIF401 4.2 57.9 1.0 CG H:HIS24 4.2 39.1 1.0 ND1 H:HIS26 4.3 41.0 1.0 ND1 H:HIS208 4.3 40.6 1.0 CG H:HIS208 4.3 38.4 1.0 C6 H:EIF401 4.5 57.6 1.0 N2 H:EIF401 4.5 57.7 1.0 C9 H:EIF401 4.5 57.8 1.0 N H:EIF401 4.6 57.8 1.0 CB H:ASP293 4.6 42.0 1.0 CE1 H:HIS232 4.8 41.2 1.0 CD2 H:HIS232 4.9 39.7 1.0 CD H:ARG105 5.0 46.8 1.0 CA H:ASP293 5.0 41.2 1.0

A.Chazot, C.Zimberger, M.Feracci, A.Moussa, S.Good, J.P.Sommadossi, K.Alvarez, F.Ferron, B.Canard. The Activation Chain of the Broad-Spectrum Antiviral Bemnifosbuvir at Atomic Resolution Plos Biol. 2024.
ISSN: ESSN 1545-7885
DOI: 10.1371/JOURNAL.PBIO.3002743