Zinc in PDB 8hu6: Amp Deaminase 2 in Complex with Amp

All present enzymatic activity of Amp Deaminase 2 in Complex with Amp:
3.5.4.6;

The structure of Amp Deaminase 2 in Complex with Amp, PDB code: 8hu6 was solved by T.Adachi, S.Doi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.35 / 2.33
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	123.665, 163.563, 289.385, 90, 90, 90
R / Rfree (%)	23.7 / 26.8

The binding sites of Zinc atom in the Amp Deaminase 2 in Complex with Amp (pdb code 8hu6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Amp Deaminase 2 in Complex with Amp, PDB code: 8hu6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Amp Deaminase 2 in Complex with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Amp Deaminase 2 in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:38.8 occ:1.00 NE2 A:HIS687 2.3 32.6 1.0 NE2 A:HIS418 2.3 34.3 1.0 NE2 A:HIS420 2.3 34.3 1.0 O A:HOH1123 2.4 36.0 1.0 OD1 A:ASP764 2.5 35.6 1.0 HE1 A:HIS418 2.9 40.4 1.0 CE1 A:HIS418 2.9 33.7 1.0 O A:HOH1085 2.9 28.6 1.0 HD2 A:HIS687 2.9 40.8 1.0 CD2 A:HIS687 3.0 34.0 1.0 CD2 A:HIS420 3.1 33.2 1.0 HD2 A:HIS420 3.2 39.9 1.0 HE2 A:HIS709 3.2 40.9 1.0 CG A:ASP764 3.3 34.0 1.0 CE1 A:HIS420 3.4 35.0 1.0 CE1 A:HIS687 3.4 32.7 1.0 CD2 A:HIS418 3.4 35.1 1.0 OD2 A:ASP764 3.6 31.2 1.0 HE1 A:HIS420 3.6 42.1 1.0 HE1 A:HIS687 3.7 39.2 1.0 HD2 A:HIS418 3.8 42.1 1.0 NE2 A:HIS709 3.9 34.1 1.0 ND1 A:HIS418 4.1 32.2 1.0 CG A:HIS687 4.2 33.4 1.0 HA A:ASP764 4.2 38.4 1.0 CG A:HIS420 4.3 34.5 1.0 CG A:HIS418 4.4 30.1 1.0 ND1 A:HIS687 4.4 37.5 1.0 ND1 A:HIS420 4.4 35.5 1.0 CB A:ASP764 4.5 30.8 1.0 HG12 A:VAL627 4.7 47.0 1.0 HE1 A:HIS709 4.7 40.0 1.0 CE1 A:HIS709 4.7 33.4 1.0 HB2 A:ASP764 4.8 37.0 1.0 OD2 A:ASP765 4.8 38.4 1.0 HD1 A:HIS418 4.8 38.6 1.0 CA A:ASP764 4.8 32.0 1.0 CD2 A:HIS709 4.8 34.4 1.0 HD2 A:HIS709 4.9 41.2 1.0 HG11 A:VAL627 5.0 47.0 1.0

Zinc binding site 2 out of 4 in the Amp Deaminase 2 in Complex with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Amp Deaminase 2 in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:30.4 occ:1.00 O B:HOH1054 2.1 31.4 1.0 NE2 B:HIS687 2.2 37.2 1.0 NE2 B:HIS418 2.3 34.5 1.0 NE2 B:HIS420 2.3 40.0 1.0 OD1 B:ASP764 2.3 36.2 1.0 HE1 B:HIS418 2.8 43.6 1.0 CE1 B:HIS418 2.8 36.3 1.0 CG B:ASP764 3.1 35.9 1.0 CD2 B:HIS420 3.1 35.0 1.0 CE1 B:HIS687 3.1 34.6 1.0 HD2 B:HIS420 3.2 42.0 1.0 CD2 B:HIS687 3.2 32.4 1.0 HE2 B:HIS709 3.2 40.0 1.0 O B:HOH1122 3.2 36.8 1.0 HE1 B:HIS687 3.3 41.5 1.0 OD2 B:ASP764 3.3 35.0 1.0 CE1 B:HIS420 3.4 37.0 1.0 HD2 B:HIS687 3.4 38.8 1.0 CD2 B:HIS418 3.4 34.8 1.0 HE1 B:HIS420 3.6 44.5 1.0 HD2 B:HIS418 3.8 41.7 1.0 ND1 B:HIS418 4.0 32.5 1.0 NE2 B:HIS709 4.0 33.4 1.0 HA B:ASP764 4.1 40.5 1.0 ND1 B:HIS687 4.2 38.9 1.0 CG B:HIS420 4.3 33.4 1.0 CB B:ASP764 4.3 31.3 1.0 CG B:HIS687 4.3 33.0 1.0 CG B:HIS418 4.3 34.0 1.0 ND1 B:HIS420 4.4 33.0 1.0 O B:HOH1107 4.4 36.0 1.0 HB2 B:ASP764 4.5 37.6 1.0 OD2 B:ASP765 4.6 42.5 1.0 CA B:ASP764 4.6 33.8 1.0 HD1 B:HIS418 4.7 39.1 1.0 HG11 B:VAL627 4.7 41.2 1.0 HE1 B:HIS709 4.7 41.0 1.0 HG12 B:VAL627 4.8 41.2 1.0 CE1 B:HIS709 4.8 34.2 1.0 CD2 B:HIS709 5.0 39.5 1.0

Zinc binding site 3 out of 4 in the Amp Deaminase 2 in Complex with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Amp Deaminase 2 in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:31.3 occ:1.00 O C:HOH1129 2.2 27.3 1.0 NE2 C:HIS418 2.2 35.8 1.0 NE2 C:HIS687 2.3 31.4 1.0 NE2 C:HIS420 2.3 27.6 1.0 OD1 C:ASP764 2.5 29.9 1.0 HE1 C:HIS418 2.8 43.6 1.0 CE1 C:HIS418 2.8 36.4 1.0 HD2 C:HIS687 2.9 31.5 1.0 CD2 C:HIS687 3.0 26.3 1.0 O C:HOH1130 3.0 29.2 1.0 HE2 C:HIS709 3.1 33.8 1.0 CD2 C:HIS420 3.2 35.3 1.0 HD2 C:HIS420 3.3 42.3 1.0 CG C:ASP764 3.3 35.6 1.0 CE1 C:HIS420 3.3 35.8 1.0 CD2 C:HIS418 3.4 34.1 1.0 CE1 C:HIS687 3.4 31.9 1.0 HE1 C:HIS420 3.6 43.0 1.0 OD2 C:ASP764 3.6 29.6 1.0 HE1 C:HIS687 3.8 38.3 1.0 HD2 C:HIS418 3.8 41.0 1.0 NE2 C:HIS709 3.9 28.1 1.0 ND1 C:HIS418 4.0 34.6 1.0 HA C:ASP764 4.1 39.2 1.0 CG C:HIS687 4.2 30.7 1.0 CG C:HIS418 4.3 29.8 1.0 CG C:HIS420 4.4 33.3 1.0 ND1 C:HIS687 4.4 28.2 1.0 ND1 C:HIS420 4.4 32.6 1.0 CB C:ASP764 4.5 34.1 1.0 HG12 C:VAL627 4.6 35.4 1.0 HB2 C:ASP764 4.7 40.9 1.0 HD1 C:HIS418 4.7 41.5 1.0 CA C:ASP764 4.8 32.7 1.0 HG11 C:VAL627 4.8 35.4 1.0 HE1 C:HIS709 4.8 35.1 1.0 CE1 C:HIS709 4.8 29.2 1.0 CD2 C:HIS709 4.9 31.2 1.0 HD2 C:HIS709 4.9 37.4 1.0 OD2 C:ASP765 4.9 44.1 1.0

Zinc binding site 4 out of 4 in the Amp Deaminase 2 in Complex with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Amp Deaminase 2 in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:32.2 occ:1.00 O D:HOH1110 2.1 33.5 1.0 NE2 D:HIS687 2.1 38.7 1.0 NE2 D:HIS420 2.1 39.0 1.0 NE2 D:HIS418 2.3 35.7 1.0 OD1 D:ASP764 2.4 34.8 1.0 HN61 D:AMP902 2.5 54.4 1.0 HE1 D:HIS418 2.7 41.2 1.0 CE1 D:HIS418 2.8 34.3 1.0 CD2 D:HIS687 3.0 36.9 1.0 CE1 D:HIS420 3.1 38.0 1.0 CD2 D:HIS420 3.1 41.5 1.0 CE1 D:HIS687 3.1 32.2 1.0 N6 D:AMP902 3.1 45.3 1.0 HD2 D:HIS687 3.2 44.3 1.0 HD2 D:HIS420 3.3 49.8 1.0 HE1 D:HIS420 3.3 45.6 1.0 CG D:ASP764 3.3 33.6 1.0 HE1 D:HIS687 3.4 38.6 1.0 HN62 D:AMP902 3.4 54.4 1.0 CD2 D:HIS418 3.5 37.1 1.0 OD2 D:ASP764 3.6 34.9 1.0 NE2 D:HIS709 3.9 36.2 1.0 HD2 D:HIS418 3.9 44.5 1.0 ND1 D:HIS418 4.0 30.9 1.0 HA D:ASP764 4.1 45.8 1.0 ND1 D:HIS420 4.2 40.2 1.0 CG D:HIS687 4.2 35.0 1.0 CG D:HIS420 4.2 40.5 1.0 ND1 D:HIS687 4.2 33.3 1.0 C6 D:AMP902 4.3 51.2 1.0 CG D:HIS418 4.4 32.0 1.0 CB D:ASP764 4.5 35.5 1.0 HG12 D:VAL627 4.5 45.9 1.0 HB2 D:ASP764 4.7 42.7 1.0 HD1 D:HIS418 4.7 37.1 1.0 N1 D:AMP902 4.7 53.2 1.0 CA D:ASP764 4.7 38.2 1.0 CE1 D:HIS709 4.7 35.4 1.0 CD2 D:HIS709 4.7 34.8 1.0 HD2 D:HIS709 4.7 41.7 1.0 HE1 D:HIS709 4.7 42.5 1.0 HG11 D:VAL627 4.9 45.9 1.0 OD1 D:ASP765 4.9 43.4 1.0 HD1 D:HIS420 4.9 48.2 1.0 HD1 D:HIS687 5.0 39.9 1.0

Y.Kitao, T.Saito, S.Watanabe, Y.Ohe, K.Takahashi, T.Akaki, T.Adachi, S.Doi, K.Yamanaka, Y.Murai, M.Oba, T.Suzuki. The Discovery of 3,3-Dimethyl-1,2,3,4-Tetrahydroquinoxaline-1-Carboxamides As AMPD2 Inhibitors with A Novel Mechanism of Action. Bioorg.Med.Chem.Lett. V. 80 2023.
ISSN: ESSN 1464-3405