Zinc in PDB 8hub: Amp Deaminase 2 in Complex with An Inhibitor

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

The structure of Amp Deaminase 2 in Complex with An Inhibitor, PDB code: 8hub 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)	98.84 / 3.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	124.516, 162.533, 289.758, 90, 90, 90
R / Rfree (%)	25.8 / 27.6

The binding sites of Zinc atom in the Amp Deaminase 2 in Complex with An Inhibitor (pdb code 8hub). 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 An Inhibitor, PDB code: 8hub:
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 An Inhibitor


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:113.5 occ:1.00 NE2 A:HIS418 2.3 112.5 1.0 NE2 A:HIS420 2.3 115.1 1.0 NE2 A:HIS687 2.3 114.3 1.0 OD1 A:ASP764 2.7 112.4 1.0 HD2 A:HIS687 2.8 136.7 1.0 CD2 A:HIS687 2.9 113.9 1.0 CE1 A:HIS418 3.0 112.1 1.0 HE1 A:HIS418 3.0 134.6 1.0 CE1 A:HIS420 3.1 115.9 1.0 OD2 A:ASP764 3.1 111.8 1.0 HE1 A:HIS709 3.1 130.8 1.0 CG A:ASP764 3.2 111.6 1.0 HE1 A:HIS420 3.2 139.1 1.0 CD2 A:HIS420 3.3 115.0 1.0 CE1 A:HIS687 3.4 114.0 1.0 CD2 A:HIS418 3.5 112.9 1.0 HD2 A:HIS420 3.5 138.0 1.0 HD2 A:HIS418 3.7 135.5 1.0 HE1 A:HIS687 3.8 136.9 1.0 HG13 A:VAL627 4.0 140.8 1.0 CE1 A:HIS709 4.0 109.0 1.0 CG A:HIS687 4.1 113.4 1.0 ND1 A:HIS420 4.2 116.7 1.0 ND1 A:HIS418 4.2 111.7 1.0 CG A:HIS420 4.3 116.2 1.0 ND1 A:HIS687 4.4 113.7 1.0 HG11 A:VAL627 4.4 140.8 1.0 CG A:HIS418 4.5 112.8 1.0 CB A:ASP764 4.6 110.4 1.0 HA A:ASP764 4.6 133.0 1.0 CG1 A:VAL627 4.7 117.3 1.0 HB2 A:ASP764 4.8 132.4 1.0 HE2 A:HIS709 4.9 129.9 1.0 NE2 A:HIS709 4.9 108.2 1.0 HD1 A:HIS420 4.9 140.0 1.0 HG22 A:VAL627 4.9 140.9 1.0 ND1 A:HIS709 5.0 108.6 1.0 HD1 A:HIS418 5.0 134.0 1.0

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


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:90.1 occ:1.00 NE2 B:HIS420 2.3 92.2 1.0 NE2 B:HIS418 2.3 89.5 1.0 NE2 B:HIS687 2.3 89.5 1.0 OD1 B:ASP764 2.7 92.4 1.0 OD2 B:ASP764 2.8 90.7 1.0 HD2 B:HIS687 2.9 105.4 1.0 HE1 B:HIS418 2.9 107.3 1.0 CE1 B:HIS418 3.0 89.4 1.0 CG B:ASP764 3.0 91.3 1.0 CD2 B:HIS687 3.0 87.8 1.0 CD2 B:HIS420 3.1 93.4 1.0 HD2 B:HIS420 3.2 112.1 1.0 CE1 B:HIS420 3.2 93.5 1.0 CE1 B:HIS687 3.5 89.6 1.0 CD2 B:HIS418 3.5 90.1 1.0 HE1 B:HIS420 3.5 112.2 1.0 HD2 B:HIS418 3.8 108.1 1.0 HE1 B:HIS687 3.8 107.5 1.0 ND1 B:HIS418 4.2 89.4 1.0 CG B:HIS420 4.2 95.2 1.0 NE2 B:HIS709 4.2 84.3 1.0 CG B:HIS687 4.2 87.5 1.0 ND1 B:HIS420 4.2 95.0 1.0 CB B:ASP764 4.3 91.7 1.0 HB2 B:ASP764 4.4 110.0 1.0 ND1 B:HIS687 4.4 88.5 1.0 CG B:HIS418 4.5 89.7 1.0 HA B:ASP764 4.5 110.4 1.0 HG21 B:VAL627 4.9 109.9 1.0 HD1 B:HIS418 4.9 107.3 1.0 CA B:ASP764 4.9 92.0 1.0 HG22 B:VAL627 5.0 109.9 1.0 HE1 B:HIS709 5.0 101.7 1.0 HB3 B:ASP764 5.0 110.0 1.0

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


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:77.3 occ:1.00 OD1 C:ASP764 2.3 75.6 1.0 NE2 C:HIS418 2.3 73.9 1.0 NE2 C:HIS420 2.3 75.7 1.0 NE2 C:HIS687 2.3 73.7 1.0 HE1 C:HIS418 2.6 88.7 1.0 CE1 C:HIS418 2.7 73.9 1.0 CG C:ASP764 3.0 74.4 1.0 OD2 C:ASP764 3.1 75.0 1.0 CD2 C:HIS420 3.1 76.6 1.0 CD2 C:HIS687 3.1 73.5 1.0 HD2 C:HIS420 3.2 91.9 1.0 HD2 C:HIS687 3.2 88.2 1.0 CE1 C:HIS420 3.2 76.7 1.0 CE1 C:HIS687 3.3 73.4 1.0 HE1 C:HIS420 3.5 92.1 1.0 HE1 C:HIS687 3.5 88.0 1.0 CD2 C:HIS418 3.6 74.2 1.0 NE2 C:HIS709 3.9 71.6 1.0 ND1 C:HIS418 4.0 74.3 1.0 HD2 C:HIS418 4.0 89.1 1.0 CG C:HIS420 4.2 77.8 1.0 ND1 C:HIS420 4.3 77.8 1.0 CG C:HIS687 4.3 72.5 1.0 ND1 C:HIS687 4.3 73.3 1.0 CB C:ASP764 4.4 74.9 1.0 HA C:ASP764 4.4 90.7 1.0 CG C:HIS418 4.4 73.9 1.0 HB2 C:ASP764 4.6 89.8 1.0 HD1 C:HIS418 4.6 89.2 1.0 HD2 C:HIS709 4.8 85.2 1.0 CD2 C:HIS709 4.8 71.0 1.0 CE1 C:HIS709 4.8 72.1 1.0 HE1 C:HIS709 4.8 86.5 1.0 CA C:ASP764 4.9 75.6 1.0 HB3 C:ASP764 5.0 89.8 1.0

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


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:67.5 occ:1.00 NE2 D:HIS418 2.3 67.6 1.0 NE2 D:HIS687 2.3 67.7 1.0 NE2 D:HIS420 2.3 69.7 1.0 OD1 D:ASP764 2.4 71.5 1.0 HE1 D:HIS418 2.6 81.8 1.0 CE1 D:HIS418 2.8 68.2 1.0 CG D:ASP764 3.0 71.1 1.0 CD2 D:HIS687 3.1 66.5 1.0 CE1 D:HIS420 3.1 70.3 1.0 OD2 D:ASP764 3.2 71.6 1.0 HD2 D:HIS687 3.2 79.8 1.0 CD2 D:HIS420 3.2 71.1 1.0 HE1 D:HIS420 3.3 84.3 1.0 CE1 D:HIS687 3.4 67.2 1.0 HD2 D:HIS420 3.4 85.3 1.0 CD2 D:HIS418 3.6 68.3 1.0 HE1 D:HIS687 3.6 80.6 1.0 NE2 D:HIS709 3.6 65.7 1.0 HD2 D:HIS418 4.0 82.0 1.0 ND1 D:HIS418 4.0 68.4 1.0 ND1 D:HIS420 4.2 71.4 1.0 HA D:ASP764 4.2 85.7 1.0 CB D:ASP764 4.3 70.8 1.0 CG D:HIS420 4.3 71.8 1.0 CG D:HIS687 4.3 65.0 1.0 HB2 D:ASP764 4.4 85.0 1.0 ND1 D:HIS687 4.4 65.6 1.0 CG D:HIS418 4.5 68.6 1.0 HE1 D:HIS709 4.5 79.1 1.0 CE1 D:HIS709 4.5 65.9 1.0 CD2 D:HIS709 4.6 64.9 1.0 HD2 D:HIS709 4.7 77.9 1.0 CA D:ASP764 4.7 71.4 1.0 HG13 D:VAL627 4.9 80.9 1.0 HD1 D:HIS420 5.0 85.7 1.0 O D:ASP764 5.0 72.4 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