Zinc in PDB 9ntf: Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site

The structure of Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site, PDB code: 9ntf was solved by G.Kaur, J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.85 / 1.56
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.344, 82.351, 211.495, 90, 92.29, 90
R / Rfree (%)	16.1 / 18.8

The binding sites of Zinc atom in the Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site (pdb code 9ntf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site, PDB code: 9ntf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:20.0 occ:1.00 O A:HOH720 1.9 19.6 1.0 NE2 A:HIS123 2.1 21.2 1.0 NE2 A:HIS121 2.2 19.5 1.0 OD1 A:ASP451 2.2 20.4 1.0 NE2 A:HIS366 2.2 19.3 1.0 CD2 A:HIS123 3.0 18.1 1.0 CD2 A:HIS121 3.1 21.4 1.0 CE1 A:HIS123 3.1 21.1 1.0 CE1 A:HIS121 3.2 21.7 1.0 CE1 A:HIS366 3.2 19.6 1.0 CG A:ASP451 3.2 21.7 1.0 CD2 A:HIS366 3.2 18.7 1.0 OD2 A:ASP451 3.5 20.6 1.0 NE2 A:HIS394 3.7 20.3 1.0 O A:HOH746 3.8 31.7 1.0 O A:HOH704 3.9 24.7 0.5 O2 A:EDO605 4.0 25.9 0.5 O1 A:EDO605 4.2 31.9 0.5 CG A:HIS123 4.2 18.3 1.0 ND1 A:HIS123 4.2 20.4 1.0 ND1 A:HIS121 4.3 21.5 1.0 CG A:HIS121 4.3 20.7 1.0 ND1 A:HIS366 4.3 18.2 1.0 CG A:HIS366 4.4 17.6 1.0 O A:HOH1050 4.5 27.8 0.5 CE1 A:HIS394 4.5 25.8 1.0 O A:HOH704 4.5 30.3 0.5 CB A:ASP451 4.6 21.8 1.0 OD1 A:ASP452 4.7 23.3 1.0 CD2 A:HIS394 4.7 20.4 1.0 C2 A:EDO605 4.8 19.8 0.5 O A:HOH712 4.8 37.1 1.0 CA A:ASP451 4.9 17.9 1.0 C1 A:EDO605 5.0 27.8 0.5

Zinc binding site 2 out of 4 in the Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:18.3 occ:1.00 O B:HOH724 1.9 19.6 1.0 NE2 B:HIS123 2.1 18.8 1.0 NE2 B:HIS121 2.2 17.6 1.0 OD1 B:ASP451 2.2 19.5 1.0 NE2 B:HIS366 2.2 16.7 1.0 CD2 B:HIS123 3.0 16.9 1.0 CD2 B:HIS121 3.1 18.0 1.0 CG B:ASP451 3.1 22.0 1.0 CE1 B:HIS123 3.1 18.5 1.0 CE1 B:HIS366 3.1 19.6 1.0 CE1 B:HIS121 3.2 19.9 1.0 CD2 B:HIS366 3.2 16.0 1.0 OD2 B:ASP451 3.4 19.9 1.0 O B:HOH739 3.6 31.7 1.0 NE2 B:HIS394 3.7 18.6 1.0 O2 B:EDO605 4.0 22.3 0.5 O B:HOH978 4.0 23.8 0.5 CG B:HIS123 4.2 17.9 1.0 ND1 B:HIS123 4.2 16.8 1.0 ND1 B:HIS121 4.3 17.7 1.0 CG B:HIS121 4.3 16.9 1.0 ND1 B:HIS366 4.3 18.3 1.0 CG B:HIS366 4.3 16.4 1.0 CE1 B:HIS394 4.5 19.4 1.0 CB B:ASP451 4.5 17.3 1.0 O B:HOH978 4.5 31.4 0.5 O B:HOH702 4.6 22.9 0.5 OD1 B:ASP452 4.6 21.1 1.0 CD2 B:HIS394 4.7 21.1 1.0 O1 B:EDO605 4.8 30.6 0.5 O B:HOH877 4.8 39.9 1.0 CA B:ASP451 4.9 13.7 1.0 C2 B:EDO605 4.9 18.5 0.5

Zinc binding site 3 out of 4 in the Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:17.6 occ:1.00 O C:HOH710 2.0 20.7 1.0 NE2 C:HIS123 2.0 20.2 1.0 OD1 C:ASP451 2.2 18.0 1.0 NE2 C:HIS121 2.2 18.3 1.0 NE2 C:HIS366 2.2 18.6 1.0 CE1 C:HIS123 3.0 17.9 1.0 CD2 C:HIS123 3.0 19.2 1.0 CD2 C:HIS121 3.1 19.9 1.0 CE1 C:HIS366 3.1 19.8 1.0 CG C:ASP451 3.2 21.1 1.0 CE1 C:HIS121 3.2 19.6 1.0 CD2 C:HIS366 3.2 16.0 1.0 OD2 C:ASP451 3.5 20.2 1.0 O C:HOH702 3.7 31.5 1.0 NE2 C:HIS394 3.8 19.1 1.0 O C:HOH1043 3.9 27.8 0.5 O1 C:EDO604 4.0 28.0 0.5 ND1 C:HIS123 4.1 19.6 1.0 CG C:HIS123 4.1 17.8 1.0 CG C:HIS121 4.3 14.8 1.0 ND1 C:HIS121 4.3 17.9 1.0 ND1 C:HIS366 4.3 19.7 1.0 CG C:HIS366 4.4 17.3 1.0 C1 C:EDO604 4.4 25.5 0.5 CB C:ASP451 4.5 16.8 1.0 O2 C:EDO604 4.6 36.6 0.5 CE1 C:HIS394 4.6 21.0 1.0 OD2 C:ASP452 4.7 20.9 1.0 O1 C:EDO604 4.7 33.1 0.5 CD2 C:HIS394 4.7 18.4 1.0 O C:HOH705 4.8 35.8 1.0 O C:HOH1062 4.8 36.7 0.5 CA C:ASP451 4.9 16.2 1.0

Zinc binding site 4 out of 4 in the Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Helix Pomatia Amp Deaminase (Hpampd) with Unknown Density in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn604 b:22.5 occ:1.00 NE2 D:HIS123 2.1 22.3 1.0 O D:HOH713 2.1 23.7 1.0 NE2 D:HIS121 2.2 19.3 1.0 NE2 D:HIS366 2.2 26.1 1.0 OD1 D:ASP451 2.2 24.9 1.0 CE1 D:HIS123 3.0 21.9 1.0 CD2 D:HIS123 3.1 21.8 1.0 CE1 D:HIS366 3.1 23.9 1.0 CD2 D:HIS121 3.1 19.9 1.0 CE1 D:HIS121 3.2 23.1 1.0 CG D:ASP451 3.2 25.2 1.0 CD2 D:HIS366 3.2 23.4 1.0 OD2 D:ASP451 3.5 26.2 1.0 O D:HOH833 3.7 34.2 1.0 NE2 D:HIS394 3.8 23.7 1.0 O1 D:EDO605 4.1 34.5 1.0 ND1 D:HIS123 4.1 25.4 1.0 CG D:HIS123 4.2 22.2 1.0 ND1 D:HIS366 4.2 21.4 1.0 ND1 D:HIS121 4.3 19.8 1.0 CG D:HIS121 4.3 19.0 1.0 CG D:HIS366 4.3 21.5 1.0 C2 D:EDO605 4.5 38.1 1.0 CB D:ASP451 4.6 21.9 1.0 CE1 D:HIS394 4.6 22.5 1.0 OD1 D:ASP452 4.7 27.3 1.0 O D:HOH751 4.7 40.8 1.0 CD2 D:HIS394 4.7 23.2 1.0 CA D:ASP451 4.8 20.8 1.0 C1 D:EDO605 4.9 33.0 1.0 O D:HOH756 4.9 39.6 1.0 O2 D:EDO605 4.9 44.4 1.0

G.Kaur, J.R.Horton, X.Cheng. Structural Basis of Substrate Specificity of Helix Pomatia Amp Deaminase and A Chimeric Adgf Adenosine Deaminase To Be Published.