Zinc in PDB 6zpa: Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and One Catalytic ZN2+ Ion

The structure of Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and One Catalytic ZN2+ Ion, PDB code: 6zpa was solved by D.Czernecki, P.Legrand, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.84 / 0.86
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	141.489, 141.489, 53.601, 90, 90, 120
R / Rfree (%)	12.9 / 13.5

The binding sites of Zinc atom in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and One Catalytic ZN2+ Ion (pdb code 6zpa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and One Catalytic ZN2+ Ion, PDB code: 6zpa:

Zinc binding site 1 out of 1 in the Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and One Catalytic ZN2+ Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cyanophage S-2L Hd Phosphohydrolase (Datz) Bound to Da and One Catalytic ZN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:13.2 occ:1.00 OD1 A:ASP119 2.1 11.5 1.0 NE2 A:HIS66 2.2 7.2 1.0 NE2 A:HIS34 2.2 6.6 1.0 OD2 A:ASP67 2.3 11.3 1.0 CE1 A:HIS34 3.1 6.3 1.0 CG A:ASP119 3.1 10.7 1.0 CD2 A:HIS66 3.1 8.7 1.0 CE1 A:HIS66 3.2 8.4 1.0 HE1 A:HIS34 3.2 62.5 1.0 HD2 A:HIS66 3.2 97.3 1.0 CG A:ASP67 3.2 9.5 1.0 CD2 A:HIS34 3.2 6.4 1.0 OD2 A:ASP119 3.4 15.9 1.0 HE1 A:HIS66 3.4 36.5 1.0 HD2 A:HIS34 3.4 8.7 1.0 OD1 A:ASP67 3.5 11.4 1.0 HH12 A:ARG19 3.7 10.8 1.0 HG23 A:VAL38 4.1 6.4 1.0 NH1 A:ARG19 4.1 6.4 1.0 HH11 A:ARG19 4.2 8.7 1.0 HZ2 A:TRP115 4.2 44.0 1.0 O A:HOH319 4.2 9.2 1.0 ND1 A:HIS34 4.2 5.6 1.0 CG A:HIS66 4.3 7.3 1.0 ND1 A:HIS66 4.3 8.6 1.0 CG A:HIS34 4.3 5.8 1.0 O A:HOH430 4.3 9.2 1.0 HE1 A:TRP115 4.4 31.2 1.0 CB A:ASP119 4.4 8.4 1.0 HB2 A:ASP119 4.5 6.7 1.0 HB2 A:ASP67 4.5 7.3 1.0 CB A:ASP67 4.5 7.7 1.0 H5' A:3D1201 4.7 33.7 1.0 HA A:ASP119 4.8 5.4 1.0 HG2 A:MET35 4.8 8.7 1.0 HD1 A:HIS34 5.0 6.0 1.0 CZ2 A:TRP115 5.0 14.8 1.0 CG2 A:VAL38 5.0 5.9 1.0

D.Czernecki, P.Legrand, M.Tekpinar, S.Rosario, P.A.Kaminski, M.Delarue. How Cyanophage S-2L Rejects Adenine and Incorporates 2-Aminoadenine to Saturate Hydrogen Bonding in Its Dna Nat Commun 2021.
ISSN: ESSN 2041-1723