Zinc in PDB 7u2s: Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State

The structure of Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State, PDB code: 7u2s was solved by S.J.Hobbs, T.Wein, A.Lu, B.R.Morehouse, J.Schnabel, R.Sorek, P.J.Kranzusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.64 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.03, 58.295, 76.188, 90, 101.9, 90
R / Rfree (%)	17.3 / 19.3

The binding sites of Zinc atom in the Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State (pdb code 7u2s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State, PDB code: 7u2s:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.0 occ:1.00 O A:HOH438 2.2 13.0 1.0 NE2 A:HIS61 2.2 10.8 1.0 ND1 A:HIS63 2.3 12.8 1.0 NE2 A:HIS146 2.3 11.4 1.0 OD2 A:ASP166 2.4 8.6 1.0 CD2 A:HIS61 3.0 11.6 1.0 CE1 A:HIS63 3.1 16.3 1.0 CD2 A:HIS146 3.2 9.9 1.0 CE1 A:HIS61 3.3 11.1 1.0 CG A:HIS63 3.3 10.9 1.0 ZN A:ZN302 3.3 14.2 1.0 CE1 A:HIS146 3.4 10.7 1.0 CG A:ASP166 3.4 9.9 1.0 O A:HOH635 3.4 21.4 1.0 CB A:HIS63 3.7 7.4 1.0 NE2 A:HIS66 3.9 10.5 1.0 CB A:ASP166 3.9 7.5 1.0 CD2 A:HIS66 4.1 9.7 1.0 CG A:HIS61 4.2 9.5 1.0 NE2 A:HIS63 4.3 15.2 1.0 ND1 A:HIS61 4.3 13.5 1.0 OD1 A:ASP166 4.3 10.9 1.0 CG A:HIS146 4.3 11.0 1.0 ND1 A:HIS146 4.4 10.6 1.0 CD2 A:HIS63 4.4 12.1 1.0 OD1 A:ASP65 4.5 8.4 1.0 CE1 A:HIS199 4.7 11.7 1.0 OD2 A:ASP65 4.9 6.7 1.0 CE1 A:HIS66 5.0 14.8 1.0

Zinc binding site 2 out of 4 in the Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.2 occ:1.00 O A:HOH438 2.2 13.0 1.0 OD2 A:ASP65 2.2 6.7 1.0 NE2 A:HIS66 2.2 10.5 1.0 OD2 A:ASP166 2.2 8.6 1.0 NE2 A:HIS220 2.2 10.1 1.0 CG A:ASP166 3.0 9.9 1.0 OD1 A:ASP166 3.0 10.9 1.0 CE1 A:HIS220 3.1 11.8 1.0 CG A:ASP65 3.2 8.8 1.0 CE1 A:HIS66 3.2 14.8 1.0 CD2 A:HIS66 3.2 9.7 1.0 CD2 A:HIS220 3.3 11.8 1.0 ZN A:ZN301 3.3 19.0 1.0 OD1 A:ASP65 3.4 8.4 1.0 O A:HOH635 3.8 21.4 1.0 O A:HOH463 4.0 7.0 1.0 NE2 A:HIS61 4.1 10.8 1.0 CE1 A:HIS61 4.2 11.1 1.0 ND1 A:HIS220 4.3 8.7 1.0 ND1 A:HIS66 4.3 10.7 1.0 CG A:HIS66 4.4 8.1 1.0 CG A:HIS220 4.4 7.8 1.0 CB A:ASP166 4.5 7.5 1.0 CB A:ASP65 4.5 6.9 1.0 CB A:ALA13 4.5 12.0 1.0 CE1 A:HIS199 4.7 11.7 1.0 CA A:ALA13 4.8 10.0 1.0 O A:HOH542 4.9 9.0 1.0 N A:ALA13 4.9 9.0 1.0

Zinc binding site 3 out of 4 in the Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.5 occ:1.00 O B:HOH442 2.2 11.8 1.0 NE2 B:HIS61 2.2 10.3 1.0 ND1 B:HIS63 2.3 12.9 1.0 NE2 B:HIS146 2.3 13.3 1.0 OD2 B:ASP166 2.4 9.9 1.0 CD2 B:HIS61 3.0 12.8 1.0 CE1 B:HIS63 3.1 14.4 1.0 CD2 B:HIS146 3.2 12.0 1.0 CE1 B:HIS61 3.3 10.6 1.0 CG B:HIS63 3.3 11.2 1.0 CE1 B:HIS146 3.4 13.0 1.0 ZN B:ZN302 3.4 14.5 1.0 CG B:ASP166 3.4 9.7 1.0 CB B:HIS63 3.7 7.0 1.0 CB B:ASP166 3.9 9.3 1.0 NE2 B:HIS66 4.0 10.9 1.0 CD2 B:HIS66 4.2 9.0 1.0 CG B:HIS61 4.2 11.5 1.0 NE2 B:HIS63 4.3 13.8 1.0 ND1 B:HIS61 4.3 12.2 1.0 OD1 B:ASP166 4.4 11.9 1.0 CG B:HIS146 4.4 11.1 1.0 ND1 B:HIS146 4.4 11.9 1.0 CD2 B:HIS63 4.4 11.2 1.0 OD1 B:ASP65 4.5 8.2 1.0 CE1 B:HIS199 4.7 11.9 1.0 OD2 B:ASP65 4.9 7.6 1.0 CE1 B:HIS66 5.0 12.5 1.0

Zinc binding site 4 out of 4 in the Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Paenibacillus Xerothermodurans APYC1 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:14.5 occ:1.00 O B:HOH442 2.1 11.8 1.0 OD2 B:ASP65 2.2 7.6 1.0 NE2 B:HIS66 2.2 10.9 1.0 OD2 B:ASP166 2.2 9.9 1.0 NE2 B:HIS220 2.3 10.6 1.0 CG B:ASP166 3.0 9.7 1.0 OD1 B:ASP166 3.1 11.9 1.0 CG B:ASP65 3.1 8.8 1.0 CD2 B:HIS66 3.2 9.0 1.0 CE1 B:HIS220 3.2 11.5 1.0 CD2 B:HIS220 3.2 12.1 1.0 CE1 B:HIS66 3.2 12.5 1.0 ZN B:ZN301 3.4 17.5 1.0 OD1 B:ASP65 3.4 8.2 1.0 O B:HOH459 4.0 7.5 1.0 NE2 B:HIS61 4.1 10.3 1.0 CE1 B:HIS61 4.3 10.6 1.0 ND1 B:HIS220 4.3 11.1 1.0 ND1 B:HIS66 4.3 11.4 1.0 CG B:HIS66 4.3 8.2 1.0 CG B:HIS220 4.4 9.1 1.0 CB B:ASP65 4.5 6.2 1.0 CB B:ASP166 4.5 9.3 1.0 CB B:ALA13 4.5 12.0 1.0 CE1 B:HIS199 4.7 11.9 1.0 CA B:ALA13 4.8 11.2 1.0 N B:ALA13 4.9 9.0 1.0 O B:HOH515 5.0 9.6 1.0

S.J.Hobbs, T.Wein, A.Lu, B.R.Morehouse, J.Schnabel, A.Leavitt, E.Yirmiya, R.Sorek, P.J.Kranzusch. Phage Anti-Cbass and Anti-Pycsar Nucleases Subvert Bacterial Immunity. Nature V. 605 522 2022.
ISSN: ESSN 1476-4687
PubMed: 35395152
DOI: 10.1038/S41586-022-04716-Y