Zinc in PDB 6ren: Crystal Structure of 3FPIZZA6-Sh with ZN2+

The structure of Crystal Structure of 3FPIZZA6-Sh with ZN2+, PDB code: 6ren was solved by H.Noguchi, D.E.Clarke, J.L.Gryspeerdt, S.D.Feyter, A.R.D.Voet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.09 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.781, 66.683, 70.534, 90.00, 97.92, 90.00
R / Rfree (%)	13.4 / 16.7

The binding sites of Zinc atom in the Crystal Structure of 3FPIZZA6-Sh with ZN2+ (pdb code 6ren). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of 3FPIZZA6-Sh with ZN2+, PDB code: 6ren:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.5 occ:1.00 NE2 A:HIS226 2.0 10.0 1.0 NE2 A:HIS142 2.0 10.4 1.0 NE2 A:HIS58 2.0 13.0 1.0 O A:HOH639 2.3 25.1 1.0 CE1 A:HIS226 3.0 10.6 1.0 CE1 A:HIS58 3.0 12.5 1.0 CE1 A:HIS142 3.0 9.5 1.0 CD2 A:HIS226 3.0 10.5 1.0 CD2 A:HIS142 3.0 11.0 1.0 CD2 A:HIS58 3.1 12.7 1.0 O A:HOH586 3.8 28.1 1.0 ND1 A:HIS142 4.1 10.1 1.0 ND1 A:HIS226 4.1 10.1 1.0 ND1 A:HIS58 4.1 12.7 1.0 CG A:HIS226 4.2 9.2 1.0 CG A:HIS142 4.2 9.5 1.0 CG A:HIS58 4.2 10.7 1.0 CB A:SER184 4.5 10.4 1.0 O A:HOH576 4.5 21.7 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.2 occ:1.00 O2 A:IPA306 2.0 16.4 1.0 NE2 A:HIS199 2.0 11.0 1.0 NE2 A:HIS241 2.0 12.8 1.0 ND1 A:HIS226 2.0 10.1 1.0 C1 A:IPA306 2.8 14.8 1.0 C2 A:IPA306 2.9 19.9 1.0 CE1 A:HIS226 3.0 10.6 1.0 CD2 A:HIS199 3.0 11.0 1.0 CE1 A:HIS241 3.0 14.2 1.0 CE1 A:HIS199 3.0 12.0 1.0 CD2 A:HIS241 3.1 12.4 1.0 CG A:HIS226 3.1 9.2 1.0 CB A:HIS226 3.6 10.4 1.0 C3 A:IPA307 3.9 30.8 1.0 ND1 A:HIS241 4.1 13.4 1.0 NE2 A:HIS226 4.1 10.0 1.0 CG A:HIS199 4.1 11.2 1.0 ND1 A:HIS199 4.1 12.5 1.0 CG A:HIS241 4.2 12.9 1.0 CD2 A:HIS226 4.2 10.5 1.0 O2 A:IPA307 4.2 29.6 1.0 C3 A:IPA306 4.3 23.2 1.0 C1 A:IPA311 4.4 25.9 1.0 CA A:HIS226 4.5 10.2 1.0 C2 A:IPA307 4.7 29.9 1.0 O A:PRO225 4.7 12.7 1.0 O A:HOH576 4.7 21.7 1.0 CG2 A:THR224 4.8 16.5 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:11.1 occ:1.00 O2 A:IPA305 2.0 15.4 1.0 NE2 A:HIS157 2.0 11.2 1.0 NE2 A:HIS115 2.0 12.2 1.0 ND1 A:HIS142 2.1 10.1 1.0 C2 A:IPA305 2.8 17.6 1.0 C1 A:IPA305 2.9 11.9 1.0 CE1 A:HIS142 3.0 9.5 1.0 CD2 A:HIS115 3.0 11.8 1.0 CD2 A:HIS157 3.0 10.4 1.0 CE1 A:HIS157 3.0 11.6 1.0 CE1 A:HIS115 3.1 12.9 1.0 CG A:HIS142 3.1 9.5 1.0 CB A:HIS142 3.6 9.7 1.0 O2 A:IPA311 3.9 29.1 1.0 C2 A:IPA311 4.1 27.5 1.0 NE2 A:HIS142 4.1 10.4 1.0 ND1 A:HIS157 4.2 12.3 1.0 CG A:HIS115 4.2 11.0 1.0 ND1 A:HIS115 4.2 12.6 1.0 CG A:HIS157 4.2 11.1 1.0 CD2 A:HIS142 4.2 11.0 1.0 C3 A:IPA305 4.3 18.4 1.0 C1 A:IPA309 4.4 25.9 1.0 O A:HOH576 4.5 21.7 1.0 C3 A:IPA311 4.5 27.9 1.0 CA A:HIS142 4.6 9.7 1.0 O A:THR140 4.6 11.8 1.0 C3 A:IPA309 4.8 30.4 1.0 C2 A:IPA309 4.8 30.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:14.9 occ:1.00 O2 A:IPA310 2.0 23.1 1.0 NE2 A:HIS73 2.0 15.0 1.0 NE2 A:HIS31 2.1 15.3 1.0 ND1 A:HIS58 2.1 12.7 1.0 CE1 A:HIS58 3.0 12.5 1.0 C2 A:IPA310 3.0 27.8 1.0 CD2 A:HIS31 3.0 15.3 1.0 CD2 A:HIS73 3.0 15.2 1.0 CE1 A:HIS73 3.0 15.5 1.0 CE1 A:HIS31 3.1 14.7 1.0 CG A:HIS58 3.1 10.7 1.0 C3 A:IPA310 3.3 27.3 1.0 CB A:HIS58 3.5 10.9 1.0 O2 A:IPA309 4.0 34.0 1.0 C1 A:IPA309 4.1 25.9 1.0 NE2 A:HIS58 4.1 13.0 1.0 ND1 A:HIS73 4.1 15.1 1.0 CG A:HIS73 4.2 13.8 1.0 CG A:HIS31 4.2 14.7 1.0 ND1 A:HIS31 4.2 17.1 1.0 CD2 A:HIS58 4.2 12.7 1.0 O A:THR56 4.3 16.4 1.0 C1 A:IPA310 4.3 30.2 1.0 O2 A:IPA307 4.4 29.6 1.0 C2 A:IPA309 4.5 30.4 1.0 CA A:HIS58 4.6 10.6 1.0 CB A:THR56 4.7 17.0 1.0 C1 A:IPA307 4.8 31.2 1.0 O A:HOH576 4.9 21.7 1.0 O A:PRO57 5.0 17.8 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:15.1 occ:1.00 NE2 B:HIS226 2.0 13.2 1.0 NE2 B:HIS142 2.0 13.5 1.0 O B:HOH591 2.1 24.1 1.0 NE2 B:HIS58 2.1 15.4 1.0 CE1 B:HIS142 3.0 14.4 1.0 CE1 B:HIS226 3.0 12.7 1.0 CD2 B:HIS226 3.0 12.6 1.0 CE1 B:HIS58 3.0 16.0 1.0 CD2 B:HIS58 3.1 14.2 1.0 CD2 B:HIS142 3.1 13.0 1.0 ND1 B:HIS226 4.1 12.9 1.0 ND1 B:HIS142 4.1 14.0 1.0 ND1 B:HIS58 4.2 14.9 1.0 CG B:HIS226 4.2 13.0 1.0 CG B:HIS58 4.2 13.7 1.0 CG B:HIS142 4.2 12.7 1.0 O B:HOH576 4.5 29.8 1.0 CB B:SER184 4.7 13.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.7 occ:1.00 O2 B:IPA307 2.0 23.4 1.0 NE2 B:HIS73 2.1 16.2 1.0 NE2 B:HIS31 2.1 16.3 1.0 ND1 B:HIS58 2.1 14.9 1.0 C2 B:IPA307 3.0 26.4 1.0 CE1 B:HIS58 3.0 16.0 1.0 CD2 B:HIS31 3.0 15.7 1.0 CE1 B:HIS73 3.0 20.7 1.0 C1 B:IPA307 3.1 25.7 1.0 CE1 B:HIS31 3.1 17.8 1.0 CD2 B:HIS73 3.1 19.4 1.0 CG B:HIS58 3.1 13.7 1.0 CB B:HIS58 3.5 14.1 1.0 NE2 B:HIS58 4.1 15.4 1.0 ND1 B:HIS73 4.1 23.3 1.0 CG B:HIS31 4.2 16.4 1.0 ND1 B:HIS31 4.2 18.8 1.0 C3 B:IPA310 4.2 27.6 1.0 CG B:HIS73 4.2 21.5 1.0 CD2 B:HIS58 4.2 14.2 1.0 C3 B:IPA307 4.3 27.0 1.0 C1 B:IPA310 4.3 25.0 1.0 O2 B:IPA308 4.4 32.3 1.0 C2 B:IPA310 4.4 29.2 1.0 C3 B:IPA308 4.5 28.4 1.0 CA B:HIS58 4.6 13.6 1.0 O B:THR56 4.7 26.0 1.0 O B:HOH576 4.9 29.8 1.0 C2 B:IPA308 5.0 29.9 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:13.9 occ:1.00 O2 B:IPA305 1.9 18.5 1.0 ND1 B:HIS226 2.0 12.9 1.0 NE2 B:HIS241 2.0 15.2 1.0 NE2 B:HIS199 2.0 13.1 1.0 C2 B:IPA305 2.8 19.9 1.0 C3 B:IPA305 2.9 16.0 1.0 CE1 B:HIS226 2.9 12.7 1.0 CD2 B:HIS199 3.0 11.9 1.0 CE1 B:HIS241 3.0 17.5 1.0 CE1 B:HIS199 3.1 14.0 1.0 CD2 B:HIS241 3.1 15.6 1.0 CG B:HIS226 3.1 13.0 1.0 O2 B:IPA309 3.4 34.2 1.0 CB B:HIS226 3.6 12.5 1.0 NE2 B:HIS226 4.1 13.2 1.0 ND1 B:HIS241 4.1 19.8 1.0 CG B:HIS199 4.1 12.4 1.0 C3 B:IPA308 4.2 28.4 1.0 ND1 B:HIS199 4.2 14.4 1.0 CG B:HIS241 4.2 17.4 1.0 CD2 B:HIS226 4.2 12.6 1.0 C1 B:IPA305 4.2 23.1 1.0 C1 B:IPA308 4.3 29.1 1.0 CG2 B:THR224 4.5 23.9 1.0 CA B:HIS226 4.5 11.4 1.0 C2 B:IPA309 4.6 30.8 1.0 O B:HOH576 4.6 29.8 1.0 C3 B:IPA309 4.8 27.5 1.0 C2 B:IPA308 4.9 29.9 1.0 O B:PRO225 4.9 18.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:15.6 occ:1.00 O2 B:IPA306 2.0 22.2 1.0 NE2 B:HIS157 2.0 14.9 1.0 NE2 B:HIS115 2.0 16.5 1.0 ND1 B:HIS142 2.1 14.0 1.0 C2 B:IPA306 3.0 25.9 1.0 CE1 B:HIS142 3.0 14.4 1.0 CD2 B:HIS115 3.0 15.4 1.0 CE1 B:HIS157 3.0 16.9 1.0 CD2 B:HIS157 3.0 15.1 1.0 CE1 B:HIS115 3.1 15.2 1.0 CG B:HIS142 3.1 12.7 1.0 C1 B:IPA306 3.1 25.2 1.0 CB B:HIS142 3.5 12.6 1.0 C1 B:IPA309 4.0 27.4 1.0 ND1 B:HIS157 4.1 17.0 1.0 NE2 B:HIS142 4.1 13.5 1.0 ND1 B:HIS115 4.1 17.0 1.0 CG B:HIS115 4.2 15.7 1.0 CG B:HIS157 4.2 16.1 1.0 CD2 B:HIS142 4.2 13.0 1.0 C3 B:IPA306 4.3 26.6 1.0 C2 B:IPA309 4.4 30.8 1.0 CG2 B:THR140 4.5 22.9 1.0 O2 B:IPA310 4.5 32.4 1.0 CA B:HIS142 4.5 12.3 1.0 C1 B:IPA310 4.5 25.0 1.0 O B:HOH576 4.9 29.8 1.0 O B:THR140 4.9 17.7 1.0 C2 B:IPA310 5.0 29.2 1.0

D.E.Clarke, H.Noguchi, J.A.G.Gryspeerdt, S.De Feyter, A.R.D.Voet. Artificial Beta-Propeller Protein-Based Hydrolases. Chem.Commun.(Camb.) V. 55 8880 2019.
ISSN: ESSN 1364-548X
PubMed: 31321399
DOI: 10.1039/C9CC04388H