Zinc in PDB 6rej: Crystal Structure of PIZZA6-Sh with ZN2+

The structure of Crystal Structure of PIZZA6-Sh with ZN2+, PDB code: 6rej 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)	39.45 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.958, 55.179, 69.399, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.6

The binding sites of Zinc atom in the Crystal Structure of PIZZA6-Sh with ZN2+ (pdb code 6rej). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of PIZZA6-Sh with ZN2+, PDB code: 6rej:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of PIZZA6-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 PIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.6 occ:0.72 NE2 A:HIS142 2.1 41.4 1.0 NE2 A:HIS226 2.2 47.8 1.0 NE2 A:HIS58 2.2 45.8 1.0 O A:HOH522 2.5 36.8 1.0 CD2 A:HIS226 2.7 41.9 1.0 CD2 A:HIS58 2.8 37.9 1.0 CE1 A:HIS142 3.0 38.5 1.0 CD2 A:HIS142 3.1 35.7 1.0 CE1 A:HIS226 3.2 42.2 1.0 CE1 A:HIS58 3.4 44.5 1.0 OG A:SER100 3.9 32.8 1.0 CG A:HIS226 3.9 41.4 1.0 OG A:SER184 3.9 34.7 1.0 CG A:HIS58 4.1 33.3 1.0 ND1 A:HIS142 4.1 33.9 1.0 ND1 A:HIS226 4.1 49.8 1.0 CG A:HIS142 4.1 25.7 1.0 OG A:SER16 4.2 40.4 1.0 ND1 A:HIS58 4.3 41.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of PIZZA6-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 PIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:34.2 occ:0.43 O A:HOH517 2.1 42.5 1.0 CE1 A:HIS31 2.1 46.2 1.0 O A:HOH402 2.4 31.8 1.0 NE2 A:HIS241 2.7 41.5 1.0 ND1 A:HIS31 2.7 44.2 1.0 CD2 A:HIS241 2.9 42.5 1.0 NE2 A:HIS31 3.1 47.8 1.0 OG A:SER16 3.1 40.4 1.0 CE1 A:HIS226 3.8 42.2 1.0 CE1 A:HIS58 3.8 44.5 1.0 CE1 A:HIS241 3.8 46.5 1.0 CG A:HIS31 3.9 44.7 1.0 CB A:SER16 3.9 33.7 1.0 O A:HOH401 4.0 32.1 1.0 CD2 A:HIS31 4.0 38.6 1.0 NE2 A:HIS226 4.0 47.8 1.0 ZN A:ZN303 4.1 34.6 0.4 CG A:HIS241 4.1 38.5 1.0 ND1 A:HIS226 4.1 49.8 1.0 O A:HOH525 4.4 45.7 1.0 ND1 A:HIS58 4.4 41.2 1.0 ND1 A:HIS241 4.5 41.5 1.0 CG A:HIS226 4.5 41.4 1.0 CD2 A:HIS226 4.6 41.9 1.0 O A:HOH520 4.6 50.1 1.0 NE2 A:HIS58 4.7 45.8 1.0 CA A:SER16 4.7 27.7 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of PIZZA6-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 PIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:34.6 occ:0.43 ND1 A:HIS226 2.1 49.8 1.0 NE2 A:HIS199 2.5 46.1 1.0 CE1 A:HIS226 2.7 42.2 1.0 O A:HOH520 2.7 50.1 1.0 O A:HOH486 2.9 51.4 1.0 CD2 A:HIS199 3.1 43.4 1.0 CG A:HIS226 3.3 41.4 1.0 CE1 A:HIS199 3.7 50.2 1.0 CG A:HIS241 3.8 38.5 1.0 CD2 A:HIS241 3.9 42.5 1.0 CB A:HIS226 3.9 28.9 1.0 NE2 A:HIS226 3.9 47.8 1.0 ZN A:ZN302 4.1 34.2 0.4 CB A:HIS241 4.1 38.6 1.0 ND1 A:HIS241 4.1 41.5 1.0 CD2 A:HIS226 4.2 41.9 1.0 O A:THR224 4.2 45.2 1.0 NE2 A:HIS241 4.3 41.5 1.0 O A:HOH517 4.3 42.5 1.0 CG A:HIS199 4.4 38.0 1.0 CE1 A:HIS241 4.4 46.5 1.0 O A:HOH525 4.5 45.7 1.0 CA A:HIS226 4.5 23.6 1.0 ND1 A:HIS199 4.6 43.9 1.0 OG1 A:THR224 4.7 51.6 1.0 CB A:THR224 4.9 44.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of PIZZA6-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 PIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:26.0 occ:0.49 ND1 A:HIS142 2.1 33.9 1.0 O A:HOH518 2.2 40.0 1.0 NE2 A:HIS115 2.2 37.6 1.0 CE1 A:HIS142 2.9 38.5 1.0 CE1 A:HIS115 3.1 31.3 1.0 CD2 A:HIS115 3.1 33.7 1.0 CG A:HIS142 3.2 25.7 1.0 CB A:HIS142 3.7 26.3 1.0 CD2 A:HIS157 3.9 38.4 1.0 NE2 A:HIS157 4.0 41.4 1.0 NE2 A:HIS142 4.1 41.4 1.0 ND1 A:HIS115 4.2 37.2 1.0 CD2 A:HIS142 4.2 35.7 1.0 CG A:HIS115 4.2 28.9 1.0 O A:HOH525 4.3 45.7 1.0 ZN A:ZN305 4.3 36.6 0.5 CG A:HIS157 4.4 38.0 1.0 CE1 A:HIS157 4.5 45.4 1.0 CA A:HIS142 4.5 17.0 1.0 ND1 A:HIS157 4.7 45.2 1.0 OG A:SER100 4.8 32.8 1.0 CG2 A:THR140 5.0 31.7 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of PIZZA6-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 PIZZA6-Sh with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:36.6 occ:0.45 NE2 A:HIS73 2.2 38.4 1.0 CD2 A:HIS73 3.1 33.5 1.0 CE1 A:HIS73 3.2 38.0 1.0 OG A:SER100 3.2 32.8 1.0 CB A:SER100 3.7 21.9 1.0 CD2 A:HIS115 3.7 33.7 1.0 CG A:HIS115 3.8 28.9 1.0 NE2 A:HIS115 3.9 37.6 1.0 ND1 A:HIS115 4.1 37.2 1.0 O A:HOH518 4.1 40.0 1.0 CE1 A:HIS115 4.1 31.3 1.0 O A:HOH401 4.1 32.1 1.0 O A:HOH525 4.2 45.7 1.0 CE1 A:HIS58 4.2 44.5 1.0 CG A:HIS73 4.3 32.9 1.0 ND1 A:HIS73 4.3 39.1 1.0 CE1 A:HIS142 4.3 38.5 1.0 ZN A:ZN304 4.3 26.0 0.5 CB A:HIS115 4.3 31.0 1.0 ND1 A:HIS58 4.4 41.2 1.0 O A:THR98 4.4 34.4 1.0 CA A:SER100 4.5 15.2 1.0 NE2 A:HIS58 4.5 45.8 1.0 ND1 A:HIS142 4.6 33.9 1.0 CG A:HIS58 4.8 33.3 1.0 CD2 A:HIS58 4.9 37.9 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