Zinc in PDB 8ihr: Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe

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Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe (pdb code 8ihr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe, PDB code: 8ihr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:50.1 occ:1.00 NE2 A:HIS83 2.3 12.3 1.0 NE2 A:HIS85 2.3 25.7 1.0 OQ1 A:KCX210 2.4 31.1 1.0 OD1 A:ASP344 2.9 33.4 1.0 CE1 A:HIS83 3.1 17.6 1.0 CE1 A:HIS85 3.2 9.5 1.0 CX A:KCX210 3.3 33.6 1.0 CD2 A:HIS85 3.3 24.0 1.0 OD2 A:ASP344 3.3 20.7 1.0 CD2 A:HIS83 3.4 22.7 1.0 CG A:ASP344 3.4 28.1 1.0 OQ2 A:KCX210 3.5 29.4 1.0 ZN A:ZN502 3.5 60.3 1.0 N A:PHE503 4.0 25.7 1.0 ND1 A:HIS83 4.3 22.7 1.0 NZ A:KCX210 4.4 28.7 1.0 ND1 A:HIS85 4.4 19.1 1.0 CG A:HIS83 4.4 20.5 1.0 CG A:HIS85 4.4 25.4 1.0 NE2 A:HIS271 4.5 22.4 1.0 CB A:ASP344 4.6 18.1 1.0 CE1 A:HIS271 4.7 25.1 1.0

Zinc binding site 2 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:60.3 occ:1.00 ND1 A:HIS251 2.3 31.1 1.0 NE2 A:HIS271 2.3 22.4 1.0 OQ2 A:KCX210 2.4 29.4 1.0 CD2 A:HIS271 3.1 18.9 1.0 CE1 A:HIS251 3.1 19.1 1.0 CX A:KCX210 3.3 33.6 1.0 CG A:HIS251 3.3 22.9 1.0 CE1 A:HIS271 3.4 25.1 1.0 OQ1 A:KCX210 3.4 31.1 1.0 ZN A:ZN501 3.5 50.1 1.0 N A:PHE503 3.6 25.7 1.0 CB A:HIS251 3.7 12.1 1.0 CA A:PHE503 4.0 32.4 1.0 CE1 A:HIS83 4.1 17.6 1.0 CG A:HIS271 4.3 19.4 1.0 NE2 A:HIS251 4.3 11.5 1.0 CD2 A:HIS251 4.4 20.5 1.0 ND1 A:HIS271 4.4 28.4 1.0 NE2 A:HIS83 4.4 12.3 1.0 NZ A:KCX210 4.5 28.7 1.0 C A:PHE503 4.6 27.9 1.0 OD2 A:ASP344 4.6 20.7 1.0 NE2 A:HIS163 4.6 24.4 1.0 CA A:HIS251 4.8 16.6 1.0 OXT A:PHE503 4.8 28.3 1.0 CB A:GLU270 4.8 23.2 1.0 CD2 A:HIS163 5.0 23.1 1.0

Zinc binding site 3 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:50.6 occ:1.00 NE2 B:HIS83 2.3 11.5 1.0 NE2 B:HIS85 2.3 24.7 1.0 OQ1 B:KCX210 2.4 31.8 1.0 OD1 B:ASP344 2.8 32.3 1.0 CE1 B:HIS83 3.1 17.0 1.0 CE1 B:HIS85 3.2 8.4 1.0 CX B:KCX210 3.3 33.5 1.0 CG B:ASP344 3.3 27.4 1.0 OD2 B:ASP344 3.3 21.1 1.0 CD2 B:HIS85 3.3 23.7 1.0 CD2 B:HIS83 3.4 22.0 1.0 OQ2 B:KCX210 3.5 29.9 1.0 ZN B:ZN502 3.5 64.7 1.0 N B:PHE503 4.0 25.8 1.0 ND1 B:HIS83 4.3 23.3 1.0 NZ B:KCX210 4.4 28.0 1.0 ND1 B:HIS85 4.4 18.8 1.0 CG B:HIS83 4.4 19.8 1.0 CG B:HIS85 4.4 25.8 1.0 NE2 B:HIS271 4.5 21.9 1.0 CB B:ASP344 4.5 17.9 1.0 CE1 B:HIS271 4.7 24.9 1.0

Zinc binding site 4 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:64.7 occ:1.00 NE2 B:HIS271 2.3 21.9 1.0 ND1 B:HIS251 2.3 30.6 1.0 OQ2 B:KCX210 2.4 29.9 1.0 CD2 B:HIS271 3.1 19.1 1.0 CE1 B:HIS251 3.1 19.0 1.0 CX B:KCX210 3.3 33.5 1.0 CG B:HIS251 3.3 21.6 1.0 CE1 B:HIS271 3.4 24.9 1.0 OQ1 B:KCX210 3.4 31.8 1.0 ZN B:ZN501 3.5 50.6 1.0 N B:PHE503 3.6 25.8 1.0 CB B:HIS251 3.7 12.2 1.0 CA B:PHE503 4.0 32.8 1.0 CE1 B:HIS83 4.1 17.0 1.0 CG B:HIS271 4.3 20.2 1.0 NE2 B:HIS251 4.3 11.8 1.0 CD2 B:HIS251 4.4 19.9 1.0 ND1 B:HIS271 4.4 28.4 1.0 NE2 B:HIS83 4.4 11.5 1.0 OD2 B:ASP344 4.5 21.1 1.0 NZ B:KCX210 4.5 28.0 1.0 C B:PHE503 4.6 29.1 1.0 NE2 B:HIS163 4.6 23.6 1.0 CA B:HIS251 4.8 16.2 1.0 OXT B:PHE503 4.8 28.6 1.0 CB B:GLU270 4.8 23.6 1.0 CD2 B:HIS163 5.0 22.0 1.0

Zinc binding site 5 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:49.1 occ:1.00 NE2 C:HIS83 2.3 12.1 1.0 NE2 C:HIS85 2.3 25.9 1.0 OQ1 C:KCX210 2.4 32.5 1.0 OD1 C:ASP344 2.8 32.2 1.0 CE1 C:HIS83 3.1 17.7 1.0 CE1 C:HIS85 3.2 8.4 1.0 CX C:KCX210 3.3 34.1 1.0 CG C:ASP344 3.3 27.9 1.0 OD2 C:ASP344 3.3 20.9 1.0 CD2 C:HIS85 3.3 24.2 1.0 CD2 C:HIS83 3.4 22.0 1.0 OQ2 C:KCX210 3.5 29.6 1.0 ZN C:ZN502 3.5 61.6 1.0 N C:PHE503 4.0 26.1 1.0 ND1 C:HIS83 4.3 23.8 1.0 NZ C:KCX210 4.4 29.2 1.0 ND1 C:HIS85 4.4 18.6 1.0 CG C:HIS83 4.4 20.7 1.0 CG C:HIS85 4.4 26.0 1.0 NE2 C:HIS271 4.5 22.7 1.0 CB C:ASP344 4.5 18.1 1.0 CE1 C:HIS271 4.7 25.0 1.0

Zinc binding site 6 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:61.6 occ:1.00 ND1 C:HIS251 2.3 32.2 1.0 NE2 C:HIS271 2.3 22.7 1.0 OQ2 C:KCX210 2.4 29.6 1.0 CD2 C:HIS271 3.1 19.5 1.0 CE1 C:HIS251 3.1 19.1 1.0 CX C:KCX210 3.3 34.1 1.0 CG C:HIS251 3.3 22.4 1.0 CE1 C:HIS271 3.4 25.0 1.0 OQ1 C:KCX210 3.4 32.5 1.0 ZN C:ZN501 3.5 49.1 1.0 N C:PHE503 3.6 26.1 1.0 CB C:HIS251 3.7 12.5 1.0 CA C:PHE503 4.0 32.7 1.0 CE1 C:HIS83 4.1 17.7 1.0 CG C:HIS271 4.3 19.8 1.0 NE2 C:HIS251 4.3 11.2 1.0 CD2 C:HIS251 4.4 20.1 1.0 ND1 C:HIS271 4.4 28.9 1.0 NE2 C:HIS83 4.4 12.1 1.0 OD2 C:ASP344 4.5 20.9 1.0 NZ C:KCX210 4.5 29.2 1.0 C C:PHE503 4.6 28.4 1.0 NE2 C:HIS163 4.6 23.4 1.0 CA C:HIS251 4.8 17.2 1.0 OXT C:PHE503 4.8 29.1 1.0 CB C:GLU270 4.8 22.8 1.0 CD2 C:HIS163 5.0 22.1 1.0

Zinc binding site 7 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:49.5 occ:1.00 NE2 D:HIS83 2.3 10.4 1.0 NE2 D:HIS85 2.3 25.4 1.0 OQ1 D:KCX210 2.4 31.7 1.0 OD1 D:ASP344 3.0 32.9 1.0 CE1 D:HIS83 3.1 16.9 1.0 CE1 D:HIS85 3.2 8.2 1.0 CX D:KCX210 3.3 33.6 1.0 CD2 D:HIS85 3.3 22.8 1.0 CD2 D:HIS83 3.4 21.5 1.0 OD2 D:ASP344 3.4 18.9 1.0 CG D:ASP344 3.4 27.2 1.0 OQ2 D:KCX210 3.5 29.4 1.0 ZN D:ZN502 3.5 62.0 1.0 N D:PHE503 4.0 26.6 1.0 ND1 D:HIS83 4.3 23.1 1.0 NZ D:KCX210 4.4 28.6 1.0 ND1 D:HIS85 4.4 18.9 1.0 CG D:HIS83 4.4 20.2 1.0 CG D:HIS85 4.4 25.0 1.0 NE2 D:HIS271 4.5 22.7 1.0 CB D:ASP344 4.7 17.6 1.0 CE1 D:HIS271 4.7 25.0 1.0

Zinc binding site 8 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:62.0 occ:1.00 NE2 D:HIS271 2.3 22.7 1.0 ND1 D:HIS251 2.3 30.2 1.0 OQ2 D:KCX210 2.4 29.4 1.0 CD2 D:HIS271 3.1 19.9 1.0 CE1 D:HIS251 3.1 18.5 1.0 CX D:KCX210 3.3 33.6 1.0 CG D:HIS251 3.3 21.9 1.0 CE1 D:HIS271 3.4 25.0 1.0 OQ1 D:KCX210 3.4 31.7 1.0 ZN D:ZN501 3.5 49.5 1.0 N D:PHE503 3.6 26.6 1.0 CB D:HIS251 3.7 11.8 1.0 CA D:PHE503 4.0 32.3 1.0 CE1 D:HIS83 4.1 16.9 1.0 CG D:HIS271 4.3 20.1 1.0 NE2 D:HIS251 4.3 13.3 1.0 CD2 D:HIS251 4.4 19.9 1.0 ND1 D:HIS271 4.4 28.5 1.0 NE2 D:HIS83 4.4 10.4 1.0 NZ D:KCX210 4.5 28.6 1.0 OD2 D:ASP344 4.6 18.9 1.0 C D:PHE503 4.6 28.1 1.0 NE2 D:HIS163 4.6 24.2 1.0 CA D:HIS251 4.8 16.2 1.0 OXT D:PHE503 4.8 28.8 1.0 CB D:GLU270 4.8 24.2 1.0 CD2 D:HIS163 5.0 22.0 1.0

Zinc binding site 9 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:58.1 occ:1.00 OQ2 E:KCX210 2.1 26.9 1.0 NE2 E:HIS83 2.3 23.7 1.0 NE2 E:HIS85 2.3 21.3 1.0 CX E:KCX210 2.9 28.0 1.0 CE1 E:HIS85 3.0 14.1 1.0 CE1 E:HIS83 3.1 17.8 1.0 OQ1 E:KCX210 3.1 30.8 1.0 OD2 E:ASP344 3.3 27.3 1.0 CD2 E:HIS83 3.4 28.4 1.0 OD1 E:ASP344 3.5 38.3 1.0 CD2 E:HIS85 3.5 21.0 1.0 ZN E:ZN502 3.5 63.1 1.0 CG E:ASP344 3.6 27.3 1.0 NZ E:KCX210 4.1 28.6 1.0 N E:PHE503 4.1 29.9 1.0 ND1 E:HIS85 4.2 18.0 1.0 ND1 E:HIS83 4.3 24.9 1.0 CG E:HIS83 4.5 21.9 1.0 CG E:HIS85 4.5 26.6 1.0 NE2 E:HIS271 4.6 24.8 1.0 CB E:LEU128 4.9 18.8 1.0 CE1 E:HIS271 4.9 21.9 1.0 CB E:ASP344 4.9 19.4 1.0

Zinc binding site 10 out of 16 in the Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of Ochratoxin A-Detoxifying Amidohydrolase ADH3 in Complex with Phe within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:63.1 occ:1.00 ND1 E:HIS251 2.2 30.5 1.0 NE2 E:HIS271 2.3 24.8 1.0 OQ1 E:KCX210 2.5 30.8 1.0 CD2 E:HIS271 3.0 23.4 1.0 CE1 E:HIS251 3.1 16.9 1.0 CG E:HIS251 3.2 20.5 1.0 N E:PHE503 3.3 29.9 1.0 CX E:KCX210 3.4 28.0 1.0 CE1 E:HIS271 3.4 21.9 1.0 CB E:HIS251 3.4 7.9 1.0 ZN E:ZN501 3.5 58.1 1.0 OQ2 E:KCX210 3.6 26.9 1.0 CA E:PHE503 3.9 33.2 1.0 CE1 E:HIS83 4.0 17.8 1.0 OD2 E:ASP344 4.2 27.3 1.0 NE2 E:HIS251 4.2 5.3 1.0 CD2 E:HIS251 4.3 18.2 1.0 CG E:HIS271 4.3 21.2 1.0 ND1 E:HIS271 4.4 27.0 1.0 NE2 E:HIS83 4.5 23.7 1.0 CA E:HIS251 4.5 14.8 1.0 NZ E:KCX210 4.6 28.6 1.0 C E:PHE503 4.7 30.6 1.0 CB E:GLU270 4.8 23.3 1.0 NE2 E:HIS163 4.8 24.8 1.0 O E:PHE503 4.9 28.2 1.0

L.Dai, D.Niu, J.W.Huang, X.Li, P.Shen, H.Li, Z.Xie, J.Min, Y.Hu, Y.Yang, R.T.Guo, C.C.Chen. Cryo-Em Structure and Rational Engineering of A Superefficient Ochratoxin A-Detoxifying Amidohydrolase. J Hazard Mater V. 458 31836 2023.
ISSN: ESSN 1873-3336
PubMed: 37331057
DOI: 10.1016/J.JHAZMAT.2023.131836