Zinc in PDB 8yag: Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis (pdb code 8yag). 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-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis, PDB code: 8yag:
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-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:58.0 occ:1.00 NE2 A:HIS83 2.3 26.9 1.0 NE2 A:HIS85 2.3 26.5 1.0 OD1 A:ASP344 2.6 39.0 1.0 CE1 A:HIS85 3.1 19.7 1.0 OQ1 A:KCX210 3.1 33.6 1.0 CE1 A:HIS83 3.2 23.4 1.0 OQ2 A:KCX210 3.2 31.5 1.0 CD2 A:HIS83 3.3 27.4 1.0 CG A:ASP344 3.3 23.6 1.0 CX A:KCX210 3.4 27.4 1.0 CD2 A:HIS85 3.4 27.9 1.0 OD2 A:ASP344 3.4 27.5 1.0 ZN A:ZN502 3.5 65.8 1.0 ND1 A:HIS85 4.3 28.0 1.0 ND1 A:HIS83 4.3 33.7 1.0 CG A:HIS83 4.4 28.3 1.0 NZ A:KCX210 4.4 33.1 1.0 CG A:HIS85 4.5 30.1 1.0 CB A:ASP344 4.6 27.1 1.0 NE2 A:HIS271 4.8 31.6 1.0

Zinc binding site 2 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:65.8 occ:1.00 NE2 A:HIS271 2.3 31.6 1.0 OQ2 A:KCX210 2.4 31.5 1.0 CD2 A:HIS251 2.6 27.9 1.0 CD2 A:HIS271 3.1 24.9 1.0 CE1 A:HIS271 3.4 33.9 1.0 ZN A:ZN501 3.5 58.0 1.0 NE2 A:HIS251 3.5 24.4 1.0 CG A:HIS251 3.6 28.7 1.0 CX A:KCX210 3.7 27.4 1.0 CB A:HIS251 4.0 22.7 1.0 CE1 A:HIS83 4.1 23.4 1.0 OD2 A:ASP344 4.2 27.5 1.0 OQ1 A:KCX210 4.3 33.6 1.0 CG A:HIS271 4.3 31.4 1.0 NE2 A:HIS83 4.4 26.9 1.0 ND1 A:HIS271 4.4 37.6 1.0 NZ A:KCX210 4.6 33.1 1.0 CE1 A:HIS251 4.7 29.6 1.0 ND1 A:HIS251 4.7 35.0 1.0 NE2 A:HIS163 4.8 31.0 1.0 CG A:ASP344 5.0 23.6 1.0

Zinc binding site 3 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:58.0 occ:1.00 NE2 B:HIS83 2.3 26.9 1.0 NE2 B:HIS85 2.3 26.5 1.0 OD1 B:ASP344 2.6 39.0 1.0 CE1 B:HIS85 3.1 19.7 1.0 OQ1 B:KCX210 3.1 33.6 1.0 CE1 B:HIS83 3.2 23.4 1.0 OQ2 B:KCX210 3.2 31.5 1.0 CD2 B:HIS83 3.3 27.4 1.0 CG B:ASP344 3.3 23.6 1.0 CX B:KCX210 3.4 27.4 1.0 CD2 B:HIS85 3.4 27.9 1.0 OD2 B:ASP344 3.4 27.5 1.0 ZN B:ZN502 3.5 65.8 1.0 ND1 B:HIS85 4.3 28.0 1.0 ND1 B:HIS83 4.3 33.7 1.0 CG B:HIS83 4.4 28.3 1.0 NZ B:KCX210 4.4 33.1 1.0 CG B:HIS85 4.5 30.1 1.0 CB B:ASP344 4.6 27.1 1.0 NE2 B:HIS271 4.8 31.6 1.0

Zinc binding site 4 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:65.8 occ:1.00 NE2 B:HIS271 2.3 31.6 1.0 OQ2 B:KCX210 2.4 31.5 1.0 CD2 B:HIS251 2.6 27.9 1.0 CD2 B:HIS271 3.1 24.9 1.0 CE1 B:HIS271 3.4 33.9 1.0 ZN B:ZN501 3.5 58.0 1.0 NE2 B:HIS251 3.5 24.4 1.0 CG B:HIS251 3.6 28.7 1.0 CX B:KCX210 3.7 27.4 1.0 CB B:HIS251 4.0 22.7 1.0 CE1 B:HIS83 4.1 23.4 1.0 OD2 B:ASP344 4.2 27.5 1.0 OQ1 B:KCX210 4.3 33.6 1.0 CG B:HIS271 4.3 31.4 1.0 NE2 B:HIS83 4.4 26.9 1.0 ND1 B:HIS271 4.4 37.6 1.0 NZ B:KCX210 4.6 33.1 1.0 CE1 B:HIS251 4.7 29.6 1.0 ND1 B:HIS251 4.7 35.0 1.0 NE2 B:HIS163 4.8 31.0 1.0 CG B:ASP344 5.0 23.6 1.0

Zinc binding site 5 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:58.0 occ:1.00 NE2 C:HIS83 2.3 26.9 1.0 NE2 C:HIS85 2.3 26.5 1.0 OD1 C:ASP344 2.6 39.0 1.0 CE1 C:HIS85 3.1 19.7 1.0 OQ1 C:KCX210 3.1 33.6 1.0 CE1 C:HIS83 3.2 23.4 1.0 OQ2 C:KCX210 3.2 31.5 1.0 CD2 C:HIS83 3.3 27.4 1.0 CG C:ASP344 3.3 23.6 1.0 CX C:KCX210 3.4 27.4 1.0 CD2 C:HIS85 3.4 27.9 1.0 OD2 C:ASP344 3.4 27.5 1.0 ZN C:ZN502 3.5 65.8 1.0 ND1 C:HIS85 4.3 28.0 1.0 ND1 C:HIS83 4.3 33.7 1.0 CG C:HIS83 4.4 28.3 1.0 NZ C:KCX210 4.4 33.1 1.0 CG C:HIS85 4.5 30.1 1.0 CB C:ASP344 4.6 27.1 1.0 NE2 C:HIS271 4.8 31.6 1.0

Zinc binding site 6 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:65.8 occ:1.00 NE2 C:HIS271 2.3 31.6 1.0 OQ2 C:KCX210 2.4 31.5 1.0 CD2 C:HIS251 2.6 27.9 1.0 CD2 C:HIS271 3.1 24.9 1.0 CE1 C:HIS271 3.4 33.9 1.0 ZN C:ZN501 3.5 58.0 1.0 NE2 C:HIS251 3.5 24.4 1.0 CG C:HIS251 3.6 28.7 1.0 CX C:KCX210 3.7 27.4 1.0 CB C:HIS251 4.0 22.7 1.0 CE1 C:HIS83 4.1 23.4 1.0 OD2 C:ASP344 4.2 27.5 1.0 OQ1 C:KCX210 4.3 33.6 1.0 CG C:HIS271 4.3 31.4 1.0 NE2 C:HIS83 4.4 26.9 1.0 ND1 C:HIS271 4.4 37.6 1.0 NZ C:KCX210 4.6 33.1 1.0 CE1 C:HIS251 4.7 29.6 1.0 ND1 C:HIS251 4.7 35.0 1.0 NE2 C:HIS163 4.8 31.0 1.0 CG C:ASP344 5.0 23.6 1.0

Zinc binding site 7 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:58.0 occ:1.00 NE2 D:HIS83 2.3 26.9 1.0 NE2 D:HIS85 2.3 26.5 1.0 OD1 D:ASP344 2.6 39.0 1.0 CE1 D:HIS85 3.1 19.7 1.0 OQ1 D:KCX210 3.1 33.6 1.0 CE1 D:HIS83 3.2 23.4 1.0 OQ2 D:KCX210 3.2 31.5 1.0 CD2 D:HIS83 3.3 27.4 1.0 CG D:ASP344 3.3 23.6 1.0 CX D:KCX210 3.4 27.4 1.0 CD2 D:HIS85 3.4 27.9 1.0 OD2 D:ASP344 3.4 27.5 1.0 ZN D:ZN502 3.5 65.8 1.0 ND1 D:HIS85 4.3 28.0 1.0 ND1 D:HIS83 4.3 33.7 1.0 CG D:HIS83 4.4 28.3 1.0 NZ D:KCX210 4.4 33.1 1.0 CG D:HIS85 4.5 30.1 1.0 CB D:ASP344 4.6 27.1 1.0 NE2 D:HIS271 4.8 31.6 1.0

Zinc binding site 8 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:65.8 occ:1.00 NE2 D:HIS271 2.3 31.6 1.0 OQ2 D:KCX210 2.4 31.5 1.0 CD2 D:HIS251 2.6 27.9 1.0 CD2 D:HIS271 3.1 24.9 1.0 CE1 D:HIS271 3.4 33.9 1.0 ZN D:ZN501 3.5 58.0 1.0 NE2 D:HIS251 3.5 24.4 1.0 CG D:HIS251 3.6 28.7 1.0 CX D:KCX210 3.7 27.4 1.0 CB D:HIS251 4.0 22.7 1.0 CE1 D:HIS83 4.1 23.4 1.0 OD2 D:ASP344 4.2 27.5 1.0 OQ1 D:KCX210 4.3 33.6 1.0 CG D:HIS271 4.3 31.4 1.0 NE2 D:HIS83 4.4 26.9 1.0 ND1 D:HIS271 4.4 37.6 1.0 NZ D:KCX210 4.6 33.1 1.0 CE1 D:HIS251 4.7 29.6 1.0 ND1 D:HIS251 4.7 35.0 1.0 NE2 D:HIS163 4.8 31.0 1.0 CG D:ASP344 5.0 23.6 1.0

Zinc binding site 9 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:58.0 occ:1.00 NE2 E:HIS83 2.3 26.9 1.0 NE2 E:HIS85 2.3 26.5 1.0 OD1 E:ASP344 2.6 39.0 1.0 CE1 E:HIS85 3.1 19.7 1.0 OQ2 E:KCX210 3.1 33.6 1.0 CE1 E:HIS83 3.2 23.4 1.0 OQ1 E:KCX210 3.2 31.5 1.0 CD2 E:HIS83 3.3 27.4 1.0 CG E:ASP344 3.3 23.6 1.0 CX E:KCX210 3.4 27.4 1.0 CD2 E:HIS85 3.4 27.9 1.0 OD2 E:ASP344 3.4 27.5 1.0 ZN E:ZN502 3.5 65.8 1.0 ND1 E:HIS85 4.3 28.0 1.0 ND1 E:HIS83 4.3 33.7 1.0 CG E:HIS83 4.4 28.3 1.0 NZ E:KCX210 4.4 33.1 1.0 CG E:HIS85 4.5 30.1 1.0 CB E:ASP344 4.6 27.1 1.0 NE2 E:HIS271 4.8 31.6 1.0

Zinc binding site 10 out of 16 in the Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Electron Microscopic Structure of An Amide Hydrolase From Pseudoxanthomonas Wuyuanensis within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:65.8 occ:1.00 NE2 E:HIS271 2.3 31.6 1.0 OQ1 E:KCX210 2.4 31.5 1.0 CD2 E:HIS251 2.6 27.9 1.0 CD2 E:HIS271 3.1 24.9 1.0 CE1 E:HIS271 3.4 33.9 1.0 ZN E:ZN501 3.5 58.0 1.0 NE2 E:HIS251 3.5 24.4 1.0 CG E:HIS251 3.6 28.7 1.0 CX E:KCX210 3.7 27.4 1.0 CB E:HIS251 4.0 22.7 1.0 CE1 E:HIS83 4.1 23.4 1.0 OD2 E:ASP344 4.2 27.5 1.0 OQ2 E:KCX210 4.3 33.6 1.0 CG E:HIS271 4.3 31.4 1.0 NE2 E:HIS83 4.4 26.9 1.0 ND1 E:HIS271 4.4 37.6 1.0 NZ E:KCX210 4.6 33.1 1.0 CE1 E:HIS251 4.7 29.6 1.0 ND1 E:HIS251 4.7 35.0 1.0 NE2 E:HIS163 4.8 31.0 1.0 CG E:ASP344 5.0 23.6 1.0

Y.Hu, L.Dai, Y.Xu, D.Niu, X.Yang, Z.Xie, P.Shen, X.Li, H.Li, L.Zhang, J.Min, R.T.Guo, C.C.Chen. Functional Characterization and Structural Basis of An Efficient Ochratoxin A-Degrading Amidohydrolase. Int.J.Biol.Macromol. V. 278 34831 2024.
ISSN: ISSN 0141-8130
PubMed: 39163957
DOI: 10.1016/J.IJBIOMAC.2024.134831