Zinc in PDB 8f6h: Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex

The binding sites of Zinc atom in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex (pdb code 8f6h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex, PDB code: 8f6h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex


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 A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:56.8 occ:1.00 HE2 A:HIS285 1.6 31.8 1.0 OD1 A:ASP287 2.1 33.8 1.0 NE2 B:HIS263 2.3 30.3 1.0 NE2 A:HIS285 2.3 31.8 1.0 HD2 A:HIS285 2.7 31.8 1.0 CD2 A:HIS285 2.8 31.8 1.0 CG A:ASP287 3.0 33.8 1.0 OD2 A:ASP287 3.2 33.8 1.0 CD2 B:HIS263 3.2 30.3 1.0 HD2 B:HIS263 3.3 30.3 1.0 CE1 B:HIS263 3.3 30.3 1.0 HE1 A:HIS250 3.4 35.4 1.0 CE1 A:HIS285 3.5 31.8 1.0 HD1 A:HIS250 3.5 35.4 1.0 HE1 B:HIS263 3.5 30.3 1.0 CE1 A:HIS250 3.9 35.4 1.0 O A:GLN286 3.9 31.2 1.0 ND1 A:HIS250 3.9 35.4 1.0 HE1 A:HIS285 3.9 31.8 1.0 ZN A:ZN302 4.0 67.4 1.0 CG A:HIS285 4.1 31.8 1.0 HA A:ASP287 4.2 33.8 1.0 CG B:HIS263 4.4 30.3 1.0 CB A:ASP287 4.4 33.8 1.0 ND1 A:HIS285 4.4 31.8 1.0 ND1 B:HIS263 4.4 30.3 1.0 CA A:ASP287 4.8 33.8 1.0 C A:GLN286 4.9 31.2 1.0 HB3 A:ASP287 4.9 33.8 1.0 HB2 A:ASP287 4.9 33.8 1.0 NE2 A:HIS250 5.0 35.4 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex


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 A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:67.4 occ:1.00 HD1 A:HIS250 1.7 35.4 1.0 HE1 A:HIS234 1.8 38.2 1.0 OD2 A:ASP287 1.9 33.8 1.0 HE2 A:HIS234 2.0 38.2 1.0 CE1 A:HIS234 2.2 38.2 1.0 NE2 A:HIS234 2.3 38.2 1.0 ND1 A:HIS250 2.3 35.4 1.0 CE1 A:HIS250 3.0 35.4 1.0 HE1 A:HIS250 3.1 35.4 1.0 CG A:ASP287 3.1 33.8 1.0 CG A:HIS250 3.3 35.4 1.0 HB3 A:HIS250 3.5 35.4 1.0 ND1 A:HIS234 3.5 38.2 1.0 CD2 A:HIS234 3.6 38.2 1.0 OD1 A:ASP287 3.8 33.8 1.0 CB A:HIS250 3.8 35.4 1.0 HB2 A:HIS250 3.9 35.4 1.0 ZN A:ZN301 4.0 56.8 1.0 NE2 A:HIS250 4.1 35.4 1.0 HB2 A:ASP287 4.2 33.8 1.0 CB A:ASP287 4.2 33.8 1.0 CG A:HIS234 4.2 38.2 1.0 HD2 A:HIS285 4.2 31.8 1.0 HD2 A:HIS234 4.3 38.2 1.0 CD2 A:HIS250 4.3 35.4 1.0 HB3 A:ASP287 4.3 33.8 1.0 HB3 A:ASP235 4.6 35.5 1.0 HB2 A:ASP235 4.8 35.5 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex


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 A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:114.1 occ:1.00 OD1 A:ASP47 2.0 101.8 1.0 NE2 A:HIS155 2.3 105.2 1.0 OD2 A:ASP51 2.4 94.3 1.0 OD1 A:ASP51 2.4 94.3 1.0 OD1 A:ASP159 2.6 114.0 1.0 CG A:ASP47 2.7 101.8 1.0 CG A:ASP51 2.7 94.3 1.0 OD2 A:ASP47 2.8 101.8 1.0 CE1 A:HIS155 2.9 105.2 1.0 HE1 A:HIS155 2.9 105.2 1.0 HB2 A:ASP159 3.3 114.0 1.0 CD2 A:HIS155 3.4 105.2 1.0 CG A:ASP159 3.4 114.0 1.0 HD2 A:HIS155 3.7 105.2 1.0 O A:ASP47 3.8 101.8 1.0 CB A:ASP159 3.9 114.0 1.0 ND1 A:HIS155 4.0 105.2 1.0 CB A:ASP47 4.1 101.8 1.0 HE21 A:GLN88 4.2 88.7 1.0 C A:ASP47 4.2 101.8 1.0 CB A:ASP51 4.3 94.3 1.0 CG A:HIS155 4.3 105.2 1.0 OD2 A:ASP159 4.4 114.0 1.0 HA A:ASP159 4.4 114.0 1.0 HB3 A:ASP47 4.4 101.8 1.0 HB3 A:ASP159 4.6 114.0 1.0 HA A:ASP47 4.6 101.8 1.0 CA A:ASP47 4.6 101.8 1.0 HB3 A:ASP51 4.6 94.3 1.0 HA A:SER48 4.6 105.5 1.0 HB2 A:ASP51 4.7 94.3 1.0 HB2 A:ASP47 4.7 101.8 1.0 HD1 A:HIS155 4.7 105.2 1.0 H A:ASP51 4.7 94.3 1.0 CA A:ASP159 4.8 114.0 1.0 HD13 A:LEU162 4.9 112.7 1.0 NE2 A:GLN88 4.9 88.7 1.0 O A:HIS155 4.9 105.2 1.0 N A:SER48 5.0 105.5 1.0 HA A:ASP51 5.0 94.3 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex


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 A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:60.8 occ:1.00 OD1 B:ASP287 2.2 32.7 1.0 NE2 A:HIS263 2.3 29.7 1.0 NE2 B:HIS285 2.3 30.3 1.0 HD2 A:HIS263 2.4 29.7 1.0 CD2 A:HIS263 2.6 29.7 1.0 CD2 B:HIS285 3.0 30.3 1.0 HD2 B:HIS285 3.1 30.3 1.0 CE1 B:HIS285 3.3 30.3 1.0 CG B:ASP287 3.4 32.7 1.0 HA B:ASP287 3.5 32.7 1.0 CE1 A:HIS263 3.6 29.7 1.0 HE1 B:HIS285 3.6 30.3 1.0 CG A:HIS263 3.9 29.7 1.0 HE1 A:HIS263 4.1 29.7 1.0 OD2 B:ASP287 4.1 32.7 1.0 HD3 B:PRO288 4.2 32.1 1.0 CG B:HIS285 4.2 30.3 1.0 ND1 B:HIS285 4.3 30.3 1.0 CA B:ASP287 4.3 32.7 1.0 ND1 A:HIS263 4.4 29.7 1.0 CB B:ASP287 4.4 32.7 1.0 HD2 B:PRO288 4.4 32.1 1.0 ZN B:ZN302 4.7 110.4 1.0 HB2 A:ASP267 4.7 30.8 1.0 N B:ASP287 4.8 32.7 1.0 CD B:PRO288 4.8 32.1 1.0 O B:GLN286 4.8 28.2 1.0 HE1 B:HIS250 4.8 34.7 1.0 ND1 B:HIS250 4.8 34.7 1.0 HB3 B:ASP287 4.9 32.7 1.0 C B:GLN286 5.0 28.2 1.0 CE1 B:HIS250 5.0 34.7 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex


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 A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:110.4 occ:1.00 OD2 B:ASP287 1.9 32.7 1.0 ND1 B:HIS250 2.3 34.7 1.0 NE2 B:HIS234 2.3 35.2 1.0 CG B:ASP287 2.9 32.7 1.0 CE1 B:HIS250 3.1 34.7 1.0 HE1 B:HIS250 3.2 34.7 1.0 CE1 B:HIS234 3.2 35.2 1.0 CD2 B:HIS234 3.3 35.2 1.0 OD1 B:ASP287 3.4 32.7 1.0 HE1 B:HIS234 3.4 35.2 1.0 CG B:HIS250 3.4 34.7 1.0 HD2 B:HIS234 3.5 35.2 1.0 HB3 B:HIS250 3.6 34.7 1.0 HB2 B:HIS250 3.7 34.7 1.0 CB B:HIS250 3.8 34.7 1.0 CB B:ASP287 4.2 32.7 1.0 NE2 B:HIS250 4.3 34.7 1.0 HB2 B:ASP287 4.3 32.7 1.0 HD2 B:HIS285 4.4 30.3 1.0 ND1 B:HIS234 4.4 35.2 1.0 CG B:HIS234 4.4 35.2 1.0 CD2 B:HIS250 4.5 34.7 1.0 HB3 B:ASP287 4.5 32.7 1.0 ZN B:ZN301 4.7 60.8 1.0 HB2 B:ASP235 4.8 37.0 1.0 OD2 B:ASP235 4.9 37.0 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex


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 A Zinc-Loaded Asymmetrical Tmd D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:189.0 occ:1.00 OD1 B:ASP51 2.1 119.8 1.0 OD1 B:ASP47 2.2 113.7 1.0 HE2 B:HIS155 2.3 136.7 1.0 NE2 B:HIS155 2.3 136.7 1.0 CE1 B:HIS155 2.3 136.7 1.0 HE1 B:HIS155 2.3 136.7 1.0 OD1 B:ASP159 2.5 133.3 1.0 OD2 B:ASP159 2.8 133.3 1.0 CG B:ASP51 2.8 119.8 1.0 CG B:ASP47 2.9 113.7 1.0 CG B:ASP159 3.0 133.3 1.0 OD2 B:ASP51 3.0 119.8 1.0 OD2 B:ASP47 3.0 113.7 1.0 ND1 B:HIS155 3.2 136.7 1.0 CD2 B:HIS155 3.2 136.7 1.0 O B:ASP47 3.6 113.7 1.0 CG B:HIS155 3.7 136.7 1.0 HD2 B:HIS155 3.8 136.7 1.0 HD21 B:LEU162 4.2 128.1 1.0 CB B:ASP47 4.2 113.7 1.0 C B:ASP47 4.2 113.7 1.0 CB B:ASP51 4.3 119.8 1.0 HA B:ASP47 4.3 113.7 1.0 H B:ASP51 4.3 119.8 1.0 O B:HIS155 4.3 136.7 1.0 CB B:ASP159 4.5 133.3 1.0 HB3 B:ALA50 4.5 109.3 1.0 CA B:ASP47 4.5 113.7 1.0 HA B:ASP51 4.6 119.8 1.0 HB3 B:ASP51 4.6 119.8 1.0 HB2 B:ASP47 4.6 113.7 1.0 N B:ASP51 4.7 119.8 1.0 HA B:ASP159 4.7 133.3 1.0 CA B:ASP51 4.8 119.8 1.0 HB3 B:ASP159 4.8 133.3 1.0 HB3 B:ASP47 4.8 113.7 1.0 HB2 B:ASP51 4.9 119.8 1.0 HB2 B:ASP159 4.9 133.3 1.0 HG B:SER158 5.0 134.7 1.0

M.L.Lopez-Redondo, A.K.Hussein, D.L.Stokes. Characterization of Individual ZN2+ Binding Sites of Yiip To Be Published.