Zinc in PDB 8f6i: Cryo-Em Structure of A Zinc-Loaded Symmetrical D70A Mutant of the Yiip-Fab Complex

The binding sites of Zinc atom in the Cryo-Em Structure of A Zinc-Loaded Symmetrical D70A Mutant of the Yiip-Fab Complex (pdb code 8f6i). 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 Symmetrical D70A Mutant of the Yiip-Fab Complex, PDB code: 8f6i:
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 Symmetrical 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 Symmetrical D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:69.3 occ:1.00 OD1 B:ASP287 2.1 57.5 1.0 NE2 B:HIS285 2.3 67.9 1.0 NE2 A:HIS263 2.3 37.9 1.0 CE1 B:HIS285 3.0 67.9 1.0 CD2 A:HIS263 3.1 37.9 1.0 CG B:ASP287 3.2 57.5 1.0 CE1 A:HIS263 3.4 37.9 1.0 CD2 B:HIS285 3.5 67.9 1.0 OD2 B:ASP287 3.8 57.5 1.0 O B:GLN286 4.0 67.9 1.0 ND1 B:HIS285 4.2 67.9 1.0 CG A:HIS263 4.3 37.9 1.0 CB B:ASP287 4.4 57.5 1.0 ND1 A:HIS263 4.4 37.9 1.0 CG B:HIS285 4.5 67.9 1.0 ZN B:ZN302 4.5 72.8 1.0 CA B:ASP287 4.6 57.5 1.0 C B:GLN286 5.0 67.9 1.0 CE1 B:HIS250 5.0 50.9 1.0 ND1 B:HIS250 5.0 50.9 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Symmetrical 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 Symmetrical D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:72.8 occ:1.00 OD2 B:ASP287 2.1 57.5 1.0 ND1 B:HIS250 2.3 50.9 1.0 NE2 B:HIS234 2.3 56.6 1.0 CE1 B:HIS234 2.4 56.6 1.0 CE1 B:HIS250 3.1 50.9 1.0 CG B:ASP287 3.1 57.5 1.0 CG B:HIS250 3.4 50.9 1.0 CD2 B:HIS234 3.6 56.6 1.0 ND1 B:HIS234 3.7 56.6 1.0 OD1 B:ASP287 3.7 57.5 1.0 CB B:HIS250 3.9 50.9 1.0 CB B:ASP287 4.1 57.5 1.0 NE2 B:HIS250 4.3 50.9 1.0 CG B:HIS234 4.3 56.6 1.0 CD2 B:HIS250 4.5 50.9 1.0 ZN B:ZN301 4.5 69.3 1.0 CD2 B:HIS285 4.9 67.9 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Symmetrical 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 Symmetrical D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:186.1 occ:1.00 OD1 B:ASP47 2.1 129.0 1.0 OD2 B:ASP51 2.1 125.3 1.0 NE2 B:HIS155 2.3 143.0 1.0 O B:ASP47 2.4 129.0 1.0 CG B:ASP51 2.8 125.3 1.0 OD1 B:ASP51 3.0 125.3 1.0 CE1 B:HIS155 3.0 143.0 1.0 OD2 B:ASP159 3.1 134.3 1.0 CG B:ASP47 3.2 129.0 1.0 C B:ASP47 3.2 129.0 1.0 CD2 B:HIS155 3.5 143.0 1.0 OD1 B:ASP159 3.7 134.3 1.0 CG B:ASP159 3.8 134.3 1.0 CA B:ASP47 3.9 129.0 1.0 OD2 B:ASP47 4.0 129.0 1.0 CB B:ASP51 4.1 125.3 1.0 N B:ASP51 4.1 125.3 1.0 CB B:ASP47 4.1 129.0 1.0 N B:SER48 4.1 123.2 1.0 CB B:ALA50 4.2 115.5 1.0 ND1 B:HIS155 4.3 143.0 1.0 CA B:SER48 4.4 123.2 1.0 CG B:HIS155 4.5 143.0 1.0 CA B:ASP51 4.6 125.3 1.0 C B:ALA50 4.8 115.5 1.0 C B:SER48 4.9 123.2 1.0 O B:SER48 4.9 123.2 1.0 CA B:ALA50 4.9 115.5 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Symmetrical 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 Symmetrical D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:73.8 occ:1.00 OD1 A:ASP287 2.1 49.2 1.0 NE2 B:HIS263 2.3 44.4 1.0 NE2 A:HIS285 2.3 36.1 1.0 CG A:ASP287 2.8 49.2 1.0 OD2 A:ASP287 2.8 49.2 1.0 CD2 B:HIS263 3.0 44.4 1.0 CD2 A:HIS285 3.0 36.1 1.0 CE1 A:HIS285 3.2 36.1 1.0 NE2 A:HIS250 3.3 46.2 1.0 CE1 B:HIS263 3.4 44.4 1.0 CE1 A:HIS250 3.4 46.2 1.0 CG A:HIS285 4.0 36.1 1.0 ND1 A:HIS285 4.1 36.1 1.0 CG B:HIS263 4.2 44.4 1.0 CB A:ASP287 4.3 49.2 1.0 ND1 B:HIS263 4.3 44.4 1.0 CD2 A:HIS250 4.6 46.2 1.0 ND1 A:HIS250 4.7 46.2 1.0 ZN A:ZN302 4.7 116.5 1.0 O A:GLN286 4.8 38.8 1.0 CA A:ASP287 4.8 49.2 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Symmetrical 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 Symmetrical D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:116.5 occ:1.00 CD2 A:HIS250 2.1 46.2 1.0 NE2 A:HIS250 2.3 46.2 1.0 NE2 A:HIS234 2.3 48.0 1.0 OD2 A:ASP287 2.4 49.2 1.0 CE1 A:HIS234 2.8 48.0 1.0 CG A:HIS250 3.4 46.2 1.0 CG A:ASP287 3.5 49.2 1.0 CE1 A:HIS250 3.5 46.2 1.0 CD2 A:HIS234 3.6 48.0 1.0 ND1 A:HIS250 4.0 46.2 1.0 ND1 A:HIS234 4.1 48.0 1.0 CB A:ASP287 4.1 49.2 1.0 CB A:HIS250 4.4 46.2 1.0 CG A:HIS234 4.5 48.0 1.0 OD1 A:ASP287 4.5 49.2 1.0 ZN A:ZN301 4.7 73.8 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of A Zinc-Loaded Symmetrical 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 Symmetrical D70A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:178.2 occ:1.00 CE1 A:HIS155 2.0 137.1 1.0 NE2 A:HIS155 2.3 137.1 1.0 ND1 A:HIS155 2.3 137.1 1.0 OD1 A:ASP159 2.3 135.2 1.0 OD1 A:ASP51 2.6 117.1 1.0 CD2 A:HIS155 2.7 137.1 1.0 CG A:HIS155 2.7 137.1 1.0 CG A:ASP159 3.1 135.2 1.0 OD2 A:ASP159 3.1 135.2 1.0 O A:HIS155 3.1 137.1 1.0 CG A:ASP51 3.3 117.1 1.0 OD2 A:ASP51 3.5 117.1 1.0 OD1 A:ASP47 3.5 109.9 1.0 C A:HIS155 3.7 137.1 1.0 CB A:HIS155 3.9 137.1 1.0 OG A:SER158 4.0 137.7 1.0 CA A:HIS155 4.1 137.1 1.0 OD2 A:ASP47 4.2 109.9 1.0 CG A:ASP47 4.2 109.9 1.0 CB A:ASP51 4.5 117.1 1.0 N A:TYR156 4.5 136.1 1.0 CB A:ASP159 4.5 135.2 1.0 O A:ASP47 4.7 109.9 1.0 CD1 A:TYR156 4.8 136.1 1.0 CA A:TYR156 4.9 136.1 1.0 N A:ASP159 4.9 135.2 1.0

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