Zinc in PDB 8f6k: Cryo-Em Structure of A Zinc-Loaded H263A/D287A Mutant of the Yiip-Fab Complex

The binding sites of Zinc atom in the Cryo-Em Structure of A Zinc-Loaded H263A/D287A Mutant of the Yiip-Fab Complex (pdb code 8f6k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of A Zinc-Loaded H263A/D287A Mutant of the Yiip-Fab Complex, PDB code: 8f6k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of A Zinc-Loaded H263A/D287A 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 H263A/D287A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:117.2 occ:1.00 OD2 A:ASP159 1.9 82.8 1.0 OD1 A:ASP51 2.1 66.0 1.0 OD2 A:ASP51 2.2 66.0 1.0 NE2 A:HIS155 2.3 86.1 1.0 CG A:ASP51 2.3 66.0 1.0 OD1 A:ASP47 2.5 58.0 1.0 CG A:ASP159 2.7 82.8 1.0 CE1 A:HIS155 2.8 86.1 1.0 HE1 A:HIS155 2.8 86.1 1.0 OD1 A:ASP159 3.1 82.8 1.0 CG A:ASP47 3.3 58.0 1.0 CD2 A:HIS155 3.4 86.1 1.0 OD2 A:ASP47 3.5 58.0 1.0 O A:ASP47 3.7 58.0 1.0 HD2 A:HIS155 3.8 86.1 1.0 CB A:ASP51 3.8 66.0 1.0 CB A:ASP159 3.9 82.8 1.0 HB3 A:ASP159 3.9 82.8 1.0 ND1 A:HIS155 3.9 86.1 1.0 HB2 A:ASP51 4.1 66.0 1.0 HB2 A:ASP159 4.2 82.8 1.0 CG A:HIS155 4.2 86.1 1.0 H A:ASP51 4.2 66.0 1.0 HA A:ASP51 4.3 66.0 1.0 HB3 A:ASP51 4.4 66.0 1.0 C A:ASP47 4.5 58.0 1.0 CA A:ASP51 4.5 66.0 1.0 N A:ASP51 4.6 66.0 1.0 HD1 A:HIS155 4.6 86.1 1.0 CB A:ASP47 4.6 58.0 1.0 HB3 A:ALA50 4.7 52.9 1.0 HA A:ASP47 4.7 58.0 1.0 HD1 A:TYR156 4.8 85.8 1.0 CA A:ASP47 4.9 58.0 1.0 HA A:SER48 4.9 61.2 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of A Zinc-Loaded H263A/D287A 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 H263A/D287A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:54.2 occ:1.00 OD2 B:ASP159 1.9 27.6 1.0 HE2 B:HIS155 2.0 25.1 1.0 OD2 B:ASP51 2.1 24.1 1.0 OD1 B:ASP159 2.2 27.6 1.0 NE2 B:HIS155 2.3 25.1 1.0 CG B:ASP159 2.3 27.6 1.0 OD1 B:ASP51 2.6 24.1 1.0 CG B:ASP51 2.7 24.1 1.0 CE1 B:HIS155 2.7 25.1 1.0 HE1 B:HIS155 2.8 25.1 1.0 OD2 B:ASP47 2.9 28.2 1.0 CD2 B:HIS155 3.2 25.1 1.0 OD1 B:ASP47 3.3 28.2 1.0 CG B:ASP47 3.4 28.2 1.0 HD2 B:HIS155 3.6 25.1 1.0 ND1 B:HIS155 3.6 25.1 1.0 CB B:ASP159 3.8 27.6 1.0 O B:ASP47 3.9 28.2 1.0 CG B:HIS155 3.9 25.1 1.0 HB3 B:ASP159 4.1 27.6 1.0 CB B:ASP51 4.1 24.1 1.0 HB2 B:ASP159 4.2 27.6 1.0 HB2 B:ASP51 4.4 24.1 1.0 HA B:SER48 4.4 26.4 1.0 O B:HIS155 4.4 25.1 1.0 C B:ASP47 4.4 28.2 1.0 H B:ASP51 4.5 24.1 1.0 HB3 B:ASP51 4.6 24.1 1.0 HA B:ASP159 4.6 27.6 1.0 HE1 B:TYR156 4.7 24.1 1.0 CB B:ASP47 4.7 28.2 1.0 CA B:ASP159 4.8 27.6 1.0 HD1 B:TYR156 4.9 24.1 1.0 HB3 B:ASP47 4.9 28.2 1.0 HB3 B:ALA50 4.9 24.4 1.0 HA B:TYR156 4.9 24.1 1.0 CE1 B:TYR156 4.9 24.1 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of A Zinc-Loaded H263A/D287A 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 H263A/D287A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:119.0 occ:1.00 OD2 C:ASP159 1.9 82.6 1.0 OD1 C:ASP51 2.0 66.1 1.0 OD2 C:ASP51 2.2 66.1 1.0 NE2 C:HIS155 2.3 86.2 1.0 CG C:ASP51 2.3 66.1 1.0 OD1 C:ASP47 2.5 57.7 1.0 CG C:ASP159 2.7 82.6 1.0 CE1 C:HIS155 2.8 86.2 1.0 HE1 C:HIS155 2.8 86.2 1.0 OD1 C:ASP159 3.1 82.6 1.0 CG C:ASP47 3.3 57.7 1.0 CD2 C:HIS155 3.4 86.2 1.0 OD2 C:ASP47 3.6 57.7 1.0 O C:ASP47 3.7 57.7 1.0 HD2 C:HIS155 3.8 86.2 1.0 CB C:ASP51 3.8 66.1 1.0 CB C:ASP159 3.9 82.6 1.0 HB3 C:ASP159 3.9 82.6 1.0 ND1 C:HIS155 3.9 86.2 1.0 HB2 C:ASP51 4.1 66.1 1.0 HB2 C:ASP159 4.2 82.6 1.0 CG C:HIS155 4.2 86.2 1.0 H C:ASP51 4.2 66.1 1.0 HA C:ASP51 4.3 66.1 1.0 HB3 C:ASP51 4.4 66.1 1.0 C C:ASP47 4.5 57.7 1.0 CA C:ASP51 4.5 66.1 1.0 N C:ASP51 4.6 66.1 1.0 HD1 C:HIS155 4.6 86.2 1.0 CB C:ASP47 4.7 57.7 1.0 HB3 C:ALA50 4.7 52.7 1.0 HA C:ASP47 4.8 57.7 1.0 HD1 C:TYR156 4.9 86.1 1.0 CA C:ASP47 4.9 57.7 1.0 HA C:SER48 5.0 61.1 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of A Zinc-Loaded H263A/D287A 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 H263A/D287A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:59.1 occ:1.00 OD2 D:ASP159 1.9 28.3 1.0 HE2 D:HIS155 2.0 25.4 1.0 OD2 D:ASP51 2.1 24.2 1.0 OD1 D:ASP159 2.2 28.3 1.0 NE2 D:HIS155 2.3 25.4 1.0 CG D:ASP159 2.3 28.3 1.0 OD1 D:ASP51 2.6 24.2 1.0 CG D:ASP51 2.7 24.2 1.0 CE1 D:HIS155 2.7 25.4 1.0 HE1 D:HIS155 2.8 25.4 1.0 OD2 D:ASP47 2.9 28.3 1.0 CD2 D:HIS155 3.2 25.4 1.0 OD1 D:ASP47 3.3 28.3 1.0 CG D:ASP47 3.4 28.3 1.0 HD2 D:HIS155 3.6 25.4 1.0 ND1 D:HIS155 3.6 25.4 1.0 CB D:ASP159 3.8 28.3 1.0 O D:ASP47 3.9 28.3 1.0 CG D:HIS155 3.9 25.4 1.0 HB3 D:ASP159 4.1 28.3 1.0 CB D:ASP51 4.1 24.2 1.0 HB2 D:ASP159 4.2 28.3 1.0 HB2 D:ASP51 4.4 24.2 1.0 HA D:SER48 4.4 26.7 1.0 O D:HIS155 4.4 25.4 1.0 C D:ASP47 4.4 28.3 1.0 H D:ASP51 4.6 24.2 1.0 HB3 D:ASP51 4.6 24.2 1.0 HA D:ASP159 4.6 28.3 1.0 HE1 D:TYR156 4.7 24.5 1.0 CB D:ASP47 4.7 28.3 1.0 CA D:ASP159 4.8 28.3 1.0 HD1 D:TYR156 4.9 24.5 1.0 HB3 D:ASP47 4.9 28.3 1.0 HB3 D:ALA50 4.9 24.1 1.0 HA D:TYR156 4.9 24.5 1.0 CE1 D:TYR156 4.9 24.5 1.0 H D:ASP159 5.0 28.3 1.0

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