Zinc in PDB 8f6j: Cryo-Em Structure of A Zinc-Loaded D287A Mutant of the Yiip-Fab Complex

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of A Zinc-Loaded D287A Mutant of the Yiip-Fab Complex (pdb code 8f6j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of A Zinc-Loaded D287A Mutant of the Yiip-Fab Complex, PDB code: 8f6j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8f6j

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:59.8
occ:1.00
ND1 B:HIS250 2.3 29.0 1.0
NE2 B:HIS234 2.3 38.7 1.0
CE1 B:HIS234 2.4 38.7 1.0
CB B:HIS250 2.8 29.0 1.0
CG B:HIS250 2.9 29.0 1.0
CD2 B:HIS234 3.4 38.7 1.0
ND1 B:HIS234 3.4 38.7 1.0
CE1 B:HIS250 3.5 29.0 1.0
CG B:HIS234 4.0 38.7 1.0
CD2 B:HIS250 4.2 29.0 1.0
ZN A:ZN304 4.2 68.3 1.0
CA B:HIS250 4.3 29.0 1.0
CB B:ALA287 4.4 16.1 1.0
NE2 B:HIS250 4.4 29.0 1.0
CD2 B:HIS285 4.6 22.2 1.0
O B:HIS234 4.7 38.7 1.0
C B:HIS250 4.8 29.0 1.0
CB B:ASP235 4.8 46.8 1.0
O B:HIS250 4.9 29.0 1.0
OD2 B:ASP235 4.9 46.8 1.0
CG B:ASP235 4.9 46.8 1.0

Zinc binding site 2 out of 8 in 8f6j

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:175.1
occ:1.00
OD2 B:ASP70 2.1 149.9 1.0
NE2 B:HIS77 2.3 141.0 1.0
ND1 B:HIS73 2.3 144.9 1.0
OD1 B:ASP70 2.7 149.9 1.0
CG B:ASP70 2.7 149.9 1.0
CE1 B:HIS77 3.0 141.0 1.0
CE1 B:HIS73 3.1 144.9 1.0
CG B:HIS73 3.4 144.9 1.0
CD2 B:HIS77 3.5 141.0 1.0
CB B:HIS73 3.9 144.9 1.0
OH B:TYR64 3.9 149.4 1.0
N B:HIS73 4.1 144.9 1.0
CB B:ASP70 4.2 149.9 1.0
ND1 B:HIS77 4.2 141.0 1.0
NE2 B:HIS73 4.3 144.9 1.0
CB B:ASP72 4.5 146.7 1.0
CG B:HIS77 4.5 141.0 1.0
CD2 B:HIS73 4.5 144.9 1.0
CA B:HIS73 4.6 144.9 1.0
OD2 B:ASP72 4.7 146.7 1.0
CZ B:TYR64 4.8 149.4 1.0
C B:ASP72 4.9 146.7 1.0

Zinc binding site 3 out of 8 in 8f6j

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:154.3
occ:1.00
OD2 B:ASP159 2.1 152.1 1.0
OD1 B:ASP51 2.4 143.6 1.0
OD1 B:ASP159 2.5 152.1 1.0
CG B:ASP159 2.6 152.1 1.0
OD1 B:ASP47 2.9 140.3 1.0
OD2 B:ASP51 3.1 143.6 1.0
CG B:ASP51 3.1 143.6 1.0
CG B:ASP47 3.6 140.3 1.0
OD2 B:ASP47 3.7 140.3 1.0
O B:ASP47 3.8 140.3 1.0
CD2 B:HIS155 4.0 153.9 1.0
O B:HIS155 4.1 153.9 1.0
CB B:ASP159 4.1 152.1 1.0
CD1 B:TYR156 4.2 155.7 1.0
CE1 B:TYR156 4.4 155.7 1.0
C B:HIS155 4.5 153.9 1.0
CB B:ASP51 4.6 143.6 1.0
CG B:HIS155 4.6 153.9 1.0
C B:ASP47 4.6 140.3 1.0
CB B:HIS155 4.7 153.9 1.0
N B:TYR156 4.9 155.7 1.0
CB B:ASP47 4.9 140.3 1.0
CA B:TYR156 5.0 155.7 1.0

Zinc binding site 4 out of 8 in 8f6j

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:61.0
occ:1.00
NE2 B:HIS263 2.3 16.7 1.0
NE2 A:HIS285 2.3 20.6 1.0
CD2 A:HIS285 2.8 20.6 1.0
CE1 B:HIS263 3.2 16.7 1.0
CD2 B:HIS263 3.3 16.7 1.0
CE1 A:HIS285 3.5 20.6 1.0
CB A:ALA287 4.0 15.1 1.0
CG A:HIS285 4.1 20.6 1.0
ZN A:ZN301 4.2 58.3 1.0
ND1 B:HIS263 4.3 16.7 1.0
CG B:HIS263 4.4 16.7 1.0
ND1 A:HIS285 4.4 20.6 1.0
ND1 A:HIS250 4.5 26.1 1.0
CA A:ALA287 4.5 15.1 1.0
OD1 B:ASP267 4.8 23.2 1.0
CE1 A:HIS250 4.8 26.1 1.0

Zinc binding site 5 out of 8 in 8f6j

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 5 of Cryo-Em Structure of A Zinc-Loaded D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:58.3
occ:1.00
ND1 A:HIS250 2.3 26.1 1.0
NE2 A:HIS234 2.3 34.4 1.0
CE1 A:HIS234 2.4 34.4 1.0
CB A:HIS250 2.8 26.1 1.0
CG A:HIS250 2.9 26.1 1.0
CD2 A:HIS234 3.4 34.4 1.0
ND1 A:HIS234 3.4 34.4 1.0
CE1 A:HIS250 3.5 26.1 1.0
CG A:HIS234 4.0 34.4 1.0
CD2 A:HIS250 4.2 26.1 1.0
CA A:HIS250 4.2 26.1 1.0
ZN B:ZN304 4.2 61.0 1.0
CB A:ALA287 4.4 15.1 1.0
NE2 A:HIS250 4.4 26.1 1.0
CD2 A:HIS285 4.6 20.6 1.0
O A:HIS234 4.7 34.4 1.0
C A:HIS250 4.8 26.1 1.0
O A:HIS250 4.8 26.1 1.0
CB A:ASP235 4.8 41.9 1.0
OD2 A:ASP235 4.9 41.9 1.0
CG A:ASP235 4.9 41.9 1.0

Zinc binding site 6 out of 8 in 8f6j

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 6 of Cryo-Em Structure of A Zinc-Loaded D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:170.5
occ:1.00
OD2 A:ASP70 2.1 147.8 1.0
ND1 A:HIS73 2.3 142.6 1.0
NE2 A:HIS77 2.3 141.0 1.0
CG A:ASP70 2.7 147.8 1.0
OD1 A:ASP70 2.7 147.8 1.0
CE1 A:HIS77 3.0 141.0 1.0
CE1 A:HIS73 3.1 142.6 1.0
CG A:HIS73 3.4 142.6 1.0
CD2 A:HIS77 3.5 141.0 1.0
CB A:HIS73 3.9 142.6 1.0
OH A:TYR64 3.9 149.0 1.0
N A:HIS73 4.2 142.6 1.0
CB A:ASP70 4.2 147.8 1.0
ND1 A:HIS77 4.2 141.0 1.0
NE2 A:HIS73 4.3 142.6 1.0
CG A:HIS77 4.5 141.0 1.0
CD2 A:HIS73 4.5 142.6 1.0
CB A:ASP72 4.5 142.8 1.0
CA A:HIS73 4.6 142.6 1.0
OD2 A:ASP72 4.8 142.8 1.0
CZ A:TYR64 4.8 149.0 1.0
C A:ASP72 5.0 142.8 1.0

Zinc binding site 7 out of 8 in 8f6j

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 7 of Cryo-Em Structure of A Zinc-Loaded D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:147.0
occ:1.00
OD2 A:ASP159 2.1 150.3 1.0
OD1 A:ASP51 2.4 142.8 1.0
OD1 A:ASP159 2.5 150.3 1.0
CG A:ASP159 2.6 150.3 1.0
OD1 A:ASP47 3.0 139.2 1.0
CG A:ASP51 3.2 142.8 1.0
OD2 A:ASP51 3.3 142.8 1.0
CG A:ASP47 3.6 139.2 1.0
O A:ASP47 3.6 139.2 1.0
OD2 A:ASP47 3.7 139.2 1.0
CB A:ASP159 4.1 150.3 1.0
CD2 A:HIS155 4.1 153.9 1.0
O A:HIS155 4.2 153.9 1.0
CD1 A:TYR156 4.3 153.8 1.0
CE1 A:TYR156 4.4 153.8 1.0
C A:ASP47 4.5 139.2 1.0
CB A:HIS155 4.6 153.9 1.0
C A:HIS155 4.6 153.9 1.0
CG A:HIS155 4.6 153.9 1.0
CB A:ASP51 4.6 142.8 1.0
CB A:ASP47 4.8 139.2 1.0
N A:ASP51 4.9 142.8 1.0
CA A:ASP47 4.9 139.2 1.0
N A:TYR156 5.0 153.8 1.0
CA A:ASP159 5.0 150.3 1.0

Zinc binding site 8 out of 8 in 8f6j

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of A Zinc-Loaded 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 8 of Cryo-Em Structure of A Zinc-Loaded D287A Mutant of the Yiip-Fab Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:68.3
occ:1.00
NE2 A:HIS263 2.3 16.4 1.0
NE2 B:HIS285 2.3 22.2 1.0
CD2 B:HIS285 2.8 22.2 1.0
CE1 A:HIS263 3.2 16.4 1.0
CD2 A:HIS263 3.3 16.4 1.0
CE1 B:HIS285 3.5 22.2 1.0
CB B:ALA287 4.0 16.1 1.0
CG B:HIS285 4.1 22.2 1.0
ZN B:ZN301 4.2 59.8 1.0
ND1 A:HIS263 4.3 16.4 1.0
CG A:HIS263 4.4 16.4 1.0
ND1 B:HIS285 4.4 22.2 1.0
ND1 B:HIS250 4.5 29.0 1.0
CA B:ALA287 4.5 16.1 1.0
OD1 A:ASP267 4.8 23.2 1.0
CE1 B:HIS250 4.8 29.0 1.0

Reference:

M.L.Lopez-Redondo, A.K.Hussein, D.L.Stokes. Characterization of Individual ZN2+ Binding Sites of Yiip To Be Published.
Page generated: Sat Apr 8 08:50:13 2023

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