Zinc in PDB 7y5g: Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc (pdb code 7y5g). 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 Eukaryotic ZNT8 in the Presence of Zinc, PDB code: 7y5g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7y5g

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc


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 Eukaryotic ZNT8 in the Presence of Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:40.0
occ:1.00
OE2 B:GLU357 2.1 24.1 1.0
ND1 B:HIS323 2.3 16.1 1.0
SG A:CYS46 2.3 39.3 1.0
NE2 B:HIS306 2.3 21.4 1.0
OE1 B:GLU357 2.4 24.1 1.0
CD B:GLU357 2.5 24.1 1.0
CE1 B:HIS323 3.1 16.1 1.0
CD2 B:HIS306 3.2 21.4 1.0
CE1 B:HIS306 3.3 21.4 1.0
CG B:HIS323 3.4 16.1 1.0
CB B:HIS323 3.8 16.1 1.0
CB A:CYS46 3.9 39.3 1.0
CG B:GLU357 4.0 24.1 1.0
NE2 B:HIS323 4.3 16.1 1.0
ND1 B:HIS306 4.4 21.4 1.0
CG B:HIS306 4.4 21.4 1.0
CD2 B:HIS323 4.5 16.1 1.0
NE2 A:HIS47 4.7 38.4 1.0
NE2 A:HIS45 4.9 37.1 1.0
CB B:GLU357 4.9 24.1 1.0

Zinc binding site 2 out of 6 in 7y5g

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc


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 Eukaryotic ZNT8 in the Presence of Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:41.8
occ:1.00
NE2 B:HIS225 2.3 12.8 1.0
NE2 B:HIS100 2.3 42.1 1.0
OD1 B:ASP229 2.4 20.9 1.0
OD2 B:ASP229 2.7 20.9 1.0
CE1 B:HIS100 2.7 42.1 1.0
CG B:ASP229 2.9 20.9 1.0
CE1 B:HIS225 2.9 12.8 1.0
OD1 B:ASP104 3.1 30.9 1.0
CD2 B:HIS225 3.2 12.8 1.0
CD2 B:HIS100 3.4 42.1 1.0
ND1 B:HIS100 3.9 42.1 1.0
ND1 B:HIS225 3.9 12.8 1.0
CG B:HIS225 4.1 12.8 1.0
CG B:ASP104 4.2 30.9 1.0
CG B:HIS100 4.2 42.1 1.0
CB B:ASP229 4.4 20.9 1.0
CG2 B:VAL103 4.5 37.6 1.0
OD2 B:ASP104 4.5 30.9 1.0
O B:HIS225 4.7 12.8 1.0
O B:HIS100 4.8 42.1 1.0

Zinc binding site 3 out of 6 in 7y5g

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc


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 Eukaryotic ZNT8 in the Presence of Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:64.7
occ:1.00
NE2 B:HIS45 2.0 36.4 1.0
ND1 B:HIS47 2.0 38.4 1.0
CE1 B:HIS47 2.3 38.4 1.0
SG A:CYS366 2.3 46.1 1.0
SG A:CYS369 2.3 39.8 1.0
CE1 B:HIS45 2.8 36.4 1.0
CD2 B:HIS45 3.1 36.4 1.0
CG B:HIS47 3.2 38.4 1.0
CB A:CYS369 3.5 39.8 1.0
NE2 B:HIS47 3.5 38.4 1.0
CB A:CYS366 3.7 46.1 1.0
ND1 B:HIS45 3.9 36.4 1.0
CD2 B:HIS47 3.9 38.4 1.0
N A:CYS369 4.0 39.8 1.0
CG B:HIS45 4.1 36.4 1.0
CB B:HIS47 4.1 38.4 1.0
CA A:CYS369 4.2 39.8 1.0
O A:SER363 4.5 37.6 1.0
C A:PHE368 4.6 42.9 1.0
CB A:PHE368 4.6 42.9 1.0
CD2 A:HIS306 4.8 21.1 1.0
O A:CYS366 4.8 46.1 1.0
CA A:CYS366 4.9 46.1 1.0
NE2 A:GLN362 4.9 39.0 1.0
C A:CYS366 5.0 46.1 1.0
CA A:PHE368 5.0 42.9 1.0
N A:PHE368 5.0 42.9 1.0

Zinc binding site 4 out of 6 in 7y5g

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc


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 Eukaryotic ZNT8 in the Presence of Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:65.2
occ:1.00
NE2 A:HIS45 2.0 37.1 1.0
ND1 A:HIS47 2.0 38.4 1.0
CE1 A:HIS47 2.3 38.4 1.0
SG B:CYS366 2.3 47.0 1.0
SG B:CYS369 2.3 39.3 1.0
CE1 A:HIS45 2.8 37.1 1.0
CD2 A:HIS45 3.0 37.1 1.0
CG A:HIS47 3.3 38.4 1.0
NE2 A:HIS47 3.5 38.4 1.0
CB B:CYS369 3.5 39.3 1.0
CB B:CYS366 3.7 47.0 1.0
ND1 A:HIS45 3.9 37.1 1.0
CD2 A:HIS47 3.9 38.4 1.0
N B:CYS369 4.0 39.3 1.0
CG A:HIS45 4.0 37.1 1.0
CB A:HIS47 4.1 38.4 1.0
CA B:CYS369 4.3 39.3 1.0
O B:SER363 4.5 38.4 1.0
C B:PHE368 4.6 42.6 1.0
CB B:PHE368 4.6 42.6 1.0
CD2 B:HIS306 4.8 21.4 1.0
O B:CYS366 4.8 47.0 1.0
CA B:CYS366 4.9 47.0 1.0
NE2 B:GLN362 4.9 40.3 1.0
CA B:PHE368 5.0 42.6 1.0
N B:PHE368 5.0 42.6 1.0
C B:CYS366 5.0 47.0 1.0

Zinc binding site 5 out of 6 in 7y5g

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc


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 Eukaryotic ZNT8 in the Presence of Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:37.9
occ:1.00
OE2 A:GLU357 2.1 22.8 1.0
ND1 A:HIS323 2.3 15.6 1.0
SG B:CYS46 2.3 38.2 1.0
NE2 A:HIS306 2.3 21.1 1.0
OE1 A:GLU357 2.4 22.8 1.0
CD A:GLU357 2.5 22.8 1.0
CE1 A:HIS323 3.1 15.6 1.0
CD2 A:HIS306 3.2 21.1 1.0
CE1 A:HIS306 3.3 21.1 1.0
CG A:HIS323 3.4 15.6 1.0
CB A:HIS323 3.9 15.6 1.0
CB B:CYS46 3.9 38.2 1.0
CG A:GLU357 4.0 22.8 1.0
NE2 A:HIS323 4.3 15.6 1.0
ND1 A:HIS306 4.4 21.1 1.0
CG A:HIS306 4.4 21.1 1.0
CD2 A:HIS323 4.5 15.6 1.0
NE2 B:HIS47 4.7 38.4 1.0
NE2 B:HIS45 4.9 36.4 1.0
CB A:GLU357 4.9 22.8 1.0
NE2 A:GLN362 4.9 39.0 1.0

Zinc binding site 6 out of 6 in 7y5g

Go back to Zinc Binding Sites List in 7y5g
Zinc binding site 6 out of 6 in the Cryo-Em Structure of A Eukaryotic ZNT8 in the Presence of Zinc


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 Eukaryotic ZNT8 in the Presence of Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:42.1
occ:1.00
NE2 A:HIS225 2.3 13.5 1.0
NE2 A:HIS100 2.3 42.6 1.0
OD1 A:ASP229 2.4 21.1 1.0
OD2 A:ASP229 2.6 21.1 1.0
CE1 A:HIS100 2.7 42.6 1.0
CG A:ASP229 2.8 21.1 1.0
CE1 A:HIS225 2.9 13.5 1.0
OD1 A:ASP104 3.2 31.4 1.0
CD2 A:HIS225 3.2 13.5 1.0
CD2 A:HIS100 3.4 42.6 1.0
ND1 A:HIS100 3.9 42.6 1.0
ND1 A:HIS225 3.9 13.5 1.0
CG A:HIS225 4.1 13.5 1.0
CG A:ASP104 4.2 31.4 1.0
CG A:HIS100 4.2 42.6 1.0
CB A:ASP229 4.3 21.1 1.0
CG2 A:VAL103 4.4 37.3 1.0
OD2 A:ASP104 4.5 31.4 1.0
O A:HIS225 4.7 13.5 1.0
O A:HIS100 4.7 42.6 1.0

Reference:

S.Zhang, C.Fu, Y.Luo, Q.Xie, T.Xu, Z.Sun, Z.Su, X.Zhou. Cryo-Em Structure of A Eukaryotic Zinc Transporter at A Low pH Suggests Its Zn 2+ -Releasing Mechanism. J.Struct.Biol. V. 215 07926 2022.
ISSN: ESSN 1095-8657
PubMed: 36464198
DOI: 10.1016/J.JSB.2022.107926
Page generated: Sat Apr 8 06:12:23 2023

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