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Cadmium in PDB 8ght: Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica (pdb code 8ght). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica, PDB code: 8ght:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 8ght

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Cadmium binding site 1 out of 6 in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:66.7
occ:1.00
 OE1 A:GLU181 2.3 95.6 1.0
OE1 A:GLU211 2.3 92.7 1.0
OE2 A:GLU211 2.3 92.7 1.0
SD A:MET99 2.3 97.1 1.0
OE1 A:GLN207 2.3 96.1 1.0
NE2 A:GLN207 2.3 96.1 1.0
NE2 A:HIS177 2.3 89.1 1.0
CD A:GLU211 2.6 92.7 1.0
CD A:GLN207 2.6 96.1 1.0
CE1 A:HIS177 3.1 89.1 1.0
CE A:MET99 3.2 97.1 1.0
CD2 A:HIS177 3.4 89.1 1.0
CD A:GLU181 3.5 95.6 1.0
CG A:MET99 3.6 97.1 1.0
OD1 A:ASP208 4.0 96.3 1.0
CG A:GLU211 4.1 92.7 1.0
CG A:GLN207 4.1 96.1 1.0
OE2 A:GLU181 4.3 95.6 1.0
ND1 A:HIS177 4.3 89.1 1.0
CG A:HIS177 4.5 89.1 1.0
CG A:GLU181 4.5 95.6 1.0
OD1 A:ASN178 4.8 92.0 1.0
O A:GLN207 4.9 96.1 1.0
CG A:ASP208 4.9 96.3 1.0
CB A:GLU211 4.9 92.7 1.0
CB A:MET99 5.0 97.1 1.0
CB A:GLN207 5.0 96.1 1.0

Cadmium binding site 2 out of 6 in 8ght

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Cadmium binding site 2 out of 6 in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:66.9
occ:1.00
 OE2 A:GLU276 2.3 88.3 1.0
NE2 A:HIS149 2.3 85.3 1.0
OE1 A:GLU276 2.3 88.3 1.0
OD1 A:ASP144 2.3 89.7 1.0
NE2 A:HIS151 2.3 75.3 1.0
OD2 A:ASP144 2.3 89.7 1.0
CG A:ASP144 2.6 89.7 1.0
CD A:GLU276 2.6 88.3 1.0
CE1 A:HIS151 2.7 75.3 1.0
CD2 A:HIS149 3.2 85.3 1.0
CE1 A:HIS149 3.3 85.3 1.0
CD2 A:HIS151 3.6 75.3 1.0
ND1 A:HIS151 4.0 75.3 1.0
CB A:ASP144 4.1 89.7 1.0
CG A:GLU276 4.1 88.3 1.0
ND1 A:HIS149 4.3 85.3 1.0
CG A:HIS149 4.4 85.3 1.0
O A:HIS275 4.4 91.8 1.0
CG A:HIS151 4.4 75.3 1.0
CB A:GLN157 4.5 81.2 1.0
O A:ASP144 4.8 89.7 1.0
CG A:GLN157 4.9 81.2 1.0

Cadmium binding site 3 out of 6 in 8ght

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Cadmium binding site 3 out of 6 in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:60.0
occ:1.00
 OE2 A:GLU240 2.3 95.5 1.0
OD1 A:ASN178 2.3 92.0 1.0
OD1 A:ASP208 2.3 96.3 1.0
OE2 A:GLU181 2.3 95.6 1.0
ND2 A:ASN178 2.3 92.0 1.0
OD2 A:ASP208 2.3 96.3 1.0
CG A:ASN178 2.5 92.0 1.0
CG A:ASP208 2.5 96.3 1.0
CD A:GLU181 3.4 95.6 1.0
CD A:GLU240 3.4 95.5 1.0
CB A:ASN178 3.7 92.0 1.0
OE1 A:GLU181 3.8 95.6 1.0
CB A:ASP208 3.8 96.3 1.0
CG A:GLU240 4.0 95.5 1.0
OG1 A:THR70 4.1 96.0 1.0
OE2 A:GLU211 4.3 92.7 1.0
CA A:ASN178 4.4 92.0 1.0
OE1 A:GLU240 4.5 95.5 1.0
CG A:GLU181 4.6 95.6 1.0
NE2 A:GLN207 4.6 96.1 1.0
CD2 A:HIS177 4.8 89.1 1.0
CA A:ASP208 4.8 96.3 1.0
CB A:GLU181 4.8 95.6 1.0

Cadmium binding site 4 out of 6 in 8ght

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Cadmium binding site 4 out of 6 in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:33.7
occ:1.00
 OE1 B:GLU181 2.3 95.6 1.0
OE1 B:GLU211 2.3 92.7 1.0
OE2 B:GLU211 2.3 92.7 1.0
SD B:MET99 2.3 97.1 1.0
OE1 B:GLN207 2.3 96.1 1.0
NE2 B:GLN207 2.3 96.1 1.0
NE2 B:HIS177 2.3 89.1 1.0
CD B:GLU211 2.6 92.7 1.0
CD B:GLN207 2.6 96.1 1.0
CE1 B:HIS177 3.1 89.1 1.0
CE B:MET99 3.2 97.1 1.0
CD2 B:HIS177 3.4 89.1 1.0
CD B:GLU181 3.5 95.6 1.0
CG B:MET99 3.6 97.1 1.0
OD1 B:ASP208 4.0 96.3 1.0
CG B:GLU211 4.1 92.7 1.0
CG B:GLN207 4.1 96.1 1.0
OE2 B:GLU181 4.3 95.6 1.0
ND1 B:HIS177 4.3 89.1 1.0
CG B:HIS177 4.5 89.1 1.0
CG B:GLU181 4.5 95.6 1.0
OD1 B:ASN178 4.8 92.0 1.0
O B:GLN207 4.9 96.1 1.0
CG B:ASP208 4.9 96.3 1.0
CB B:GLU211 4.9 92.7 1.0
CB B:MET99 5.0 97.1 1.0
CB B:GLN207 5.0 96.1 1.0

Cadmium binding site 5 out of 6 in 8ght

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Cadmium binding site 5 out of 6 in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd503

b:46.9
occ:0.60
 OE2 B:GLU276 2.3 88.3 1.0
NE2 B:HIS149 2.3 85.3 1.0
OD1 B:ASP144 2.3 89.7 1.0
OE1 B:GLU276 2.3 88.3 1.0
NE2 B:HIS151 2.3 75.3 1.0
OD2 B:ASP144 2.3 89.7 1.0
CG B:ASP144 2.6 89.7 1.0
CD B:GLU276 2.6 88.3 1.0
CE1 B:HIS151 2.7 75.3 1.0
CD2 B:HIS149 3.2 85.3 1.0
CE1 B:HIS149 3.3 85.3 1.0
CD2 B:HIS151 3.6 75.3 1.0
ND1 B:HIS151 4.0 75.3 1.0
CB B:ASP144 4.1 89.7 1.0
CG B:GLU276 4.1 88.3 1.0
ND1 B:HIS149 4.3 85.3 1.0
CG B:HIS149 4.4 85.3 1.0
O B:HIS275 4.4 91.8 1.0
CG B:HIS151 4.4 75.3 1.0
CB B:GLN157 4.5 81.2 1.0
O B:ASP144 4.8 89.7 1.0
CG B:GLN157 4.9 81.2 1.0

Cadmium binding site 6 out of 6 in 8ght

Go back to Cadmium Binding Sites List in 8ght
Cadmium binding site 6 out of 6 in the Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Cryo-Electron Microscopy Structure of the Zinc Transporter From Bordetella Bronchiseptica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd504

b:60.0
occ:1.00
 OE2 B:GLU240 2.3 95.5 1.0
OD1 B:ASN178 2.3 92.0 1.0
OD1 B:ASP208 2.3 96.3 1.0
OE2 B:GLU181 2.3 95.6 1.0
ND2 B:ASN178 2.3 92.0 1.0
OD2 B:ASP208 2.3 96.3 1.0
CG B:ASN178 2.5 92.0 1.0
CG B:ASP208 2.5 96.3 1.0
CD B:GLU181 3.4 95.6 1.0
CD B:GLU240 3.4 95.5 1.0
CB B:ASN178 3.7 92.0 1.0
OE1 B:GLU181 3.8 95.6 1.0
CB B:ASP208 3.8 96.3 1.0
CG B:GLU240 4.0 95.5 1.0
OG1 B:THR70 4.1 96.0 1.0
OE2 B:GLU211 4.3 92.7 1.0
CA B:ASN178 4.4 92.0 1.0
OE1 B:GLU240 4.5 95.5 1.0
CG B:GLU181 4.6 95.6 1.0
NE2 B:GLN207 4.6 96.1 1.0
CD2 B:HIS177 4.8 89.1 1.0
CA B:ASP208 4.8 96.3 1.0
CB B:GLU181 4.8 95.6 1.0

Reference:

C.Pang, J.Chai, P.Zhu, J.Shanklin, Q.Liu. Structural Mechanism of Intracellular Autoregulation of Zinc Uptake in Zip Transporters. Nat Commun V. 14 3404 2023.
ISSN: ESSN 2041-1723
PubMed: 37296139
DOI: 10.1038/S41467-023-39010-6
Page generated: Fri Jul 19 20:25:51 2024

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