Cadmium in PDB 7z6m: Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State

The structure of Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State, PDB code: 7z6m was solved by A.Wiuf, J.H.Steffen, E.R.Becares, C.Groenberg, D.R.Mahato, S.G.F.Rasmussen, M.Andersson, T.Croll, K.Gotfryd, P.Gourdon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.51 / 2.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.211, 61.656, 55.262, 90, 108.9, 90
R / Rfree (%)	23 / 27.8

The binding sites of Cadmium atom in the Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State (pdb code 7z6m). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State, PDB code: 7z6m:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:159.5 occ:0.83 OD2 A:ASP144 2.7 129.9 1.0 NE2 A:HIS149 2.7 125.5 1.0 CD2 A:HIS275 2.8 116.3 1.0 OD1 A:ASP144 2.8 131.9 1.0 NE2 A:HIS275 3.1 118.9 1.0 CG A:ASP144 3.1 126.6 1.0 CD2 A:HIS149 3.6 121.6 1.0 CE1 A:HIS149 3.6 126.2 1.0 CG A:HIS275 4.1 108.8 1.0 CE1 A:HIS275 4.4 109.9 1.0 CB A:ASP144 4.6 111.2 1.0 ND1 A:HIS149 4.6 130.1 1.0 CG A:HIS149 4.7 124.1 1.0 ND1 A:HIS275 4.9 112.7 1.0 CB A:HIS275 5.0 103.7 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:125.9 occ:1.00 NH2 A:ARG228 2.7 112.3 1.0 NH1 A:ARG228 2.8 107.0 1.0 CZ A:ARG228 2.9 118.1 1.0 CD2 A:LEU224 3.8 81.8 1.0 NE A:ARG228 4.0 109.2 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:104.4 occ:1.00 OD1 A:ASP208 2.8 84.9 1.0 OE1 A:GLU181 2.8 96.2 1.0 OD1 A:ASN178 2.8 90.2 1.0 OE2 A:GLU240 2.8 109.0 1.0 CD A:GLU240 3.2 101.5 1.0 CG A:ASN178 3.3 89.8 1.0 OE1 A:GLU240 3.4 97.3 1.0 CD A:GLU181 3.4 87.5 1.0 CG A:ASP208 3.5 85.8 1.0 OE2 A:GLU181 3.5 98.6 1.0 ND2 A:ASN178 3.7 94.4 1.0 OD2 A:ASP208 3.7 92.1 1.0 OE1 A:GLU211 3.9 86.8 1.0 NE2 A:GLN207 4.3 76.1 1.0 CG A:GLU240 4.3 94.1 1.0 CB A:ASN178 4.3 93.0 1.0 OG1 A:THR70 4.4 73.1 1.0 CA A:ASN178 4.6 88.6 1.0 CG A:GLU181 4.6 90.9 1.0 CB A:GLU181 4.6 91.8 1.0 CB A:ASP208 4.7 72.7 1.0 CD A:CD404 4.7 80.9 1.0 CD2 A:HIS177 4.8 76.0 1.0 CA A:ASP208 4.9 81.5 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of ZN2+-Transporter Bbzip in A Cadmium Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:80.9 occ:1.00 NE2 A:HIS177 2.5 63.1 1.0 OE2 A:GLU181 2.6 98.6 1.0 OE1 A:GLN207 2.7 80.0 1.0 OE1 A:GLU211 2.7 86.8 1.0 OE2 A:GLU211 2.7 78.7 1.0 SD A:MET99 2.8 86.9 1.0 CD A:GLU211 2.9 84.8 1.0 NE2 A:GLN207 3.1 76.1 1.0 CD A:GLU181 3.2 87.5 1.0 CD A:GLN207 3.3 82.2 1.0 CE1 A:HIS177 3.3 74.9 1.0 OE1 A:GLU181 3.5 96.2 1.0 CD2 A:HIS177 3.6 76.0 1.0 CG A:MET99 3.7 79.2 1.0 CE A:MET99 3.8 89.8 1.0 CG A:GLU181 4.3 90.9 1.0 CG A:GLU211 4.3 78.0 1.0 ND1 A:HIS177 4.5 90.8 1.0 CD A:CD403 4.7 104.4 1.0 CG A:HIS177 4.7 84.3 1.0 CG A:GLN207 4.8 82.2 1.0 CB A:ALA95 4.9 69.7 1.0 O A:ALA95 5.0 75.6 1.0

A.Wiuf, J.H.Steffen, E.R.Becares, C.Gronberg, D.R.Mahato, S.G.F.Rasmussen, M.Andersson, T.Croll, K.Gotfryd, P.Gourdon. The Two-Domain Elevator-Type Mechanism of Zinc-Transporting Zip Proteins. Sci Adv V. 8 N4331 2022.
ISSN: ESSN 2375-2548
PubMed: 35857505
DOI: 10.1126/SCIADV.ABN4331