Cadmium in PDB 8j1m: Crystal Structure of A Crosslinked Variant of Bbzip

The structure of Crystal Structure of A Crosslinked Variant of Bbzip, PDB code: 8j1m was solved by T.Zhang, Y.Zhang, D.Sui, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.44 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.407, 51.012, 51.817, 90, 113.92, 90
R / Rfree (%)	17.1 / 20

The structure of Crystal Structure of A Crosslinked Variant of Bbzip also contains other interesting chemical elements:

Mercury	(Hg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Cadmium atom in the Crystal Structure of A Crosslinked Variant of Bbzip (pdb code 8j1m). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of A Crosslinked Variant of Bbzip, PDB code: 8j1m:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of A Crosslinked Variant of Bbzip


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 A Crosslinked Variant of Bbzip within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:36.3 occ:0.42 OD1 A:ASN178 2.2 31.0 1.0 OE2 A:GLU240 2.3 40.0 1.0 OE1 A:GLU181 2.3 29.5 1.0 OD1 A:ASP208 2.4 29.8 1.0 O A:HOH523 2.4 34.5 1.0 OE1 A:GLU211 2.4 29.4 1.0 CG A:ASN178 3.4 34.5 1.0 CD A:GLU181 3.5 34.6 1.0 CG A:ASP208 3.5 34.9 1.0 CD A:GLU240 3.5 42.6 1.0 CD A:GLU211 3.5 36.8 1.0 CG A:GLU211 4.0 28.9 1.0 OD2 A:ASP208 4.0 33.4 1.0 OE2 A:GLU181 4.1 33.4 1.0 NE2 A:GLN207 4.1 29.2 1.0 OE1 A:GLU240 4.2 39.1 1.0 O A:HOH527 4.3 35.0 1.0 CB A:ASN178 4.3 28.5 1.0 ND2 A:ASN178 4.3 48.7 1.0 CD A:CD402 4.3 27.7 0.8 CG A:GLU240 4.5 36.6 1.0 CB A:GLU181 4.5 29.7 1.0 CG A:GLU181 4.5 31.0 1.0 OG1 A:THR70 4.6 33.0 1.0 OE2 A:GLU211 4.6 37.5 1.0 CB A:ASP208 4.6 31.2 1.0 CB A:GLU211 4.7 32.6 1.0 CA A:ASN178 4.8 29.9 1.0 CA A:ASP208 4.9 30.6 1.0 OE1 A:GLN207 4.9 38.7 1.0 CD2 A:HIS177 4.9 29.2 1.0 CD A:GLN207 5.0 38.0 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of A Crosslinked Variant of Bbzip


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 A Crosslinked Variant of Bbzip within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:27.7 occ:0.85 OE2 A:GLU181 2.2 33.4 1.0 OE1 A:GLN207 2.3 38.7 1.0 OE2 A:GLU211 2.3 37.5 1.0 NE2 A:HIS177 2.3 29.2 1.0 OE1 A:GLU211 2.4 29.4 1.0 CL A:CL405 2.6 42.8 0.8 CD A:GLU211 2.7 36.8 1.0 CD A:GLU181 3.2 34.6 1.0 CD2 A:HIS177 3.2 29.2 1.0 CE1 A:HIS177 3.4 27.5 1.0 CD A:GLN207 3.4 38.0 1.0 OE1 A:GLU181 3.4 29.5 1.0 O A:HOH534 3.6 49.0 1.0 NE2 A:GLN207 3.9 29.2 1.0 CG A:MET99 4.0 36.2 1.0 CG A:GLU211 4.2 28.9 1.0 CD A:CD401 4.3 36.3 0.4 CG A:HIS177 4.4 27.1 1.0 ND1 A:HIS177 4.5 27.4 1.0 CG A:GLU181 4.5 31.0 1.0 SD A:MET99 4.5 50.4 1.0 O A:HOH537 4.7 36.8 1.0 CG A:GLN207 4.7 30.3 1.0 O A:HOH519 4.8 32.2 1.0 CB A:GLU211 4.8 32.6 1.0 O A:HOH544 4.8 44.3 1.0 OD1 A:ASN178 4.8 31.0 1.0 CB A:CYS95 4.9 35.0 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of A Crosslinked Variant of Bbzip


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 A Crosslinked Variant of Bbzip within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:32.3 occ:0.86 NE2 A:HIS149 2.3 33.7 1.0 NE2 A:HIS151 2.3 33.2 1.0 OD1 A:ASP144 2.3 37.2 1.0 OE2 A:GLU276 2.4 34.5 1.0 OE1 A:GLU276 2.4 31.6 1.0 O A:HOH501 2.4 41.9 1.0 CD A:GLU276 2.7 33.2 1.0 CD2 A:HIS149 3.2 33.3 1.0 CG A:ASP144 3.2 36.4 1.0 CD2 A:HIS151 3.3 31.4 1.0 CE1 A:HIS151 3.3 35.8 1.0 CE1 A:HIS149 3.3 28.2 1.0 OD2 A:ASP144 3.4 42.3 1.0 O A:HOH545 4.1 51.6 1.0 CG A:GLU276 4.2 27.6 1.0 OE1 A:GLN157 4.3 58.6 1.0 CE1 A:HIS275 4.3 40.5 1.0 ND1 A:HIS275 4.3 37.3 1.0 CG A:HIS149 4.4 28.7 1.0 ND1 A:HIS149 4.4 28.5 1.0 ND1 A:HIS151 4.4 33.2 1.0 CG A:HIS151 4.4 33.7 1.0 CB A:ASP144 4.6 29.0 1.0 CG A:GLN157 4.7 43.9 1.0 CD A:GLN157 5.0 55.9 1.0 CB A:GLU276 5.0 27.1 1.0

Y.Zhang, M.Jafari, T.Zhang, D.Sui, L.Sagresti, K.M.Merz Jr., J.Hu. Molecular Insights Into Substrate Translocation in An Elevator-Type Metal Transporter. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39345646
DOI: 10.1101/2024.09.18.613805