Cadmium in PDB 4tq6: Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+

The structure of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+, PDB code: 4tq6 was solved by H.Huang, E.J.Levin, Y.Bai, M.Zhou, New York Consortium On Membraneprotein Structure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.34 / 3.07
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.938, 89.871, 341.230, 90.00, 90.00, 90.00
R / Rfree (%)	26.5 / 30.1

The binding sites of Cadmium atom in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ (pdb code 4tq6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+, PDB code: 4tq6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:0.2 occ:1.00 OE1 A:GLU200 2.7 0.6 1.0 OE2 A:GLU200 2.8 0.2 1.0 CD A:GLU200 3.0 0.4 1.0 CG A:GLU200 4.2 0.4 1.0

Cadmium binding site 2 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:0.3 occ:1.00 CE1 A:HIS49 2.8 90.8 1.0 O A:ALA120 2.8 81.2 1.0 NE2 A:HIS49 3.5 91.3 1.0 ND1 A:HIS49 3.7 93.6 1.0 C A:ALA120 4.0 72.5 1.0 O A:ILE121 4.1 75.2 1.0 CA A:ILE121 4.6 72.7 1.0 CD2 A:HIS49 4.7 91.6 1.0 CG A:HIS49 4.7 92.5 1.0 N A:ILE121 4.8 71.2 1.0 C A:ILE121 4.8 72.1 1.0 CD1 A:LEU52 5.0 79.3 1.0

Cadmium binding site 3 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:0.0 occ:1.00 OD2 A:ASP72 2.8 91.8 1.0 CB A:ASP72 3.2 95.6 1.0 ND2 A:ASN68 3.3 91.7 1.0 CG A:ASP72 3.3 95.2 1.0 NZ A:LYS146 3.9 98.3 1.0 CG A:ASN68 4.1 87.7 1.0 OD1 A:ASN68 4.2 91.4 1.0 OD1 A:ASP72 4.4 92.0 1.0 NH1 A:ARG22 4.6 0.2 1.0 CA A:ASP72 4.7 93.1 1.0 O A:ASN68 4.9 89.2 1.0

Cadmium binding site 4 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:0.5 occ:1.00 OD2 A:ASP202 3.2 0.5 1.0 OD1 A:ASP202 3.5 0.3 1.0 CB A:ASP198 3.7 0.9 1.0 CG A:ASP202 3.7 0.3 1.0 OD2 A:ASP198 3.9 0.7 1.0 O A:ASP198 4.3 1.0 1.0 CG A:ASP198 4.3 0.5 1.0 CA A:ASP198 5.0 0.5 1.0

Cadmium binding site 5 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd401 b:0.4 occ:0.80 OD2 B:ASP72 2.9 0.8 1.0 CG B:ASP72 3.8 0.0 1.0 CB B:ASP72 3.8 0.3 1.0 ND2 B:ASN68 3.9 0.7 1.0 NZ B:LYS146 4.0 1.0 1.0 CZ B:PHE201 4.1 0.8 1.0 CE2 B:PHE201 4.5 0.1 1.0 CG B:ASN68 4.8 0.4 1.0 OD1 B:ASN68 4.8 0.5 1.0 OD1 B:ASP72 4.9 0.1 1.0

Cadmium binding site 6 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd402 b:0.6 occ:0.80 OD2 B:ASP202 2.7 0.5 1.0 OD1 B:ASP202 2.8 0.7 1.0 CG B:ASP202 3.1 0.8 1.0 CB B:ASP198 3.4 0.3 1.0 OD2 B:ASP198 3.7 0.7 1.0 CD2 B:PHE201 3.7 0.7 1.0 CE2 B:PHE201 4.0 0.1 1.0 CG B:ASP198 4.0 0.9 1.0 O B:ASP198 4.3 0.8 1.0 CB B:ASP202 4.6 0.0 1.0 CA B:ASP198 4.8 0.7 1.0 CG B:PHE201 4.9 0.8 1.0 C B:ASP198 5.0 0.5 1.0

Cadmium binding site 7 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd403 b:1.0 occ:1.00 O B:ALA120 2.8 0.6 1.0 CE1 B:HIS49 2.9 0.5 1.0 NE2 B:HIS49 3.4 0.2 1.0 ND1 B:HIS49 4.0 0.3 1.0 C B:ALA120 4.1 0.1 1.0 O B:ILE121 4.3 0.7 1.0 CD2 B:HIS49 4.6 0.5 1.0 CA B:ILE121 4.8 1.0 1.0 N B:ILE121 4.9 0.7 1.0 CG B:HIS49 4.9 0.9 1.0

Cadmium binding site 8 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd404 b:0.1 occ:0.70 OE1 B:GLU242 2.9 0.8 1.0 CD B:GLU242 3.5 0.7 1.0 OE2 B:GLU242 3.5 0.6 1.0 CG B:GLU242 4.8 0.3 1.0

H.Huang, E.J.Levin, S.Liu, Y.Bai, S.W.Lockless, M.Zhou. Structure of A Membrane-Embedded Prenyltransferase Homologous to UBIAD1. Plos Biol. V. 12 01911 2014.
ISSN: ESSN 1545-7885
PubMed: 25051182
DOI: 10.1371/JOURNAL.PBIO.1001911