Cadmium in PDB 2fcq: X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group

The structure of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group, PDB code: 2fcq was solved by D.Bang, A.V.Gribenko, V.Tereshko, A.A.Kossiakoff, S.B.Kent, G.I.Makhatadze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.30
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.059, 105.059, 105.059, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.6

The binding sites of Cadmium atom in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group (pdb code 2fcq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group, PDB code: 2fcq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd100 b:85.0 occ:1.00 OE1 A:GLU64 2.4 85.0 1.0 OE2 A:GLU64 2.6 85.0 1.0 CD A:GLU64 2.8 85.0 1.0 CG A:GLU64 4.2 85.0 1.0 NZ A:LYS63 4.4 85.0 1.0 CE A:LYS63 4.6 85.0 1.0 CD A:LYS63 4.6 85.0 1.0 CB A:GLU64 5.0 85.0 1.0

Cadmium binding site 2 out of 7 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd200 b:85.0 occ:0.50 OD2 A:ASP21 2.2 85.0 1.0 OD1 A:ASP21 2.2 85.0 1.0 OE1 A:GLU18 2.3 85.0 1.0 CG A:ASP21 2.6 85.0 1.0 NZ A:LYS29 2.9 85.0 1.0 CD A:GLU18 2.9 85.0 1.0 CE A:LYS29 3.4 85.0 1.0 CG A:GLU18 3.6 85.0 1.0 OE2 A:GLU18 3.7 85.0 1.0 N A:GLU18 4.2 85.0 1.0 CB A:GLU18 4.2 85.0 1.0 CB A:ASP21 4.2 85.0 1.0 ND2 A:ASN25 4.2 85.0 1.0 CB A:ASN25 4.7 85.0 1.0 CA A:GLU18 4.8 85.0 1.0 CD A:LYS29 4.9 85.0 1.0 CG A:ASN25 5.0 85.0 1.0

Cadmium binding site 3 out of 7 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:85.0 occ:1.00 OE1 A:GLU16 2.2 85.0 1.0 OE2 A:GLU16 2.6 85.0 1.0 CD A:GLU16 2.7 85.0 1.0 N A:LEU1 2.7 85.0 1.0 O A:LEU1 3.1 85.0 1.0 C A:LEU1 3.3 85.0 1.0 CA A:LEU1 3.5 85.0 1.0 N A:GLN2 4.1 85.0 1.0 CG A:GLU16 4.2 85.0 1.0 CB A:GLN2 4.8 85.0 1.0 CA A:GLN2 4.8 85.0 1.0 CB A:LEU1 4.8 85.0 1.0

Cadmium binding site 4 out of 7 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd400 b:85.0 occ:0.25 OD1 A:ASP52 2.2 85.0 1.0 CG A:ASP52 3.5 85.0 1.0 OD2 A:ASP52 4.1 85.0 1.0 OD1 A:ASP39 4.2 85.0 1.0 CG A:GLU24 4.5 85.0 1.0 CB A:ASP52 4.5 85.0 1.0 CB A:PRO38 4.9 85.0 1.0

Cadmium binding site 5 out of 7 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd600 b:85.0 occ:0.50 OE1 B:GLU18 2.2 85.0 1.0 OD2 B:ASP21 2.2 85.0 1.0 OD1 B:ASP21 2.3 85.0 1.0 NZ B:LYS29 2.7 85.0 1.0 CG B:ASP21 2.7 85.0 1.0 CD B:GLU18 3.1 85.0 1.0 CG B:GLU18 3.4 85.0 1.0 CE B:LYS29 3.6 85.0 1.0 CB B:ASP21 4.2 85.0 1.0 OE2 B:GLU18 4.3 85.0 1.0 CB B:GLU18 4.3 85.0 1.0 ND2 B:ASN25 4.4 85.0 1.0 N B:GLU18 4.5 85.0 1.0

Cadmium binding site 6 out of 7 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd700 b:85.0 occ:1.00 OE2 B:GLU16 2.5 85.0 1.0 N B:LEU1 2.8 85.0 1.0 OE1 B:GLU16 2.8 85.0 1.0 CD B:GLU16 3.0 85.0 1.0 O B:LEU1 3.0 85.0 1.0 C B:LEU1 3.3 85.0 1.0 CA B:LEU1 3.4 85.0 1.0 N B:GLN2 4.2 85.0 1.0 CG B:GLU16 4.4 85.0 1.0 CB B:GLN2 4.5 85.0 1.0 O B:VAL17 4.8 85.0 1.0 CB B:LEU1 4.9 85.0 1.0 CA B:GLN2 4.9 85.0 1.0

Cadmium binding site 7 out of 7 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd800 b:85.0 occ:0.25 NE2 B:HIS68 2.2 85.0 1.0 CE1 B:HIS68 2.7 85.0 1.0 CD2 B:HIS68 3.0 85.0 1.0 ND1 B:HIS68 3.6 85.0 1.0 CG B:HIS68 3.8 85.0 1.0 CE B:LYS6 4.6 85.0 1.0

D.Bang, A.V.Gribenko, V.Tereshko, A.A.Kossiakoff, S.B.Kent, G.I.Makhatadze. Dissecting the Energetics of Protein Alpha-Helix C-Cap Termination Through Chemical Protein Synthesis. Nat.Chem.Biol. V. 2 139 2006.
ISSN: ISSN 1552-4450
PubMed: 16446709
DOI: 10.1038/NCHEMBIO766