Cadmium in PDB 2fcm: X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin with A Cubic Space Group

The structure of X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin with A Cubic Space Group, PDB code: 2fcm 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 / 2.20
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.532, 105.532, 105.532, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 28.3

The binding sites of Cadmium atom in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin with A Cubic Space Group (pdb code 2fcm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin with A Cubic Space Group, PDB code: 2fcm:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd100 b:54.0 occ:1.00 O A:ACT101 2.2 55.0 1.0 OE2 A:GLU64 2.2 52.9 1.0 OE1 A:GLU64 2.2 47.8 1.0 OXT A:ACT101 2.2 54.9 1.0 C A:ACT101 2.3 55.2 1.0 CD A:GLU64 2.5 48.6 1.0 O A:HOH102 2.8 52.7 1.0 CH3 A:ACT101 3.4 55.7 1.0 CG A:GLU64 4.0 50.4 1.0 NZ A:LYS63 4.3 54.4 1.0 CE A:LYS63 4.7 54.0 1.0 CB A:GLU64 4.9 50.7 1.0

Cadmium binding site 2 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd200 b:65.9 occ:1.00 OE1 A:GLU18 2.3 33.8 1.0 OD1 A:ASP21 2.5 46.0 1.0 OD2 A:ASP21 2.6 43.1 1.0 O A:HOH201 2.7 47.2 1.0 CG A:ASP21 2.9 41.6 1.0 CD A:GLU18 3.2 47.2 1.0 NZ A:LYS29 3.7 54.7 1.0 CG A:GLU18 3.7 48.5 1.0 CE A:LYS29 3.8 52.1 1.0 ND2 A:ASN25 4.0 42.6 1.0 OE2 A:GLU18 4.3 40.1 1.0 CB A:GLU18 4.4 45.4 1.0 CB A:ASP21 4.4 42.2 1.0 N A:GLU18 4.7 45.1 1.0 CG A:ASN25 4.8 43.2 1.0 CB A:ASN25 4.8 44.3 1.0

Cadmium binding site 3 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:63.3 occ:1.00 N A:LEU1 2.2 57.1 1.0 OE2 A:GLU16 2.2 61.0 1.0 O A:ACT301 2.5 63.8 1.0 OXT A:ACT301 2.6 63.7 1.0 CD A:GLU16 2.9 56.5 1.0 OE1 A:GLU16 2.9 57.6 1.0 C A:ACT301 3.0 63.6 1.0 CA A:LEU1 3.3 55.6 1.0 C A:LEU1 3.5 55.1 1.0 O A:LEU1 3.7 55.0 1.0 N A:GLN2 4.2 53.0 1.0 CG A:GLU16 4.3 53.3 1.0 CH3 A:ACT301 4.4 64.0 1.0 CB A:LEU1 4.6 56.6 1.0 O A:VAL17 4.8 44.8 1.0

Cadmium binding site 4 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd400 b:50.4 occ:0.50 OD1 A:ASP52 2.1 58.5 1.0 OE1 A:GLU24 2.2 61.9 1.0 O A:HOH401 2.3 45.5 1.0 OE2 A:GLU24 2.7 60.2 1.0 CD A:GLU24 2.8 58.1 1.0 CG A:ASP52 3.1 57.9 1.0 CB A:ASP52 3.5 56.3 1.0 OD2 A:ASP52 4.2 64.5 1.0 CG A:GLU24 4.3 50.9 1.0 NZ A:LYS27 4.7 47.5 1.0 O A:HOH1025 4.8 72.6 1.0 CB A:GLU24 4.9 47.0 1.0

Cadmium binding site 5 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:87.8 occ:0.50 OD2 A:ASP58 2.2 60.6 1.0 O A:HOH403 2.6 81.8 1.0 CG A:ASP58 3.0 57.3 1.0 OD1 A:ASP58 3.0 60.7 1.0 O A:HOH404 3.1 79.5 1.0 NH1 A:ARG54 3.8 60.6 1.0 CZ A:ARG54 4.0 60.4 1.0 NE A:ARG54 4.3 59.6 1.0 CB A:ASP58 4.4 57.2 1.0 CD A:ARG54 4.5 56.8 1.0 NH2 A:ARG54 4.5 60.3 1.0 CA A:ARG54 4.5 53.0 1.0 N A:THR55 4.7 50.5 1.0 OG1 A:THR55 4.8 51.5 1.0 O A:GLY53 4.9 54.7 1.0 CB A:ARG54 5.0 53.2 1.0

Cadmium binding site 6 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd500 b:73.3 occ:0.50 OE1 B:GLU64 2.2 64.8 1.0 O B:HOH502 2.4 57.0 1.0 OE2 B:GLU64 2.8 65.8 1.0 O B:HOH501 2.8 51.9 1.0 CD B:GLU64 2.8 63.5 1.0 O B:HOH503 3.3 50.7 1.0 CG B:GLU64 4.3 63.0 1.0 NZ B:LYS63 4.8 68.4 1.0

Cadmium binding site 7 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd600 b:55.4 occ:0.50 OD1 B:ASP21 2.2 61.5 1.0 O B:HOH601 2.2 37.7 0.5 O B:HOH602 2.2 40.2 0.5 OD2 B:ASP21 2.2 62.5 1.0 CG B:ASP21 2.6 63.5 1.0 OE1 B:GLU18 3.8 60.7 1.0 NZ B:LYS29 3.9 57.7 0.5 CB B:ASP21 4.1 62.0 1.0 CE B:LYS29 4.1 59.7 0.5 CB B:GLU18 4.5 60.8 1.0 N B:GLU18 4.5 61.6 1.0 ND2 B:ASN25 4.6 56.3 1.0 CG B:GLU18 4.6 61.6 1.0 CD B:GLU18 4.6 61.2 1.0 CB B:ASN25 4.8 57.1 1.0 CA B:ASP21 4.9 61.9 1.0

Cadmium binding site 8 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 8 of X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd700 b:69.3 occ:0.25 N B:LEU1 2.1 69.6 1.0 OE2 B:GLU16 2.2 68.5 1.0 OE1 B:GLU16 2.8 66.8 1.0 CD B:GLU16 2.8 66.6 1.0 CA B:LEU1 3.2 70.3 1.0 C B:LEU1 3.4 70.1 1.0 O B:LEU1 3.7 69.7 1.0 N B:GLN2 3.9 70.4 1.0 CG B:GLU16 4.3 65.9 1.0 CB B:LEU1 4.4 70.2 1.0 O B:VAL17 4.7 62.2 1.0 CA B:GLN2 4.9 70.8 1.0

Cadmium binding site 9 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 9 of X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd800 b:56.6 occ:0.25 OD1 B:ASP52 2.2 61.7 1.0 OE2 B:GLU24 2.2 62.9 1.0 OE1 B:GLU24 2.2 66.7 1.0 O B:HOH801 2.3 31.0 0.2 CD B:GLU24 2.5 64.0 1.0 CG B:ASP52 3.2 64.1 1.0 CB B:ASP52 3.8 64.8 1.0 CG B:GLU24 4.0 60.5 1.0 OD2 B:ASP52 4.0 66.8 1.0 O B:HOH2001 4.1 59.2 1.0 CB B:GLU24 4.8 58.9 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