Cadmium in PDB 2fcn: X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]Ubiquitin with A Cubic Space Group

The structure of X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]Ubiquitin with A Cubic Space Group, PDB code: 2fcn 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 (°)	106.152, 106.152, 106.152, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]Ubiquitin with A Cubic Space Group (pdb code 2fcn). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]Ubiquitin with A Cubic Space Group, PDB code: 2fcn:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd100 b:45.5 occ:1.00 OXT A:ACT101 2.2 47.5 1.0 OXT A:ACT102 2.2 54.7 1.0 OE2 A:GLU64 2.2 43.8 1.0 O A:ACT101 2.6 46.9 1.0 OE1 A:GLU64 2.6 45.5 1.0 CD A:GLU64 2.7 43.7 1.0 O A:HOH103 2.7 47.5 1.0 C A:ACT101 2.8 48.0 1.0 C A:ACT102 3.2 54.4 1.0 O A:ACT102 3.7 53.1 1.0 O A:HOH1012 4.0 59.8 1.0 CG A:GLU64 4.2 43.9 1.0 CH3 A:ACT101 4.2 48.3 1.0 CH3 A:ACT102 4.3 53.0 1.0 NZ A:LYS63 4.7 51.4 1.0 CD A:LYS63 4.8 50.2 1.0 CE A:LYS63 4.9 51.0 1.0

Cadmium binding site 2 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd200 b:56.0 occ:1.00 OD1 A:ASP21 2.4 37.0 1.0 OD2 A:ASP21 2.5 39.7 1.0 CG A:ASP21 2.8 41.8 1.0 O A:HOH201 2.9 41.7 1.0 CE A:LYS29 3.4 43.5 1.0 NZ A:LYS29 3.6 40.7 1.0 CG A:GLU18 3.7 40.2 1.0 OE2 A:GLU18 4.1 44.2 1.0 ND2 A:ASN25 4.2 34.9 1.0 CB A:GLU18 4.3 41.7 1.0 CB A:ASP21 4.3 40.4 1.0 N A:GLU18 4.3 42.0 1.0 CD A:GLU18 4.5 42.6 1.0 CB A:ASN25 4.8 37.4 1.0 CD A:LYS29 4.8 42.7 1.0 CG A:ASN25 4.9 35.9 1.0 CA A:GLU18 5.0 42.0 1.0

Cadmium binding site 3 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:60.0 occ:1.00 OXT A:ACT301 2.2 62.1 1.0 OE1 A:GLU16 2.2 60.5 1.0 N A:LEU1 2.2 50.6 1.0 O A:ACT301 2.6 63.6 1.0 C A:ACT301 2.8 63.7 1.0 CD A:GLU16 2.8 57.5 1.0 OE2 A:GLU16 2.9 61.7 1.0 CA A:LEU1 3.2 49.0 1.0 C A:LEU1 3.4 48.3 1.0 O A:LEU1 3.4 47.4 1.0 N A:GLN2 4.2 47.5 1.0 CH3 A:ACT301 4.3 64.1 1.0 CG A:GLU16 4.3 50.6 1.0 CB A:LEU1 4.6 49.4 1.0 O A:HOH1025 4.7 49.1 1.0 O A:HOH1004 4.8 50.5 1.0 CB A:GLN2 4.9 48.2 1.0 O A:HOH1021 5.0 44.0 1.0 CA A:GLN2 5.0 47.7 1.0

Cadmium binding site 4 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd400 b:56.6 occ:1.00 OE1 A:GLU24 2.2 45.6 1.0 OD1 A:ASP52 2.5 57.7 1.0 CD A:GLU24 3.1 42.5 1.0 OE2 A:GLU24 3.2 41.6 1.0 CG A:ASP52 3.5 54.6 1.0 CB A:ASP52 3.8 52.2 1.0 NZ A:LYS27 4.3 35.2 1.0 CD A:CD401 4.4 51.9 0.5 CG A:GLU24 4.5 40.4 1.0 OD2 A:ASP52 4.5 63.3 1.0 CD A:LYS27 5.0 32.8 1.0

Cadmium binding site 5 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:51.9 occ:0.50 OD1 A:ASP39 2.2 51.9 1.0 CG A:ASP39 3.1 50.1 1.0 OD2 A:ASP39 3.4 56.9 1.0 CD A:CD400 4.4 56.6 1.0 CB A:ASP39 4.5 44.7 1.0

Cadmium binding site 6 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:64.2 occ:0.25 OD2 A:ASP58 2.2 53.8 1.0 OD1 A:ASP58 2.6 50.9 1.0 CG A:ASP58 2.8 52.1 1.0 CG2 A:THR55 4.2 46.6 1.0 CB A:ASP58 4.3 50.2 1.0 OG1 A:THR55 4.4 46.8 1.0 N A:THR55 4.5 49.1 1.0 NH1 A:ARG54 4.5 71.9 0.0 CA A:ARG54 4.6 51.4 1.0 O A:GLY53 4.9 49.7 1.0 CB A:THR55 4.9 47.1 1.0 C A:ARG54 5.0 50.0 1.0

Cadmium binding site 7 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd500 b:57.5 occ:0.25 ND1 B:HIS68 2.2 58.0 1.0 CG B:HIS68 3.1 56.5 1.0 CE1 B:HIS68 3.2 59.4 1.0 CB B:HIS68 3.3 56.9 1.0 O B:HOH2005 3.9 55.5 1.0 NZ B:LYS6 4.1 59.7 0.5 CD B:LYS6 4.2 58.9 0.5 CD2 B:HIS68 4.3 56.5 1.0 NE2 B:HIS68 4.3 56.7 1.0 CE B:LYS6 4.4 59.4 0.5 CA B:HIS68 4.4 56.3 1.0 CG B:LYS6 4.7 58.8 0.5

Cadmium binding site 8 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd600 b:72.4 occ:1.00 OD1 B:ASP21 2.2 49.6 1.0 OD2 B:ASP21 2.9 53.0 1.0 CG B:ASP21 2.9 52.0 1.0 OE1 B:GLU18 2.9 58.5 1.0 NZ B:LYS29 3.5 62.7 1.0 CD B:GLU18 4.1 54.1 1.0 ND2 B:ASN25 4.2 53.8 1.0 CB B:GLU18 4.2 52.2 1.0 CE B:LYS29 4.4 61.6 1.0 CB B:ASP21 4.4 51.4 1.0 CG B:GLU18 4.5 54.3 1.0 N B:GLU18 4.5 54.2 1.0 CA B:ASP21 5.0 51.8 1.0 CG B:ASN25 5.0 54.7 1.0

Cadmium binding site 9 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd700 b:64.3 occ:0.50 OE2 B:GLU16 2.2 58.4 1.0 N B:LEU1 2.2 66.8 1.0 CD B:GLU16 3.0 55.7 1.0 OE1 B:GLU16 3.2 60.0 1.0 CA B:LEU1 3.3 66.9 1.0 C B:LEU1 3.3 66.6 1.0 O B:LEU1 3.3 65.8 1.0 O B:VAL17 4.0 54.7 1.0 N B:GLN2 4.0 66.2 1.0 CB B:LEU1 4.2 67.3 1.0 CG B:GLU16 4.3 57.0 1.0 CA B:GLN2 4.9 65.4 1.0 N B:VAL17 5.0 56.0 1.0

Cadmium binding site 10 out of 12 in the X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]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 10 of X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]Ubiquitin with A Cubic Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd800 b:46.9 occ:0.50 OD1 B:ASP52 2.1 51.6 1.0 OE1 B:GLU24 2.9 67.3 1.0 CG B:ASP52 3.1 58.0 1.0 OE2 B:GLU24 3.2 60.3 1.0 CD B:GLU24 3.3 60.2 1.0 CB B:ASP52 3.7 57.5 1.0 OD2 B:ASP52 4.1 60.1 1.0 CD B:CD801 4.4 55.9 0.5 OD1 B:ASP39 4.5 61.9 1.0 CG B:GLU24 4.7 54.0 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