Copper in PDB 8pf0: Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin

The structure of Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin, PDB code: 8pf0 was solved by C.Parthier, A.Katzschmann, E.Fiedler, U.Haupts, A.Reimann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.05 / 2.20
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	62.767, 62.767, 67.841, 90, 90, 90
R / Rfree (%)	19.3 / 22.6

The binding sites of Copper atom in the Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin (pdb code 8pf0). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin, PDB code: 8pf0:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:68.9 occ:1.00 N1 A:IMD206 1.9 56.4 1.0 OD1 A:ASP100 1.9 48.4 1.0 C5 A:IMD206 2.2 46.9 1.0 CG A:ASP100 2.9 38.7 1.0 O A:HOH315 3.0 44.4 1.0 OD2 A:ASP100 3.1 37.7 1.0 C2 A:IMD206 3.2 52.8 1.0 C4 A:IMD206 3.6 50.7 1.0 N3 A:IMD206 4.0 51.4 1.0 OD1 A:ASN104 4.0 52.8 1.0 CB A:ASP100 4.2 31.2 1.0 NZ A:LYS108 4.5 58.9 1.0 O A:HOH355 4.5 38.7 1.0 CA A:ASP100 4.6 35.3 1.0 CB A:GLU97 4.8 52.8 1.0 CG A:GLU97 4.8 66.9 1.0 N A:ASP100 5.0 31.8 1.0

Copper binding site 2 out of 4 in the Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:66.5 occ:1.00 N3 A:IMD205 1.9 47.0 1.0 O A:HOH335 2.2 56.6 1.0 O A:HOH308 2.2 54.9 1.0 C4 A:IMD205 2.2 54.2 1.0 OD1 A:ASP111 2.4 47.8 1.0 C2 A:IMD205 3.2 52.2 1.0 CG A:ASP111 3.5 46.9 1.0 C5 A:IMD205 3.5 52.2 1.0 N1 A:IMD205 3.9 53.4 1.0 OD2 A:ASP111 3.9 51.1 1.0 OE1 A:GLN110 4.1 39.3 1.0 O A:ALA107 4.5 32.5 1.0 CD A:GLN110 4.6 45.6 1.0 CB A:ASP111 4.7 38.3 1.0 CG A:GLN110 4.7 41.6 1.0 N A:ASP111 4.8 41.0 1.0 CA A:ASP111 4.8 40.6 1.0 O A:HOH307 4.9 47.7 1.0

Copper binding site 3 out of 4 in the Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu203 b:57.3 occ:1.00 NE2 A:HIS85 2.1 40.9 1.0 O A:HOH302 2.2 38.4 1.0 ND1 A:HIS147 2.4 54.9 1.0 CD2 A:HIS85 2.9 39.9 1.0 CG A:HIS147 3.2 44.6 1.0 CE1 A:HIS85 3.2 48.4 1.0 CB A:HIS147 3.3 39.0 1.0 CE1 A:HIS147 3.4 56.4 1.0 CG A:HIS85 4.2 44.5 1.0 ND1 A:HIS85 4.3 50.4 1.0 CD2 A:HIS147 4.4 53.4 1.0 NE2 A:HIS147 4.5 58.4 1.0 CA A:HIS147 4.8 39.7 1.0

Copper binding site 4 out of 4 in the Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Diubiquitin-Derived Artificial Binding Protein (Affilin) Variant AF1 Specific to Oncofetal Fibronectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu204 b:56.2 occ:1.00 O A:HOH301 2.1 34.3 1.0 NE2 A:HIS6 2.1 41.5 1.0 ND1 A:HIS68 2.3 53.1 1.0 CD2 A:HIS6 2.9 38.9 1.0 CG A:HIS68 3.1 42.4 1.0 CE1 A:HIS6 3.2 48.8 1.0 CB A:HIS68 3.3 39.5 1.0 CE1 A:HIS68 3.3 54.0 1.0 CG A:HIS6 4.1 45.5 1.0 ND1 A:HIS6 4.2 50.8 1.0 CD2 A:HIS68 4.3 50.4 1.0 NE2 A:HIS68 4.4 57.5 1.0 CA A:HIS68 4.7 37.3 1.0

A.Katzschmann, E.Fiedler, U.Haupts, A.Reimann, F.Settele, M.Gloser-Braeunig, C.Parthier. Ubiquitin-Derived Artificial Binding Proteins Targeting Oncofetal Fibronectin Reveal Scaffold Plasticity By Beta-Strand Slippage To Be Published.