Copper in PDB 7tc5: All Phe-Azurin Variant - F15Y

The structure of All Phe-Azurin Variant - F15Y, PDB code: 7tc5 was solved by B.P.Fedoretz-Maxwell, L.J.Worrall, N.C.J.Strynadka, J.J.Warren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.97 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.451, 53.83, 133.791, 90, 90, 90
R / Rfree (%)	18.3 / 21.4

The structure of All Phe-Azurin Variant - F15Y also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Copper atom in the All Phe-Azurin Variant - F15Y (pdb code 7tc5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the All Phe-Azurin Variant - F15Y, PDB code: 7tc5:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the All Phe-Azurin Variant - F15Y


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of All Phe-Azurin Variant - F15Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:15.6 occ:1.00 ND1 A:HIS117 2.0 15.5 1.0 ND1 A:HIS46 2.0 13.6 1.0 SG A:CYS112 2.2 14.9 1.0 CE1 A:HIS46 2.9 14.4 1.0 O A:GLY45 3.0 14.3 1.0 CE1 A:HIS117 3.0 16.6 1.0 CG A:HIS117 3.0 16.2 1.0 CG A:HIS46 3.1 14.0 1.0 SD A:MET121 3.3 16.4 1.0 CB A:CYS112 3.3 15.0 1.0 CA A:HIS46 3.4 12.7 1.0 CB A:HIS117 3.4 15.4 1.0 CB A:HIS46 3.5 15.3 1.0 CE A:MET121 3.8 18.9 1.0 CB A:PHE114 3.8 14.7 1.0 C A:GLY45 3.8 14.2 1.0 N A:HIS46 4.0 14.3 1.0 NE2 A:HIS46 4.1 14.5 1.0 NE2 A:HIS117 4.2 16.3 1.0 CD2 A:HIS117 4.2 16.5 1.0 CD2 A:HIS46 4.2 15.0 1.0 C A:HIS46 4.5 14.1 1.0 N A:ASN47 4.5 13.5 1.0 CA A:CYS112 4.7 13.8 1.0 CG A:MET121 4.7 16.8 1.0 CG A:PHE114 4.7 14.3 1.0 N A:PHE114 4.8 14.0 1.0 CA A:HIS117 4.9 14.8 1.0 CA A:PHE114 4.9 13.7 1.0 CB A:MET121 4.9 15.8 1.0

Copper binding site 2 out of 3 in the All Phe-Azurin Variant - F15Y


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of All Phe-Azurin Variant - F15Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:26.1 occ:1.00 NE2 A:HIS124 1.9 18.1 1.0 NE2 B:HIS124 2.0 17.1 1.0 O2 B:NO3201 2.1 25.8 1.0 O3 B:NO3201 2.1 26.2 1.0 N B:NO3201 2.4 29.4 1.0 CE1 B:HIS124 2.9 18.8 1.0 CE1 A:HIS124 2.9 20.8 1.0 CD2 A:HIS124 2.9 18.9 1.0 CD2 B:HIS124 3.0 19.9 1.0 SD A:MET109 3.1 21.6 1.0 SD B:MET109 3.3 23.1 1.0 CE A:MET109 3.6 19.9 1.0 CE B:MET109 3.6 22.1 1.0 O1 B:NO3201 3.7 27.1 1.0 ND1 A:HIS124 4.1 19.3 1.0 ND1 B:HIS124 4.1 18.2 1.0 CG A:HIS124 4.1 17.1 1.0 CG A:MET109 4.1 19.6 1.0 CG B:HIS124 4.1 16.2 1.0 O B:HOH308 4.4 41.2 1.0 CG B:MET109 4.4 20.9 1.0

Copper binding site 3 out of 3 in the All Phe-Azurin Variant - F15Y


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of All Phe-Azurin Variant - F15Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu202 b:16.8 occ:1.00 ND1 B:HIS117 2.1 15.9 1.0 ND1 B:HIS46 2.1 16.2 1.0 SG B:CYS112 2.1 16.0 1.0 CE1 B:HIS117 3.0 15.3 1.0 CE1 B:HIS46 3.0 15.3 1.0 O B:GLY45 3.0 17.2 1.0 CG B:HIS117 3.1 14.9 1.0 CG B:HIS46 3.1 15.7 1.0 CB B:CYS112 3.2 15.4 1.0 SD B:MET121 3.2 20.5 1.0 CA B:HIS46 3.3 15.9 1.0 CB B:HIS117 3.4 15.2 1.0 CB B:HIS46 3.5 15.9 1.0 CE B:MET121 3.8 21.9 1.0 C B:GLY45 3.9 16.2 1.0 CB B:PHE114 3.9 16.5 1.0 N B:HIS46 4.0 15.5 1.0 NE2 B:HIS46 4.1 15.4 1.0 NE2 B:HIS117 4.2 16.7 1.0 CD2 B:HIS117 4.2 14.8 1.0 CD2 B:HIS46 4.2 16.0 1.0 C B:HIS46 4.5 18.0 1.0 N B:ASN47 4.5 16.7 1.0 CA B:CYS112 4.6 15.0 1.0 CG B:MET121 4.7 17.6 1.0 N B:PHE114 4.8 16.6 1.0 CG B:PHE114 4.8 16.2 1.0 CB B:MET121 4.9 17.8 1.0 CA B:HIS117 4.9 15.2 1.0 CA B:PHE114 4.9 17.5 1.0

B.P.Fedoretz-Maxwell, C.H.Shin, G.A.Macneil, L.J.Worrall, R.Park, N.C.J.Strynadka, C.J.Walsby, J.J.Warren. The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins. Inorg.Chem. V. 61 5563 2022.
ISSN: ISSN 0020-1669
PubMed: 35347989
DOI: 10.1021/ACS.INORGCHEM.2C00030