Copper in PDB 5yt7: Crystal Structure of Circularly Permutated Azurin 3

The structure of Crystal Structure of Circularly Permutated Azurin 3, PDB code: 5yt7 was solved by H.H.Chen, H.P.Liu, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.02 / 1.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.888, 87.968, 66.096, 90.00, 110.22, 90.00
R / Rfree (%)	16.2 / 21.7

The structure of Crystal Structure of Circularly Permutated Azurin 3 also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	3 atoms

The binding sites of Copper atom in the Crystal Structure of Circularly Permutated Azurin 3 (pdb code 5yt7). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Circularly Permutated Azurin 3, PDB code: 5yt7:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Circularly Permutated Azurin 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:19.2 occ:1.00 ND1 A:HIS65 2.1 19.2 1.0 ND1 A:HIS3 2.1 19.0 1.0 SG A:CYS131 2.2 17.7 1.0 O A:GLY64 2.7 18.6 1.0 CE1 A:HIS65 3.0 18.6 1.0 CG A:HIS3 3.1 18.1 1.0 CE1 A:HIS3 3.1 21.0 1.0 CG A:HIS65 3.1 17.9 1.0 SD A:MET7 3.3 17.7 1.0 CB A:CYS131 3.3 17.9 1.0 CA A:HIS65 3.3 18.0 1.0 CB A:HIS3 3.3 16.4 1.0 CB A:HIS65 3.5 18.2 1.0 C A:GLY64 3.7 19.0 1.0 CB A:PHE133 3.8 16.8 1.0 CE A:MET7 3.8 18.3 1.0 N A:HIS65 3.9 20.1 1.0 NE2 A:HIS65 4.1 17.6 1.0 NE2 A:HIS3 4.2 24.2 1.0 CD2 A:HIS3 4.2 21.8 1.0 CD2 A:HIS65 4.2 19.9 1.0 C A:HIS65 4.5 17.8 1.0 CG A:PHE133 4.6 18.2 1.0 N A:ASN66 4.6 17.6 1.0 CA A:CYS131 4.7 16.1 1.0 CG A:MET7 4.7 18.7 1.0 N A:PHE133 4.8 18.2 1.0 CA A:HIS3 4.9 17.1 1.0 CA A:PHE133 4.9 20.3 1.0 CD1 A:PHE133 5.0 19.9 1.0 CB A:MET7 5.0 17.7 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Circularly Permutated Azurin 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:15.2 occ:1.00 ND1 B:HIS3 2.1 15.7 1.0 ND1 B:HIS65 2.1 14.7 1.0 SG B:CYS131 2.2 14.8 1.0 O B:GLY64 2.8 14.0 1.0 CE1 B:HIS65 3.0 15.6 1.0 CE1 B:HIS3 3.1 16.9 1.0 CG B:HIS3 3.1 14.3 1.0 CG B:HIS65 3.1 13.4 1.0 CB B:CYS131 3.3 14.5 1.0 CB B:HIS3 3.3 13.3 1.0 CA B:HIS65 3.3 12.8 1.0 SD B:MET7 3.4 14.6 1.0 CB B:HIS65 3.5 13.2 1.0 C B:GLY64 3.7 14.0 1.0 CB B:PHE133 3.8 17.5 1.0 N B:HIS65 4.0 14.0 1.0 CE B:MET7 4.0 15.2 1.0 NE2 B:HIS65 4.2 15.9 1.0 NE2 B:HIS3 4.2 18.1 1.0 CD2 B:HIS3 4.2 15.7 1.0 CD2 B:HIS65 4.2 14.5 1.0 C B:HIS65 4.6 13.7 1.0 CG B:PHE133 4.6 17.4 1.0 N B:ASN66 4.6 14.1 1.0 CA B:CYS131 4.7 14.2 1.0 N B:PHE133 4.7 17.4 1.0 CG B:MET7 4.8 13.9 1.0 CA B:PHE133 4.8 19.5 1.0 CA B:HIS3 4.9 14.1 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Circularly Permutated Azurin 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu201 b:19.7 occ:1.00 ND1 C:HIS3 2.1 17.0 1.0 SG C:CYS131 2.1 17.9 1.0 ND1 C:HIS65 2.1 20.2 1.0 O C:GLY64 2.8 18.2 1.0 CE1 C:HIS3 3.0 17.5 1.0 CE1 C:HIS65 3.1 20.1 1.0 CG C:HIS3 3.1 16.7 1.0 CG C:HIS65 3.2 17.9 1.0 SD C:MET7 3.2 18.4 1.0 CB C:CYS131 3.3 17.2 1.0 CB C:HIS3 3.4 18.1 1.0 CA C:HIS65 3.4 18.8 1.0 CB C:HIS65 3.6 17.9 1.0 C C:GLY64 3.8 19.2 1.0 CB C:PHE133 3.8 20.2 1.0 CE C:MET7 3.9 19.3 1.0 N C:HIS65 4.0 18.5 1.0 NE2 C:HIS3 4.1 17.9 1.0 CD2 C:HIS3 4.2 19.0 1.0 NE2 C:HIS65 4.2 18.8 1.0 CD2 C:HIS65 4.3 18.5 1.0 C C:HIS65 4.5 17.8 1.0 N C:ASN66 4.6 16.7 1.0 CG C:PHE133 4.6 20.6 1.0 CA C:CYS131 4.7 17.5 1.0 CG C:MET7 4.7 18.7 1.0 N C:PHE133 4.8 20.0 1.0 CA C:PHE133 4.9 21.0 1.0 CA C:HIS3 4.9 18.5 1.0 CB C:MET7 5.0 17.4 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Circularly Permutated Azurin 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu201 b:20.0 occ:1.00 ND1 D:HIS65 2.1 18.3 1.0 ND1 D:HIS3 2.1 16.5 1.0 SG D:CYS131 2.2 17.9 1.0 O D:GLY64 2.8 21.8 1.0 CE1 D:HIS65 3.0 19.4 1.0 CG D:HIS3 3.1 18.1 1.0 CE1 D:HIS3 3.1 20.1 1.0 CG D:HIS65 3.1 19.9 1.0 SD D:MET7 3.2 18.1 1.0 CB D:CYS131 3.3 17.6 1.0 CA D:HIS65 3.3 18.8 1.0 CB D:HIS3 3.4 17.6 1.0 CB D:HIS65 3.5 19.4 1.0 C D:GLY64 3.7 19.1 1.0 CE D:MET7 3.8 17.6 1.0 CB D:PHE133 3.8 21.8 1.0 N D:HIS65 4.0 17.9 1.0 NE2 D:HIS65 4.1 21.7 1.0 NE2 D:HIS3 4.2 22.0 1.0 CD2 D:HIS3 4.2 20.9 1.0 CD2 D:HIS65 4.2 21.2 1.0 C D:HIS65 4.5 17.9 1.0 N D:ASN66 4.6 17.4 1.0 CG D:PHE133 4.6 21.1 1.0 CA D:CYS131 4.6 17.2 1.0 CG D:MET7 4.7 19.1 1.0 N D:PHE133 4.8 20.1 1.0 CA D:PHE133 4.9 21.6 1.0 CA D:HIS3 4.9 19.4 1.0

H.H.Chen, B.Su, T.T.Zhang, A.Huang, H.P.Liu, Y.Yu, J.Wang. Engineering the Metal-Binding Loop of A Blue Copper Protein By Circular Permutation Rsc Adv 56093 2017.
ISSN: ESSN 2046-2069
DOI: 10.1039/C7RA11512A