Copper in PDB 5syd: Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence

The structure of Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence, PDB code: 5syd was solved by I.Petrik, Y.Yang, R.Howard, L.Yi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.84 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.436, 115.436, 83.145, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 25.1

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

Copper binding site 1 out of 4 in the Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:0.8 occ:0.92 NE2 A:HIS43 2.6 60.2 1.0 O A:HOH338 3.0 81.6 1.0 CD2 A:HIS43 3.3 56.1 1.0 O A:HOH322 3.4 75.5 1.0 O A:HOH330 3.4 73.8 1.0 CE1 A:HIS43 3.8 61.4 1.0 O A:HOH334 4.3 61.4 1.0 O A:HOH335 4.3 64.9 1.0 CG A:HIS43 4.5 59.7 1.0 O A:HOH323 4.7 58.5 1.0 ND1 A:HIS43 4.7 62.1 1.0

Copper binding site 2 out of 4 in the Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:52.5 occ:1.00 ND1 A:HIS6 2.3 38.8 1.0 ND1 A:HIS77 2.4 53.7 1.0 SG A:CYS72 2.5 59.2 1.0 SD A:MET81 2.9 53.2 1.0 O A:GLY5 3.0 46.5 1.0 CG A:HIS6 3.2 52.9 1.0 CG A:HIS77 3.2 54.4 1.0 CE1 A:HIS6 3.3 64.2 1.0 CB A:CYS72 3.3 59.0 1.0 CA A:HIS6 3.3 53.2 1.0 CB A:HIS77 3.4 56.7 1.0 CE1 A:HIS77 3.4 64.7 1.0 CB A:HIS6 3.5 49.2 1.0 CE A:MET81 3.5 55.4 1.0 CB A:PHE74 3.8 47.1 1.0 C A:GLY5 3.9 63.0 1.0 N A:HIS6 4.1 57.3 1.0 NE2 A:HIS6 4.4 60.9 1.0 CD2 A:HIS6 4.4 52.7 1.0 CD2 A:HIS77 4.4 65.0 1.0 NE2 A:HIS77 4.5 66.3 1.0 C A:HIS6 4.5 53.9 1.0 N A:ASN7 4.5 48.9 1.0 CG A:MET81 4.5 62.2 1.0 CG A:PHE74 4.6 58.4 1.0 CA A:CYS72 4.8 61.8 1.0 CA A:HIS77 4.9 60.9 1.0 N A:PHE74 4.9 55.9 1.0 CA A:PHE74 4.9 53.5 1.0 CB A:MET81 4.9 49.6 1.0 CD1 A:PHE74 5.0 56.1 1.0

Copper binding site 3 out of 4 in the Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu203 b:67.4 occ:1.00 O A:MET1 2.2 67.8 1.0 N B:GLY2 2.3 64.3 1.0 N B:MET1 2.7 80.4 1.0 N A:MET1 2.9 58.9 1.0 C A:MET1 3.2 64.3 1.0 CA B:GLY2 3.2 63.2 1.0 CA B:MET1 3.2 63.3 1.0 C B:MET1 3.2 65.7 1.0 O A:HOH316 3.3 50.4 1.0 CB B:MET1 3.4 52.5 1.0 CA A:MET1 3.5 66.3 1.0 CB A:MET1 4.1 69.9 1.0 CG B:MET1 4.3 64.4 1.0 O A:HOH321 4.3 59.0 1.0 N A:GLY2 4.4 59.8 1.0 O B:MET1 4.4 58.9 1.0 CG A:MET1 4.5 62.9 1.0 C B:GLY2 4.6 59.6 1.0 O B:GLY2 5.0 68.6 1.0

Copper binding site 4 out of 4 in the Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Circularly Permutated Azurin (Cpaz) Based on P. Aeruginosa Azurin Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:57.2 occ:1.00 ND1 B:HIS6 2.4 52.8 1.0 ND1 B:HIS77 2.4 47.3 1.0 SG B:CYS72 2.5 69.9 1.0 O B:GLY5 2.8 55.2 1.0 SD B:MET81 3.1 56.9 1.0 CB B:CYS72 3.2 46.2 1.0 CG B:HIS77 3.3 62.3 1.0 CG B:HIS6 3.3 63.8 1.0 CE1 B:HIS6 3.4 62.3 1.0 CA B:HIS6 3.4 56.3 1.0 CB B:HIS77 3.4 58.0 1.0 CE1 B:HIS77 3.4 64.8 1.0 CB B:HIS6 3.6 56.5 1.0 C B:GLY5 3.8 64.9 1.0 CE B:MET81 3.8 49.7 1.0 CB B:PHE74 3.9 47.0 1.0 N B:HIS6 4.0 65.9 1.0 CD2 B:HIS77 4.4 57.0 1.0 NE2 B:HIS6 4.5 61.6 1.0 CD2 B:HIS6 4.5 62.8 1.0 NE2 B:HIS77 4.5 70.5 1.0 C B:HIS6 4.5 57.8 1.0 N B:ASN7 4.5 55.2 1.0 CG B:MET81 4.6 63.9 1.0 CA B:CYS72 4.7 55.2 1.0 CG B:PHE74 4.8 59.5 1.0 CA B:HIS77 4.9 59.0 1.0 N B:PHE74 4.9 59.5 1.0 CB B:MET81 4.9 47.2 1.0

Y.Yu, I.Petrik, K.N.Chacon, P.Hosseinzadeh, N.Blackburn, L.Yi. Circular Permutation of Azurin Results in the Same Type 1 Blue Copper with Different Reduction Potentials To Be Published.