Copper in PDB 5yw3: X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant

The structure of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant, PDB code: 5yw3 was solved by C.Sakai, T.Yamaguchi, T.Kohzuma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.72 / 1.19
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.699, 51.227, 57.723, 88.88, 77.16, 86.58
R / Rfree (%)	12.7 / 17.3

The structure of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Copper atom in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant (pdb code 5yw3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant, PDB code: 5yw3:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:7.2 occ:1.00 ND1 A:HIS40 2.0 5.4 1.0 ND1 A:HIS81 2.0 7.0 1.0 SG A:CYS78 2.2 6.4 1.0 SD A:MET86 2.7 5.6 1.0 CE1 A:HIS40 2.9 6.2 1.0 CE1 A:HIS81 3.0 6.9 1.0 CG A:HIS40 3.0 4.8 1.0 CG A:HIS81 3.1 6.7 1.0 CB A:CYS78 3.2 5.8 1.0 CB A:HIS40 3.4 5.1 1.0 CB A:HIS81 3.4 6.3 1.0 CE A:MET86 3.4 6.5 1.0 CA A:HIS40 3.6 5.5 1.0 O A:GLY39 3.9 7.9 1.0 CG A:MET86 4.0 5.0 1.0 NE2 A:HIS40 4.1 6.3 1.0 CD2 A:HIS40 4.1 5.9 1.0 NE2 A:HIS81 4.2 7.0 1.0 CD2 A:HIS81 4.2 7.4 1.0 CG A:PRO80 4.5 8.9 1.0 N A:HIS40 4.5 5.6 1.0 C A:GLY39 4.5 6.7 1.0 CE A:MET16 4.5 8.6 1.0 N A:HIS81 4.6 7.4 1.0 CB A:MET86 4.6 5.6 1.0 CA A:CYS78 4.6 5.1 1.0 CA A:HIS81 4.6 7.0 1.0 N A:ASN41 4.7 5.8 1.0 C A:HIS40 4.8 5.5 1.0 C A:CYS78 5.0 5.6 1.0 CD A:PRO80 5.0 7.8 1.0

Copper binding site 2 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:5.9 occ:1.00 ND1 B:HIS81 2.0 5.1 1.0 ND1 B:HIS40 2.0 5.1 1.0 SG B:CYS78 2.2 5.7 1.0 SD B:MET86 2.6 4.7 1.0 CE1 B:HIS81 3.0 6.2 1.0 CE1 B:HIS40 3.0 6.2 1.0 CG B:HIS81 3.0 4.7 1.0 CG B:HIS40 3.1 5.2 1.0 CB B:CYS78 3.2 6.2 1.0 CB B:HIS81 3.3 4.9 1.0 CE B:MET86 3.4 6.2 1.0 CB B:HIS40 3.4 5.3 1.0 CA B:HIS40 3.7 5.0 1.0 O B:GLY39 3.9 9.4 1.0 CG B:MET86 4.0 5.1 1.0 NE2 B:HIS81 4.1 6.0 1.0 CD2 B:HIS81 4.1 5.8 1.0 NE2 B:HIS40 4.1 6.1 1.0 CD2 B:HIS40 4.2 5.9 1.0 N B:HIS40 4.5 5.4 1.0 C B:GLY39 4.5 6.7 1.0 CG B:PRO80 4.5 6.3 1.0 CB B:MET86 4.5 4.2 1.0 CA B:HIS81 4.5 4.7 1.0 N B:HIS81 4.5 5.2 1.0 CE B:MET16 4.6 12.6 1.0 CA B:CYS78 4.6 5.2 1.0 N B:ASN41 4.7 5.5 1.0 C B:HIS40 4.8 5.0 1.0

Copper binding site 3 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu201 b:6.6 occ:0.93 ND1 C:HIS40 2.0 6.4 1.0 ND1 C:HIS81 2.0 7.2 1.0 SG C:CYS78 2.2 6.8 1.0 SD C:MET86 2.6 6.1 1.0 CE1 C:HIS40 2.9 6.8 1.0 CE1 C:HIS81 2.9 8.8 1.0 CG C:HIS81 3.0 7.0 1.0 CG C:HIS40 3.1 6.1 1.0 CB C:CYS78 3.2 6.2 1.0 CB C:HIS81 3.3 7.3 1.0 CE C:MET86 3.4 7.1 1.0 CB C:HIS40 3.5 5.5 1.0 CA C:HIS40 3.7 5.8 1.0 O C:GLY39 3.9 9.4 1.0 CG C:MET86 3.9 5.7 1.0 NE2 C:HIS81 4.1 11.3 1.0 NE2 C:HIS40 4.1 7.0 1.0 CD2 C:HIS81 4.1 9.6 1.0 CD2 C:HIS40 4.2 6.7 1.0 CG C:PRO80 4.4 10.5 1.0 CB C:MET86 4.5 5.9 1.0 N C:HIS81 4.5 7.0 1.0 C C:GLY39 4.5 6.7 1.0 CA C:HIS81 4.5 7.4 1.0 N C:HIS40 4.5 6.3 1.0 CA C:CYS78 4.6 6.1 1.0 N C:ASN41 4.8 6.7 1.0 C C:HIS40 4.8 6.3 1.0 C C:CYS78 5.0 5.8 1.0

Copper binding site 4 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu201 b:8.3 occ:1.00 ND1 D:HIS40 2.0 7.8 1.0 ND1 D:HIS81 2.0 7.9 1.0 SG D:CYS78 2.2 8.5 1.0 SD D:MET86 2.9 7.1 1.0 CE1 D:HIS40 2.9 7.8 1.0 CE1 D:HIS81 2.9 9.8 1.0 CG D:HIS81 3.0 8.1 1.0 CG D:HIS40 3.0 7.1 1.0 CB D:CYS78 3.1 7.1 1.0 CB D:HIS81 3.4 7.8 1.0 CB D:HIS40 3.5 7.2 1.0 CE D:MET86 3.5 7.7 1.0 CA D:HIS40 3.6 7.2 1.0 O D:GLY39 3.7 10.6 1.0 NE2 D:HIS40 4.1 8.1 1.0 NE2 D:HIS81 4.1 11.9 1.0 CD2 D:HIS40 4.1 8.1 1.0 CD2 D:HIS81 4.2 11.3 1.0 CG D:MET86 4.2 6.4 1.0 CG D:PRO80 4.3 9.4 1.0 C D:GLY39 4.3 8.8 1.0 N D:HIS81 4.4 8.1 1.0 N D:HIS40 4.4 8.1 1.0 CA D:HIS81 4.5 8.2 1.0 CA D:CYS78 4.6 5.9 1.0 N D:ASN41 4.7 6.7 1.0 C D:HIS40 4.7 7.1 1.0 CB D:MET86 4.8 6.4 1.0 CD D:PRO80 4.8 8.4 1.0 SD D:MET16 4.9 10.7 1.0 C D:CYS78 4.9 7.2 1.0

T.Yamaguchi, C.Sakai, T.Kohzuma. X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant To Be Published.