Copper in PDB 6l1v: Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer

The structure of Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer, PDB code: 6l1v was solved by R.N.Cahyono, M.Yamanaka, S.Nagao, N.Shibata, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.451, 167.809, 116.988, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23

The binding sites of Copper atom in the Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer (pdb code 6l1v). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer, PDB code: 6l1v:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu200 b:43.7 occ:1.00 ND1 A:HIS46 2.0 48.4 1.0 ND1 A:HIS117 2.0 50.2 1.0 SG A:CYS112 2.3 41.0 1.0 CE1 A:HIS46 2.9 56.1 1.0 CE1 A:HIS117 2.9 49.2 1.0 O A:GLY45 3.0 40.6 1.0 CG A:HIS46 3.1 48.8 1.0 CG A:HIS117 3.1 50.5 1.0 SD A:MET121 3.3 69.8 1.0 CB A:CYS112 3.3 42.0 1.0 CA A:HIS46 3.3 39.8 1.0 CB A:HIS117 3.5 46.0 1.0 CB A:HIS46 3.5 42.6 1.0 CB A:PHE114 3.8 40.2 1.0 C A:GLY45 3.9 40.7 1.0 N A:HIS46 4.0 37.1 1.0 NE2 A:HIS46 4.1 57.3 1.0 NE2 A:HIS117 4.1 52.4 1.0 CD2 A:HIS46 4.2 50.4 1.0 CD2 A:HIS117 4.2 52.2 1.0 CE A:MET121 4.3 55.0 1.0 C A:HIS46 4.5 39.5 1.0 N A:ASN47 4.5 36.8 1.0 CG A:PHE114 4.6 41.0 1.0 CA A:CYS112 4.7 41.0 1.0 CG A:MET121 4.7 57.2 1.0 CA A:HIS117 4.9 46.1 1.0 CA A:PHE114 5.0 42.9 1.0 N A:PHE114 5.0 43.2 1.0 CD1 A:PHE114 5.0 41.3 1.0

Copper binding site 2 out of 4 in the Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu200 b:44.4 occ:1.00 ND1 C:HIS46 2.0 40.8 1.0 ND1 C:HIS117 2.0 49.6 1.0 SG C:CYS112 2.2 41.8 1.0 CE1 C:HIS46 2.9 49.6 1.0 CE1 C:HIS117 3.0 42.1 1.0 O C:GLY45 3.0 44.6 1.0 CG C:HIS46 3.1 44.0 1.0 CG C:HIS117 3.1 45.8 1.0 CB C:CYS112 3.3 41.0 1.0 CA C:HIS46 3.3 39.5 1.0 SD C:MET121 3.4 64.6 1.0 CB C:HIS117 3.4 44.6 1.0 CB C:HIS46 3.5 39.9 1.0 CB C:PHE114 3.7 40.7 1.0 C C:GLY45 3.8 42.2 1.0 N C:HIS46 4.0 39.0 1.0 NE2 C:HIS46 4.1 50.3 1.0 NE2 C:HIS117 4.1 43.0 1.0 CD2 C:HIS46 4.2 48.1 1.0 CD2 C:HIS117 4.2 45.6 1.0 CE C:MET121 4.4 56.0 1.0 C C:HIS46 4.5 40.1 1.0 N C:ASN47 4.5 39.3 1.0 CG C:PHE114 4.5 42.8 1.0 CA C:CYS112 4.7 39.5 1.0 CG C:MET121 4.8 51.3 1.0 CA C:PHE114 4.9 41.2 1.0 CA C:HIS117 4.9 45.7 1.0 N C:PHE114 4.9 40.1 1.0 CD1 C:PHE114 5.0 47.3 1.0

Copper binding site 3 out of 4 in the Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu200 b:41.7 occ:1.00 ND1 E:HIS46 2.0 38.2 1.0 ND1 E:HIS117 2.1 49.7 1.0 SG E:CYS112 2.2 38.5 1.0 CE1 E:HIS46 2.9 43.6 1.0 SD E:MET121 3.0 49.0 1.0 CG E:HIS117 3.1 44.6 1.0 CG E:HIS46 3.1 39.3 1.0 CE1 E:HIS117 3.1 46.1 1.0 CB E:CYS112 3.2 39.8 1.0 O E:GLY45 3.2 40.9 1.0 CB E:HIS117 3.4 44.6 1.0 CA E:HIS46 3.4 40.0 1.0 CB E:HIS46 3.5 39.4 1.0 CE E:MET121 3.9 47.9 1.0 CB E:PHE114 3.9 39.7 1.0 NE2 E:HIS46 4.0 44.9 1.0 C E:GLY45 4.1 45.9 1.0 CD2 E:HIS46 4.1 42.6 1.0 N E:HIS46 4.1 44.0 1.0 NE2 E:HIS117 4.2 45.0 1.0 CD2 E:HIS117 4.2 45.7 1.0 N E:ASN47 4.5 38.5 1.0 CG E:MET121 4.5 46.4 1.0 C E:HIS46 4.5 38.2 1.0 CA E:CYS112 4.6 37.6 1.0 CG E:PHE114 4.7 40.2 1.0 CA E:HIS117 4.9 42.5 1.0 CB E:MET121 4.9 46.5 1.0 N E:PHE114 5.0 35.1 1.0 CA E:PHE114 5.0 38.6 1.0

Copper binding site 4 out of 4 in the Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Domain-Swapped Alcaligenes Xylosoxidans Azurin Dimer within 5.0Å range: probe atom residue distance (Å) B Occ G:Cu200 b:39.6 occ:1.00 ND1 G:HIS46 2.0 36.6 1.0 ND1 G:HIS117 2.1 46.8 1.0 SG G:CYS112 2.2 38.9 1.0 CE1 G:HIS46 2.9 44.7 1.0 CG G:HIS117 3.1 45.0 1.0 SD G:MET121 3.1 50.1 1.0 CG G:HIS46 3.1 37.6 1.0 CE1 G:HIS117 3.1 43.4 1.0 CB G:CYS112 3.2 38.8 1.0 O G:GLY45 3.3 41.6 1.0 CB G:HIS117 3.3 45.7 1.0 CA G:HIS46 3.4 37.5 1.0 CB G:HIS46 3.5 37.9 1.0 CB G:PHE114 3.9 40.9 1.0 CE G:MET121 4.0 44.3 1.0 NE2 G:HIS46 4.1 50.0 1.0 C G:GLY45 4.1 45.0 1.0 CD2 G:HIS46 4.1 42.9 1.0 N G:HIS46 4.1 41.1 1.0 CD2 G:HIS117 4.2 45.5 1.0 NE2 G:HIS117 4.2 43.2 1.0 N G:ASN47 4.5 35.2 1.0 C G:HIS46 4.5 35.3 1.0 CG G:MET121 4.6 47.8 1.0 CA G:CYS112 4.6 39.3 1.0 CG G:PHE114 4.7 42.2 1.0 CA G:HIS117 4.8 43.4 1.0 CB G:MET121 4.9 45.4 1.0 N G:PHE114 4.9 37.5 1.0 CA G:PHE114 4.9 38.1 1.0

R.N.Cahyono, M.Yamanaka, S.Nagao, N.Shibata, Y.Higuchi, S.Hirota. 3D Domain Swapping of Azurin From Alcaligenes Xylosoxidans. Metallomics 2020.
ISSN: ESSN 1756-591X
PubMed: 31956880
DOI: 10.1039/C9MT00255C