Copper in PDB 2x88: Crystal Structure of Holocota

The structure of Crystal Structure of Holocota, PDB code: 2x88 was solved by I.Bento, C.S.Silva, Z.Chen, L.O.Martins, P.F.Lindley, C.M.Soares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.85 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.444, 101.444, 137.257, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 20.6

The binding sites of Copper atom in the Crystal Structure of Holocota (pdb code 2x88). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Crystal Structure of Holocota, PDB code: 2x88:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in the Crystal Structure of Holocota


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 Holocota within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1512 b:17.1 occ:1.00 ND1 A:HIS497 2.1 15.9 1.0 ND1 A:HIS419 2.1 16.3 1.0 SG A:CYS492 2.2 14.9 1.0 CE1 A:HIS419 3.0 17.3 1.0 CE1 A:HIS497 3.0 16.3 1.0 CG A:HIS497 3.1 15.7 1.0 CG A:HIS419 3.1 16.9 1.0 CB A:CYS492 3.3 13.8 1.0 SD A:MET502 3.3 16.7 1.0 CB A:HIS497 3.4 15.4 1.0 CB A:HIS419 3.5 16.4 1.0 CD1 A:ILE494 3.8 14.7 1.0 CE A:MET502 4.0 16.6 1.0 CB A:ILE494 4.1 13.5 1.0 CA A:HIS419 4.1 16.3 1.0 NE2 A:HIS419 4.1 17.1 1.0 NE2 A:HIS497 4.2 16.4 1.0 CD2 A:HIS497 4.2 15.6 1.0 CD2 A:HIS419 4.2 17.2 1.0 CG1 A:ILE494 4.4 13.6 1.0 CD1 A:LEU386 4.7 22.6 1.0 O A:HOH2454 4.7 24.9 1.0 CA A:CYS492 4.7 13.7 1.0 CD A:PRO420 4.7 14.9 1.0 CG A:MET502 4.9 15.8 1.0 CG2 A:ILE494 4.9 13.3 1.0 O A:THR418 4.9 18.1 1.0 CA A:HIS497 4.9 15.3 1.0 N A:ILE494 5.0 13.6 1.0

Copper binding site 2 out of 5 in the Crystal Structure of Holocota


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 Holocota within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1513 b:14.9 occ:1.00 ND1 A:HIS107 2.0 12.2 1.0 NE2 A:HIS153 2.1 12.6 1.0 NE2 A:HIS493 2.1 13.3 1.0 O2 A:OXY1516 2.5 16.6 1.0 O1 A:OXY1516 2.8 16.9 1.0 CE1 A:HIS107 3.0 12.3 1.0 CE1 A:HIS153 3.0 13.4 1.0 CG A:HIS107 3.1 12.3 1.0 CE1 A:HIS493 3.1 13.3 1.0 CD2 A:HIS153 3.1 13.2 1.0 CD2 A:HIS493 3.1 13.0 1.0 CB A:HIS107 3.5 12.3 1.0 CZ2 A:TRP151 3.8 12.9 1.0 CD2 A:HIS105 4.1 12.1 1.0 NE2 A:HIS107 4.1 12.0 1.0 ND1 A:HIS153 4.1 12.7 1.0 CU A:CU1515 4.1 18.0 1.0 CE2 A:TRP151 4.2 12.4 1.0 O A:HOH2525 4.2 24.8 1.0 CD2 A:HIS107 4.2 12.4 1.0 ND1 A:HIS493 4.2 13.0 1.0 CG A:HIS153 4.2 12.5 1.0 CG A:HIS493 4.3 13.4 1.0 NE1 A:TRP151 4.3 11.7 1.0 CB A:ALA297 4.4 12.5 1.0 CH2 A:TRP151 4.5 13.1 1.0 NE2 A:HIS105 4.6 12.2 1.0 CD2 A:HIS422 4.6 12.6 1.0 CA A:HIS107 4.6 12.4 1.0 NE2 A:HIS422 4.7 13.2 1.0 CU A:CU1514 4.8 16.2 1.0

Copper binding site 3 out of 5 in the Crystal Structure of Holocota


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 Holocota within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1514 b:16.2 occ:1.00 NE2 A:HIS424 2.0 14.6 1.0 NE2 A:HIS491 2.0 14.3 1.0 NE2 A:HIS155 2.1 15.0 1.0 O1 A:OXY1516 2.3 16.9 1.0 O2 A:OXY1516 2.4 16.6 1.0 CE1 A:HIS424 3.0 14.3 1.0 CD2 A:HIS491 3.0 14.5 1.0 CD2 A:HIS155 3.1 14.9 1.0 CE1 A:HIS491 3.1 14.4 1.0 CD2 A:HIS424 3.1 13.9 1.0 CE1 A:HIS155 3.1 15.2 1.0 O A:HOH2525 3.8 24.8 1.0 CU A:CU1515 3.8 18.0 1.0 CD2 A:HIS422 3.9 12.6 1.0 CG2 A:VAL489 4.1 14.0 0.6 ND1 A:HIS424 4.1 13.9 1.0 CG A:HIS491 4.1 13.9 1.0 ND1 A:HIS491 4.1 14.2 1.0 CD2 A:HIS105 4.1 12.1 1.0 CG A:HIS424 4.2 14.1 1.0 CG A:HIS155 4.2 14.2 1.0 ND1 A:HIS155 4.2 15.3 1.0 NE2 A:HIS105 4.2 12.2 1.0 NE2 A:HIS422 4.4 13.2 1.0 O A:HOH2169 4.5 32.8 1.0 OE2 A:GLU498 4.6 17.6 1.0 CU A:CU1513 4.8 14.9 1.0 CG A:HIS105 4.8 11.7 1.0 CE1 A:HIS105 5.0 12.6 1.0

Copper binding site 4 out of 5 in the Crystal Structure of Holocota


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 Holocota within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1515 b:18.0 occ:1.00 NE2 A:HIS422 2.0 13.2 1.0 NE2 A:HIS105 2.0 12.2 1.0 O2 A:OXY1516 2.7 16.6 1.0 CD2 A:HIS422 2.9 12.6 1.0 O A:HOH2151 2.9 13.2 1.0 CD2 A:HIS105 2.9 12.1 1.0 CE1 A:HIS105 3.0 12.6 1.0 CE1 A:HIS422 3.1 13.8 1.0 NE2 A:HIS424 3.2 14.6 1.0 CD2 A:HIS424 3.2 13.9 1.0 ND1 A:HIS107 3.5 12.2 1.0 CG A:HIS107 3.7 12.3 1.0 CE1 A:HIS424 3.8 14.3 1.0 CU A:CU1514 3.8 16.2 1.0 CG A:HIS424 3.8 14.1 1.0 CA A:HIS107 3.8 12.4 1.0 O1 A:OXY1516 3.8 16.9 1.0 CE1 A:HIS107 3.9 12.3 1.0 CG A:HIS422 4.0 13.2 1.0 ND1 A:HIS105 4.1 12.0 1.0 ND1 A:HIS424 4.1 13.9 1.0 CG A:HIS105 4.1 11.7 1.0 CB A:HIS107 4.1 12.3 1.0 ND1 A:HIS422 4.1 13.2 1.0 CU A:CU1513 4.1 14.9 1.0 CD2 A:HIS107 4.2 12.4 1.0 N A:GLY108 4.3 12.8 1.0 NE2 A:HIS107 4.3 12.0 1.0 CA A:HIS424 4.5 14.1 1.0 C A:HIS107 4.6 12.6 1.0 CB A:HIS424 4.7 14.0 1.0 N A:HIS107 4.8 12.3 1.0 O A:HOH2167 4.8 16.2 1.0 O A:HOH2458 4.9 14.1 1.0 O A:LEU106 4.9 12.4 1.0 O A:LEU423 5.0 14.0 1.0

Copper binding site 5 out of 5 in the Crystal Structure of Holocota


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Holocota within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1517 b:28.9 occ:0.50 NE2 A:HIS89 1.6 26.2 0.5 ND1 A:HIS86 2.2 25.2 0.5 O A:HOH2132 2.3 21.4 1.0 CE1 A:HIS89 2.4 26.2 0.5 CD2 A:HIS89 2.7 26.1 0.5 O A:HOH2144 2.7 53.4 1.0 CE1 A:HIS86 2.8 25.4 0.5 CD2 A:HIS86 3.4 25.8 0.5 ND1 A:HIS89 3.5 26.2 0.5 CG A:HIS86 3.5 25.1 0.5 O A:HOH2140 3.6 25.3 1.0 CG A:HIS89 3.6 26.0 0.5 NE2 A:HIS86 4.1 25.6 0.5 CB A:HIS86 4.1 24.9 0.5 CG A:HIS86 4.1 25.4 0.5 CA A:HIS86 4.2 24.8 0.5 CA A:HIS86 4.2 24.8 0.5 O A:HOH2224 4.3 31.4 1.0 NZ A:LYS101 4.3 23.2 1.0 CB A:HIS86 4.3 25.0 0.5 CD2 A:HIS86 4.4 25.3 0.5 NE2 A:HIS86 4.4 26.0 0.5 O A:HIS89 4.7 25.5 0.5 O A:HIS86 4.7 25.1 1.0 CG2 A:ILE84 4.8 22.0 1.0 C A:HIS86 5.0 24.9 1.0

I.Bento, C.S.Silva, Z.Chen, L.O.Martins, P.F.Lindley, C.M.Soares. Mechanisms Underlying Dioxygen Reduction in Laccases. Structural and Modelling Studies Focusing on Proton Transfer. Bmc Struct.Biol. V. 10 29 2010.
ISSN: ESSN 1472-6807
PubMed: 20822511
DOI: 10.1186/1472-6807-10-28