Copper in PDB 1w6w: 3D Structure of Cota Incubated with Sodium Azide

The structure of 3D Structure of Cota Incubated with Sodium Azide, PDB code: 1w6w was solved by I.Bento, L.O.Martins, G.G.Lopes, M.A.Carrondo, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.28 / 2.2
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.831, 101.831, 137.360, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 19.7

The binding sites of Copper atom in the 3D Structure of Cota Incubated with Sodium Azide (pdb code 1w6w). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the 3D Structure of Cota Incubated with Sodium Azide, PDB code: 1w6w:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the 3D Structure of Cota Incubated with Sodium Azide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of 3D Structure of Cota Incubated with Sodium Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1511 b:23.9 occ:1.00 ND1 A:HIS419 2.0 24.1 1.0 ND1 A:HIS497 2.1 22.2 1.0 SG A:CYS492 2.2 24.1 1.0 CE1 A:HIS419 2.9 26.1 1.0 CE1 A:HIS497 3.0 25.8 1.0 CG A:HIS419 3.1 22.9 1.0 CG A:HIS497 3.1 20.6 1.0 CB A:CYS492 3.3 20.1 1.0 SD A:MET502 3.3 26.8 1.0 CB A:HIS497 3.5 21.6 1.0 CB A:HIS419 3.6 21.0 1.0 CE A:MET502 3.7 34.9 1.0 CD1 A:ILE494 4.0 23.6 1.0 NE2 A:HIS419 4.0 25.8 1.0 CB A:ILE494 4.1 19.7 1.0 NE2 A:HIS497 4.1 21.7 1.0 CD2 A:HIS419 4.2 27.5 1.0 CD2 A:HIS497 4.2 20.4 1.0 CA A:HIS419 4.2 21.4 1.0 CG1 A:ILE494 4.5 21.5 1.0 CA A:CYS492 4.6 19.9 1.0 CD A:PRO420 4.7 18.9 1.0 CG A:MET502 4.8 24.6 1.0 CG2 A:ILE494 4.8 19.7 1.0 CD1 A:LEU386 4.9 33.2 1.0 O A:HOH2413 4.9 33.5 1.0 N A:ILE494 5.0 19.4 1.0

Copper binding site 2 out of 4 in the 3D Structure of Cota Incubated with Sodium Azide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of 3D Structure of Cota Incubated with Sodium Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1512 b:26.1 occ:1.00 ND1 A:HIS107 2.0 21.6 1.0 NE2 A:HIS493 2.1 14.8 1.0 NE2 A:HIS153 2.2 19.4 1.0 N1 A:AZI1515 2.4 24.7 1.0 N2 A:AZI1515 2.8 32.8 1.0 CE1 A:HIS107 2.9 24.7 1.0 CE1 A:HIS153 2.9 18.9 1.0 CG A:HIS107 3.1 19.2 1.0 CD2 A:HIS493 3.1 18.4 1.0 CE1 A:HIS493 3.1 17.2 1.0 CD2 A:HIS153 3.3 20.9 1.0 CB A:HIS107 3.5 18.6 1.0 N3 A:AZI1515 3.7 29.9 1.0 CZ2 A:TRP151 3.9 15.6 1.0 CD2 A:HIS105 3.9 16.0 1.0 NE2 A:HIS107 4.0 22.3 1.0 ND1 A:HIS153 4.1 18.8 1.0 CD2 A:HIS107 4.1 23.7 1.0 CU A:CU1514 4.1 25.0 0.8 CE2 A:TRP151 4.2 16.1 1.0 ND1 A:HIS493 4.2 17.3 1.0 CG A:HIS493 4.2 18.7 1.0 CG A:HIS153 4.3 17.2 1.0 NE1 A:TRP151 4.3 17.7 1.0 NE2 A:HIS105 4.4 17.1 1.0 CD2 A:HIS422 4.5 17.6 1.0 CB A:ALA297 4.5 18.1 1.0 CU A:CU1513 4.5 24.7 1.0 NE2 A:HIS422 4.5 15.0 1.0 CH2 A:TRP151 4.6 14.2 1.0 CA A:HIS107 4.7 17.1 1.0

Copper binding site 3 out of 4 in the 3D Structure of Cota Incubated with Sodium Azide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of 3D Structure of Cota Incubated with Sodium Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1513 b:24.7 occ:1.00 NE2 A:HIS491 2.0 20.3 1.0 NE2 A:HIS424 2.0 19.3 1.0 N1 A:AZI1515 2.2 24.7 1.0 NE2 A:HIS155 2.2 23.6 1.0 N2 A:AZI1515 2.6 32.8 1.0 CE1 A:HIS424 2.8 18.4 1.0 CD2 A:HIS491 2.9 21.6 1.0 CD2 A:HIS155 3.0 24.0 1.0 CE1 A:HIS491 3.0 18.9 1.0 CD2 A:HIS424 3.2 18.3 1.0 CE1 A:HIS155 3.3 26.6 1.0 N3 A:AZI1515 3.4 29.9 1.0 CD2 A:HIS422 3.7 17.6 1.0 CU A:CU1514 3.8 25.0 0.8 CD2 A:HIS105 3.9 16.0 1.0 ND1 A:HIS424 4.0 17.4 1.0 NE2 A:HIS105 4.0 17.1 1.0 CG A:HIS491 4.1 18.0 1.0 CG2 A:VAL489 4.1 19.9 1.0 ND1 A:HIS491 4.1 20.0 1.0 CG A:HIS424 4.2 18.4 1.0 NE2 A:HIS422 4.2 15.0 1.0 CG A:HIS155 4.2 20.4 1.0 ND1 A:HIS155 4.3 25.4 1.0 CU A:CU1512 4.5 26.1 1.0 CG A:HIS105 4.7 16.3 1.0 CE1 A:HIS105 4.8 18.4 1.0 OE2 A:GLU498 4.9 25.0 1.0 O A:HOH2157 4.9 40.9 1.0 CG A:HIS422 5.0 17.3 1.0 NE2 A:HIS493 5.0 14.8 1.0 CD2 A:HIS493 5.0 18.4 1.0

Copper binding site 4 out of 4 in the 3D Structure of Cota Incubated with Sodium Azide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of 3D Structure of Cota Incubated with Sodium Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1514 b:25.0 occ:0.80 NE2 A:HIS105 2.0 17.1 1.0 NE2 A:HIS422 2.0 15.0 1.0 O A:HOH2143 2.7 18.8 1.0 CD2 A:HIS424 2.8 18.3 1.0 CE1 A:HIS105 2.9 18.4 1.0 CD2 A:HIS422 2.9 17.6 1.0 NE2 A:HIS424 3.0 19.3 1.0 CE1 A:HIS422 3.0 17.4 1.0 CD2 A:HIS105 3.0 16.0 1.0 N1 A:AZI1515 3.5 24.7 1.0 CG A:HIS107 3.6 19.2 1.0 CG A:HIS424 3.6 18.4 1.0 CE1 A:HIS424 3.7 18.4 1.0 ND1 A:HIS107 3.7 21.6 1.0 CA A:HIS107 3.7 17.1 1.0 CU A:CU1513 3.8 24.7 1.0 CD2 A:HIS107 3.9 23.7 1.0 CB A:HIS107 3.9 18.6 1.0 ND1 A:HIS424 4.0 17.4 1.0 CE1 A:HIS107 4.0 24.7 1.0 ND1 A:HIS105 4.0 16.2 1.0 ND1 A:HIS422 4.1 19.0 1.0 CG A:HIS422 4.1 17.3 1.0 CG A:HIS105 4.1 16.3 1.0 CU A:CU1512 4.1 26.1 1.0 NE2 A:HIS107 4.1 22.3 1.0 N A:GLY108 4.3 16.7 1.0 CA A:HIS424 4.4 19.3 1.0 CB A:HIS424 4.4 20.7 1.0 C A:HIS107 4.6 17.3 1.0 O A:HOH2144 4.7 19.5 1.0 N A:HIS107 4.7 16.2 1.0 N2 A:AZI1515 4.7 32.8 1.0 O A:HOH2415 4.8 23.7 1.0 O A:LEU106 4.9 15.2 1.0 O A:LEU423 4.9 18.8 1.0 N A:HIS424 4.9 19.8 1.0

I.Bento, L.O.Martins, G.G.Lopes, M.A.Carrondo, P.F.Lindley. Dioxygen Reduction By Multi-Copper Oxidases; A Structural Perspective. Dalton Trans. V. 7 3507 2005.
ISSN: ISSN 1477-9226
PubMed: 16234932
DOI: 10.1039/B504806K