Copper in PDB 3g5w: Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea

The structure of Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea, PDB code: 3g5w was solved by T.J.Lawton, L.A.Sayavedra-Soto, D.J.Arp, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.28 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.140, 76.254, 105.145, 81.48, 73.38, 61.84
R / Rfree (%)	16.6 / 19.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea (pdb code 3g5w). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea, PDB code: 3g5w:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


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 Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1 b:23.2 occ:1.00 ND1 A:HIS154 2.1 21.3 1.0 SG A:CYS147 2.1 17.0 1.0 ND1 A:HIS99 2.2 18.1 1.0 SD A:MET160 2.8 19.5 1.0 CE1 A:HIS154 3.1 21.6 1.0 CG A:HIS154 3.1 20.8 1.0 CE1 A:HIS99 3.1 19.6 1.0 CB A:CYS147 3.2 16.7 1.0 CG A:HIS99 3.2 19.9 1.0 CB A:HIS154 3.5 21.1 1.0 CB A:HIS99 3.5 19.8 1.0 CE A:MET160 3.6 18.7 1.0 CA A:HIS99 3.8 19.9 1.0 O A:PRO98 3.9 21.9 1.0 CB A:VAL149 4.0 19.1 1.0 O A:VAL149 4.1 19.4 1.0 NE2 A:HIS154 4.2 20.5 1.0 CD2 A:HIS154 4.2 20.1 1.0 NE2 A:HIS99 4.3 18.6 1.0 CD2 A:HIS99 4.3 18.3 1.0 CG A:MET160 4.5 18.0 1.0 CA A:CYS147 4.6 16.4 1.0 N A:VAL149 4.6 18.6 1.0 CG2 A:VAL149 4.7 19.3 1.0 C A:PRO98 4.7 21.9 1.0 N A:THR100 4.7 19.0 1.0 N A:HIS99 4.7 21.0 1.0 CG1 A:VAL149 4.7 19.4 1.0 CA A:VAL149 4.7 19.1 1.0 C A:VAL149 4.8 19.6 1.0 C A:HIS99 4.8 19.6 1.0 CA A:HIS154 4.9 21.2 1.0 CB A:MET160 5.0 17.8 1.0

Copper binding site 2 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


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 Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu2 b:23.0 occ:1.00 CU4 A:C1O2 0.0 23.0 1.0 NE2 A:HIS246 1.9 16.1 1.0 NE2 C:HIS102 2.0 17.1 1.0 O3 A:C1O2 2.8 14.2 1.0 CD2 A:HIS246 2.9 16.7 1.0 CE1 A:HIS246 2.9 17.0 1.0 CE1 C:HIS102 2.9 17.2 1.0 CD2 C:HIS102 3.0 16.8 1.0 NE2 A:HIS248 3.3 17.5 1.0 O1 C:C2O362 3.4 23.4 1.0 CD2 A:HIS248 3.4 16.7 1.0 ND1 C:HIS104 3.5 16.5 1.0 CG C:HIS104 3.7 17.4 1.0 CE1 A:HIS248 3.8 17.8 1.0 CA C:HIS104 3.9 17.3 1.0 CG A:HIS248 4.0 16.6 1.0 CE1 C:HIS104 4.0 17.0 1.0 ND1 A:HIS246 4.0 16.7 1.0 CB C:HIS104 4.0 16.5 1.0 CU3 C:C2O362 4.0 20.2 1.0 CG A:HIS246 4.0 16.6 1.0 ND1 C:HIS102 4.0 15.8 1.0 CU2 C:C2O362 4.1 22.1 1.0 CG C:HIS102 4.1 17.0 1.0 ND1 A:HIS248 4.2 16.5 1.0 CD2 C:HIS104 4.2 16.7 1.0 NE2 C:HIS104 4.3 17.4 1.0 O A:HOH1398 4.5 31.9 1.0 N C:GLY105 4.6 17.5 1.0 C C:HIS104 4.7 17.3 1.0 N C:HIS104 4.8 17.4 1.0 O C:HOH967 4.8 24.9 1.0 CA A:HIS248 4.8 16.8 1.0 CB A:HIS248 4.9 16.2 1.0 O C:TRP103 5.0 18.1 1.0

Copper binding site 3 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


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 Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu3 b:21.9 occ:1.00 CU2 B:C2O3 0.0 21.9 1.0 O1 B:C2O3 2.0 41.7 1.0 NE2 B:HIS294 2.0 18.3 1.0 NE2 B:HIS248 2.0 19.4 1.0 NE2 A:HIS148 2.1 21.0 1.0 CE1 B:HIS248 2.8 18.7 1.0 CE1 B:HIS294 2.9 18.8 1.0 CD2 B:HIS294 3.0 18.5 1.0 CE1 A:HIS148 3.1 21.6 1.0 CD2 A:HIS148 3.1 19.0 1.0 CD2 B:HIS248 3.2 18.1 1.0 CD2 B:HIS246 3.8 14.7 1.0 ND1 B:HIS248 4.0 18.8 1.0 ND1 B:HIS294 4.0 18.7 1.0 CU4 B:C1O2 4.1 22.9 1.0 CG B:HIS294 4.1 17.2 1.0 CG B:HIS248 4.2 17.9 1.0 ND1 A:HIS148 4.2 20.8 1.0 CD2 A:HIS102 4.3 17.3 1.0 CG A:HIS148 4.3 19.5 1.0 NE2 A:HIS102 4.3 17.3 1.0 NE2 B:HIS246 4.3 14.8 1.0 O B:HOH1832 4.3 37.5 1.0 CB B:MET292 4.5 19.8 1.0 CG B:MET292 4.9 23.1 1.0 CE1 A:HIS102 4.9 18.4 1.0 CG A:HIS102 4.9 17.2 1.0 CG B:HIS246 4.9 15.5 1.0

Copper binding site 4 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


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 Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu3 b:20.5 occ:1.00 CU3 B:C2O3 0.0 20.5 1.0 ND1 A:HIS104 2.0 15.2 1.0 NE2 A:HIS146 2.1 16.6 1.0 NE2 B:HIS296 2.1 15.4 1.0 CE1 A:HIS104 2.9 17.3 1.0 CE1 A:HIS146 3.0 16.3 1.0 CG A:HIS104 3.1 16.8 1.0 CD2 A:HIS146 3.1 16.4 1.0 O1 B:C2O3 3.1 41.7 1.0 CE1 B:HIS296 3.1 15.8 1.0 CD2 B:HIS296 3.2 16.2 1.0 CB A:HIS104 3.5 17.1 1.0 CZ2 A:TRP144 3.6 16.3 1.0 CE2 A:TRP144 4.0 16.1 1.0 CD2 A:HIS102 4.0 17.3 1.0 NE2 A:HIS104 4.1 17.7 1.0 CU4 B:C1O2 4.1 22.9 1.0 ND1 A:HIS146 4.1 17.0 1.0 NE1 A:TRP144 4.1 15.7 1.0 CD2 A:HIS104 4.2 17.4 1.0 CG A:HIS146 4.2 16.5 1.0 ND1 B:HIS296 4.2 16.0 1.0 CG B:HIS296 4.3 16.5 1.0 CH2 A:TRP144 4.3 16.1 1.0 NE2 A:HIS102 4.4 17.3 1.0 NE2 B:HIS246 4.5 14.8 1.0 CD2 B:HIS246 4.5 14.7 1.0 O B:HOH1832 4.5 37.5 1.0 CA A:HIS104 4.7 17.2 1.0 CD2 A:TRP144 5.0 15.9 1.0

Copper binding site 5 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


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 Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2 b:22.9 occ:1.00 CU4 B:C1O2 0.0 22.9 1.0 NE2 B:HIS246 1.9 14.8 1.0 NE2 A:HIS102 2.0 17.3 1.0 O3 B:C1O2 2.7 10.4 1.0 CE1 A:HIS102 2.9 18.4 1.0 CE1 B:HIS246 2.9 15.7 1.0 CD2 B:HIS246 3.0 14.7 1.0 CD2 A:HIS102 3.1 17.3 1.0 NE2 B:HIS248 3.3 19.4 1.0 CD2 B:HIS248 3.4 18.1 1.0 O1 B:C2O3 3.5 41.7 1.0 ND1 A:HIS104 3.6 15.2 1.0 CG A:HIS104 3.7 16.8 1.0 CE1 B:HIS248 3.8 18.7 1.0 CA A:HIS104 3.8 17.2 1.0 CG B:HIS248 3.9 17.9 1.0 CE1 A:HIS104 4.0 17.3 1.0 CB A:HIS104 4.0 17.1 1.0 ND1 B:HIS246 4.0 16.2 1.0 ND1 A:HIS102 4.0 17.7 1.0 CU2 B:C2O3 4.1 21.9 1.0 CD2 A:HIS104 4.1 17.4 1.0 CG B:HIS246 4.1 15.5 1.0 ND1 B:HIS248 4.1 18.8 1.0 CU3 B:C2O3 4.1 20.5 1.0 CG A:HIS102 4.1 17.2 1.0 NE2 A:HIS104 4.3 17.7 1.0 N A:GLY105 4.6 18.1 1.0 C A:HIS104 4.7 17.6 1.0 N A:HIS104 4.8 16.8 1.0 CA B:HIS248 4.8 17.2 1.0 CB B:HIS248 4.9 17.5 1.0 O A:HOH744 4.9 20.3 1.0

Copper binding site 6 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu1 b:21.5 occ:1.00 ND1 B:HIS154 2.1 21.4 1.0 SG B:CYS147 2.1 15.8 1.0 ND1 B:HIS99 2.2 20.4 1.0 SD B:MET160 2.9 17.9 1.0 CE1 B:HIS154 3.1 22.4 1.0 CE1 B:HIS99 3.1 20.0 1.0 CG B:HIS99 3.2 19.9 1.0 CB B:CYS147 3.2 15.6 1.0 CG B:HIS154 3.2 20.5 1.0 CB B:HIS99 3.5 19.2 1.0 CB B:HIS154 3.5 19.7 1.0 CE B:MET160 3.6 16.5 1.0 CA B:HIS99 3.7 19.0 1.0 O B:PRO98 3.8 20.9 1.0 CB B:VAL149 4.0 18.3 1.0 O B:VAL149 4.1 19.2 1.0 NE2 B:HIS154 4.2 21.9 1.0 NE2 B:HIS99 4.2 20.2 1.0 CD2 B:HIS99 4.3 20.0 1.0 CD2 B:HIS154 4.3 21.2 1.0 CG B:MET160 4.5 17.8 1.0 CA B:CYS147 4.6 15.6 1.0 C B:PRO98 4.6 21.0 1.0 N B:HIS99 4.6 20.0 1.0 N B:VAL149 4.7 17.6 1.0 N B:THR100 4.7 17.7 1.0 CG2 B:VAL149 4.7 17.5 1.0 CG1 B:VAL149 4.7 18.4 1.0 CA B:VAL149 4.7 18.3 1.0 C B:HIS99 4.8 18.4 1.0 C B:VAL149 4.8 18.6 1.0 CA B:HIS154 4.9 19.6 1.0

Copper binding site 7 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu3 b:21.0 occ:1.00 CU2 C:C2O3 0.0 21.0 1.0 NE2 C:HIS248 2.0 16.5 1.0 NE2 C:HIS294 2.0 21.0 1.0 O1 C:C2O3 2.1 34.0 1.0 NE2 B:HIS148 2.1 17.9 1.0 CE1 C:HIS248 2.7 16.4 1.0 CD2 C:HIS294 2.9 20.5 1.0 CE1 B:HIS148 3.0 18.1 1.0 CE1 C:HIS294 3.1 19.8 1.0 CD2 C:HIS248 3.1 15.7 1.0 CD2 B:HIS148 3.2 17.6 1.0 CD2 C:HIS246 3.8 15.3 1.0 ND1 C:HIS248 3.9 16.7 1.0 CG C:HIS294 4.0 18.1 1.0 CU4 C:C1O2 4.0 21.6 1.0 ND1 C:HIS294 4.1 20.1 1.0 CG C:HIS248 4.1 16.0 1.0 ND1 B:HIS148 4.1 18.3 1.0 CG B:HIS148 4.3 17.3 1.0 NE2 C:HIS246 4.4 16.9 1.0 CD2 B:HIS102 4.4 13.6 1.0 NE2 B:HIS102 4.4 13.8 1.0 CB C:MET292 4.4 19.8 1.0 CG C:MET292 4.9 22.4 1.0 CE1 B:HIS102 5.0 15.8 1.0 CG B:HIS102 5.0 15.0 1.0 CG C:HIS246 5.0 15.6 1.0

Copper binding site 8 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu3 b:19.4 occ:1.00 CU3 C:C2O3 0.0 19.4 1.0 ND1 B:HIS104 2.0 16.7 1.0 NE2 B:HIS146 2.1 16.1 1.0 NE2 C:HIS296 2.2 19.0 1.0 CE1 B:HIS104 2.9 18.1 1.0 CG B:HIS104 3.0 17.1 1.0 CD2 B:HIS146 3.0 14.5 1.0 CE1 B:HIS146 3.0 16.2 1.0 O1 C:C2O3 3.1 34.0 1.0 CE1 C:HIS296 3.1 18.1 1.0 CD2 C:HIS296 3.2 17.9 1.0 CB B:HIS104 3.4 16.2 1.0 CZ2 B:TRP144 3.5 15.7 1.0 CE2 B:TRP144 3.9 15.8 1.0 CU4 C:C1O2 4.0 21.6 1.0 NE2 B:HIS104 4.1 19.1 1.0 NE1 B:TRP144 4.1 14.7 1.0 CD2 B:HIS102 4.1 13.6 1.0 CD2 B:HIS104 4.1 17.9 1.0 ND1 B:HIS146 4.1 14.6 1.0 CG B:HIS146 4.2 15.1 1.0 ND1 C:HIS296 4.2 18.0 1.0 CH2 B:TRP144 4.3 15.8 1.0 CG C:HIS296 4.3 17.6 1.0 NE2 C:HIS246 4.3 16.9 1.0 CD2 C:HIS246 4.4 15.3 1.0 NE2 B:HIS102 4.5 13.8 1.0 CA B:HIS104 4.6 15.9 1.0 CD2 B:TRP144 4.9 15.1 1.0

Copper binding site 9 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu2 b:21.6 occ:1.00 CU4 C:C1O2 0.0 21.6 1.0 NE2 C:HIS246 1.9 16.9 1.0 NE2 B:HIS102 2.0 13.8 1.0 O3 C:C1O2 2.8 12.3 1.0 CE1 C:HIS246 2.9 16.8 1.0 CD2 C:HIS246 2.9 15.3 1.0 CE1 B:HIS102 3.0 15.8 1.0 CD2 B:HIS102 3.0 13.6 1.0 NE2 C:HIS248 3.2 16.5 1.0 CD2 C:HIS248 3.3 15.7 1.0 O1 C:C2O3 3.5 34.0 1.0 ND1 B:HIS104 3.6 16.7 1.0 CG B:HIS104 3.7 17.1 1.0 CE1 C:HIS248 3.7 16.4 1.0 CA B:HIS104 3.9 15.9 1.0 CG C:HIS248 3.9 16.0 1.0 CB B:HIS104 4.0 16.2 1.0 CU3 C:C2O3 4.0 19.4 1.0 ND1 C:HIS246 4.0 15.7 1.0 CE1 B:HIS104 4.0 18.1 1.0 CU2 C:C2O3 4.0 21.0 1.0 ND1 C:HIS248 4.1 16.7 1.0 CG C:HIS246 4.1 15.6 1.0 ND1 B:HIS102 4.1 14.6 1.0 CG B:HIS102 4.1 15.0 1.0 CD2 B:HIS104 4.2 17.9 1.0 NE2 B:HIS104 4.4 19.1 1.0 N B:GLY105 4.6 16.2 1.0 C B:HIS104 4.8 16.0 1.0 N B:HIS104 4.8 15.4 1.0 CA C:HIS248 4.8 16.5 1.0 O C:HOH1599 4.8 44.1 1.0 CB C:HIS248 4.8 16.3 1.0 O B:HOH778 5.0 24.2 1.0

Copper binding site 10 out of 24 in the Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Blue Copper Oxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu362 b:22.1 occ:1.00 CU2 C:C2O362 0.0 22.1 1.0 NE2 A:HIS248 2.0 17.5 1.0 NE2 A:HIS294 2.0 20.9 1.0 NE2 C:HIS148 2.2 21.7 1.0 O1 C:C2O362 2.4 23.4 1.0 CE1 A:HIS248 2.8 17.8 1.0 CD2 A:HIS294 2.9 20.4 1.0 CE1 A:HIS294 3.1 21.0 1.0 CE1 C:HIS148 3.1 22.7 1.0 CD2 A:HIS248 3.2 16.7 1.0 CD2 C:HIS148 3.2 20.1 1.0 CD2 A:HIS246 3.8 16.7 1.0 ND1 A:HIS248 4.0 16.5 1.0 CG A:HIS294 4.0 19.2 1.0 CU4 A:C1O2 4.1 23.0 1.0 ND1 A:HIS294 4.1 20.6 1.0 CG A:HIS248 4.2 16.6 1.0 ND1 C:HIS148 4.2 20.8 1.0 CD2 C:HIS102 4.3 16.8 1.0 CG C:HIS148 4.3 19.7 1.0 NE2 C:HIS102 4.3 17.1 1.0 NE2 A:HIS246 4.3 16.1 1.0 CB A:MET292 4.5 21.1 1.0 CG C:HIS102 5.0 17.0 1.0 CG A:HIS246 5.0 16.6 1.0 CG A:MET292 5.0 24.5 1.0 CD2 A:HIS296 5.0 20.2 1.0

T.J.Lawton, L.A.Sayavedra-Soto, D.J.Arp, A.C.Rosenzweig. Crystal Structure of A Two-Domain Multicopper Oxidase: Implications For the Evolution of Multicopper Blue Proteins. J.Biol.Chem. V. 284 10174 2009.
ISSN: ISSN 0021-9258
PubMed: 19224923
DOI: 10.1074/JBC.M900179200