Copper in PDB 2zwn: Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome

The structure of Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome, PDB code: 2zwn was solved by H.Komori, K.Miyazaki, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.01 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.669, 100.945, 124.106, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.3

The structure of Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome (pdb code 2zwn). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome, PDB code: 2zwn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1001 b:15.4 occ:1.00 ND1 A:HIS112 2.0 14.2 1.0 ND1 A:HIS57 2.1 11.5 1.0 SG A:CYS105 2.2 14.3 1.0 SD A:MET118 2.8 12.8 1.0 CE1 A:HIS112 2.9 14.1 1.0 CE1 A:HIS57 3.0 12.6 1.0 CG A:HIS112 3.1 13.9 1.0 CG A:HIS57 3.1 12.8 1.0 CB A:CYS105 3.2 13.3 1.0 CB A:HIS57 3.4 13.4 1.0 CB A:HIS112 3.5 13.9 1.0 CE A:MET118 3.5 12.9 1.0 CA A:HIS57 3.7 13.4 1.0 O A:PRO56 3.9 14.0 1.0 O A:VAL107 3.9 16.1 1.0 NE2 A:HIS112 4.0 15.0 1.0 CD2 A:HIS112 4.1 15.1 1.0 NE2 A:HIS57 4.2 12.5 1.0 CD2 A:HIS57 4.2 12.9 1.0 CB A:VAL107 4.3 15.6 1.0 CG A:MET118 4.4 12.5 1.0 CA A:CYS105 4.6 12.8 1.0 N A:HIS57 4.7 13.8 1.0 C A:PRO56 4.7 14.3 1.0 C A:VAL107 4.7 16.0 1.0 N A:THR58 4.8 12.8 1.0 N A:VAL107 4.8 14.9 1.0 C A:HIS57 4.8 13.2 1.0 CA A:VAL107 4.9 15.4 1.0 CA A:HIS112 4.9 14.1 1.0 CB A:MET118 4.9 11.7 1.0

Copper binding site 2 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1002 b:15.2 occ:0.90 CU2 A:C2O1002 0.0 15.2 0.9 NE2 B:HIS206 2.0 12.6 1.0 NE2 B:HIS252 2.0 16.2 1.0 NE2 A:HIS106 2.1 14.6 1.0 O1 A:C2O1002 2.4 14.8 0.9 CE1 B:HIS206 2.8 11.8 1.0 CD2 B:HIS252 3.0 14.8 1.0 CE1 A:HIS106 3.0 15.5 1.0 CE1 B:HIS252 3.0 15.7 1.0 CD2 B:HIS206 3.1 11.4 1.0 CD2 A:HIS106 3.2 14.4 1.0 CG2 B:ILE250 4.0 11.9 1.0 CD2 B:HIS204 4.0 10.2 1.0 ND1 B:HIS206 4.0 11.6 1.0 CU B:CU1003 4.1 19.5 0.7 ND1 B:HIS252 4.1 15.6 1.0 CG B:HIS206 4.2 10.6 1.0 CG B:HIS252 4.2 13.9 1.0 ND1 A:HIS106 4.2 14.2 1.0 CG A:HIS106 4.3 13.8 1.0 CD2 A:HIS60 4.4 11.6 1.0 NE2 A:HIS60 4.5 11.1 1.0 NE2 B:HIS204 4.6 10.4 1.0 CE1 A:HIS104 4.9 11.4 1.0 CD2 B:HIS254 4.9 14.1 1.0 CU3 A:C2O1002 5.0 15.0 0.9

Copper binding site 3 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1002 b:15.0 occ:0.90 CU3 A:C2O1002 0.0 15.0 0.9 ND1 A:HIS62 2.0 13.0 1.0 NE2 A:HIS104 2.0 11.8 1.0 NE2 B:HIS254 2.1 13.9 1.0 O1 A:C2O1002 2.6 14.8 0.9 CE1 A:HIS62 3.0 12.3 1.0 CD2 A:HIS104 3.0 11.4 1.0 CE1 A:HIS104 3.0 11.4 1.0 CG A:HIS62 3.1 11.9 1.0 CE1 B:HIS254 3.1 13.7 1.0 CD2 B:HIS254 3.1 14.1 1.0 CB A:HIS62 3.4 11.6 1.0 CZ2 A:TRP102 3.5 10.6 1.0 CE2 A:TRP102 3.9 10.4 1.0 CU B:CU1003 3.9 19.5 0.7 CD2 A:HIS60 4.0 11.6 1.0 NE1 A:TRP102 4.0 10.6 1.0 NE2 A:HIS62 4.1 13.1 1.0 CG A:HIS104 4.1 10.9 1.0 ND1 A:HIS104 4.1 11.2 1.0 CD2 A:HIS62 4.2 12.6 1.0 ND1 B:HIS254 4.2 13.8 1.0 CH2 A:TRP102 4.3 10.5 1.0 CG B:HIS254 4.3 13.4 1.0 CD2 B:HIS204 4.3 10.2 1.0 NE2 B:HIS204 4.4 10.4 1.0 NE2 A:HIS60 4.4 11.1 1.0 CA A:HIS62 4.7 11.6 1.0 CD2 A:TRP102 4.9 9.9 1.0 CU2 A:C2O1002 5.0 15.2 0.9

Copper binding site 4 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu340 b:14.1 occ:0.90 CU2 A:C2O340 0.0 14.1 0.9 ND1 C:HIS62 2.0 10.9 1.0 NE2 C:HIS104 2.0 10.1 1.0 NE2 A:HIS254 2.2 14.2 1.0 O1 A:C2O340 2.6 13.6 0.9 CE1 C:HIS62 3.0 10.9 1.0 CD2 C:HIS104 3.0 9.8 1.0 CE1 C:HIS104 3.0 10.9 1.0 CG C:HIS62 3.0 10.8 1.0 CD2 A:HIS254 3.1 14.3 1.0 CE1 A:HIS254 3.2 14.5 1.0 CB C:HIS62 3.4 10.8 1.0 CZ2 C:TRP102 3.5 10.1 1.0 CU A:CU1003 3.9 19.0 0.7 CE2 C:TRP102 3.9 9.5 1.0 CD2 C:HIS60 4.0 10.4 1.0 NE1 C:TRP102 4.0 10.0 1.0 NE2 C:HIS62 4.1 10.7 1.0 ND1 C:HIS104 4.1 9.8 1.0 CG C:HIS104 4.1 9.7 1.0 CD2 C:HIS62 4.2 11.0 1.0 ND1 A:HIS254 4.3 13.2 1.0 CD2 A:HIS204 4.3 10.7 1.0 CG A:HIS254 4.3 13.4 1.0 CH2 C:TRP102 4.3 9.3 1.0 NE2 A:HIS204 4.4 10.7 1.0 NE2 C:HIS60 4.4 9.4 1.0 CA C:HIS62 4.7 10.7 1.0 CD2 C:TRP102 4.9 8.9 1.0 CU3 A:C2O340 4.9 14.3 0.9

Copper binding site 5 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu340 b:14.3 occ:0.90 CU3 A:C2O340 0.0 14.3 0.9 NE2 A:HIS252 2.0 15.5 1.0 NE2 A:HIS206 2.0 11.0 1.0 NE2 C:HIS106 2.1 12.6 1.0 O1 A:C2O340 2.4 13.6 0.9 CE1 A:HIS206 2.8 9.8 1.0 CE1 A:HIS252 3.0 14.7 1.0 CD2 A:HIS252 3.0 14.6 1.0 CE1 C:HIS106 3.0 13.5 1.0 CD2 C:HIS106 3.2 12.0 1.0 CD2 A:HIS206 3.2 10.4 1.0 CG2 A:ILE250 3.9 11.0 1.0 CD2 A:HIS204 3.9 10.7 1.0 ND1 A:HIS206 4.0 9.4 1.0 ND1 A:HIS252 4.1 14.3 1.0 CG A:HIS252 4.1 13.2 1.0 CU A:CU1003 4.1 19.0 0.7 ND1 C:HIS106 4.1 13.0 1.0 CG A:HIS206 4.2 9.5 1.0 CG C:HIS106 4.3 12.6 1.0 CD2 C:HIS60 4.4 10.4 1.0 NE2 C:HIS60 4.5 9.4 1.0 NE2 A:HIS204 4.6 10.7 1.0 CE1 C:HIS104 4.9 10.9 1.0 CU2 A:C2O340 4.9 14.1 0.9 CD2 A:HIS254 5.0 14.3 1.0

Copper binding site 6 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1003 b:19.0 occ:0.70 NE2 A:HIS204 1.8 10.7 1.0 NE2 C:HIS60 1.9 9.4 1.0 CD2 A:HIS204 2.7 10.7 1.0 CE1 C:HIS60 2.8 9.8 1.0 CD2 C:HIS60 2.9 10.4 1.0 CE1 A:HIS204 3.0 10.7 1.0 O C:HOH365 3.0 11.7 1.0 NE2 A:HIS206 3.2 11.0 1.0 O1 A:C2O340 3.2 13.6 0.9 CD2 A:HIS206 3.3 10.4 1.0 ND1 C:HIS62 3.5 10.9 1.0 CG C:HIS62 3.5 10.8 1.0 CE1 A:HIS206 3.6 9.8 1.0 CA C:HIS62 3.7 10.7 1.0 CB C:HIS62 3.8 10.8 1.0 CG A:HIS206 3.8 9.5 1.0 CU2 A:C2O340 3.9 14.1 0.9 CG A:HIS204 3.9 10.1 1.0 ND1 C:HIS60 4.0 10.0 1.0 ND1 A:HIS206 4.0 9.4 1.0 ND1 A:HIS204 4.0 10.3 1.0 CE1 C:HIS62 4.0 10.9 1.0 CG C:HIS60 4.0 10.1 1.0 CU3 A:C2O340 4.1 14.3 0.9 CD2 C:HIS62 4.1 11.0 1.0 NE2 C:HIS62 4.4 10.7 1.0 N C:GLY63 4.5 10.8 1.0 N C:HIS62 4.6 10.7 1.0 C C:HIS62 4.6 10.7 1.0 CA A:HIS206 4.7 9.0 1.0 CB A:HIS206 4.8 9.1 1.0 O C:HOH373 4.8 12.7 1.0 O C:TRP61 4.9 11.1 1.0 NE2 C:HIS104 4.9 10.1 1.0

Copper binding site 7 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu1003 b:19.5 occ:0.70 NE2 A:HIS60 1.9 11.1 1.0 NE2 B:HIS204 1.9 10.4 1.0 CD2 B:HIS204 2.8 10.2 1.0 CE1 A:HIS60 2.8 11.5 1.0 CD2 A:HIS60 2.9 11.6 1.0 CE1 B:HIS204 3.0 11.5 1.0 O A:HOH351 3.0 11.1 1.0 O1 A:C2O1002 3.1 14.8 0.9 NE2 B:HIS206 3.2 12.6 1.0 CD2 B:HIS206 3.3 11.4 1.0 ND1 A:HIS62 3.4 13.0 1.0 CG A:HIS62 3.6 11.9 1.0 CE1 B:HIS206 3.6 11.8 1.0 CA A:HIS62 3.7 11.6 1.0 CG B:HIS206 3.8 10.6 1.0 CB A:HIS62 3.8 11.6 1.0 ND1 A:HIS60 3.9 11.4 1.0 CU3 A:C2O1002 3.9 15.0 0.9 CG B:HIS204 3.9 10.5 1.0 ND1 B:HIS206 3.9 11.6 1.0 CG A:HIS60 4.0 11.9 1.0 CE1 A:HIS62 4.0 12.3 1.0 ND1 B:HIS204 4.0 10.8 1.0 CU2 A:C2O1002 4.1 15.2 0.9 CD2 A:HIS62 4.2 12.6 1.0 NE2 A:HIS62 4.4 13.1 1.0 N A:GLY63 4.5 11.9 1.0 CA B:HIS206 4.7 10.2 1.0 C A:HIS62 4.7 11.6 1.0 N A:HIS62 4.7 11.2 1.0 CB B:HIS206 4.7 10.5 1.0 O A:HOH380 4.8 13.7 1.0 O A:TRP61 4.9 10.5 1.0 NE2 A:HIS104 4.9 11.8 1.0

Copper binding site 8 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu1001 b:13.2 occ:1.00 ND1 B:HIS112 2.0 12.7 1.0 ND1 B:HIS57 2.1 10.2 1.0 SG B:CYS105 2.3 12.4 1.0 SD B:MET118 2.8 11.0 1.0 CE1 B:HIS112 3.0 12.9 1.0 CE1 B:HIS57 3.0 10.1 1.0 CG B:HIS112 3.1 12.2 1.0 CG B:HIS57 3.1 9.8 1.0 CB B:CYS105 3.2 11.1 1.0 CB B:HIS112 3.4 12.0 1.0 CB B:HIS57 3.5 10.6 1.0 CE B:MET118 3.5 10.0 1.0 CA B:HIS57 3.8 11.0 1.0 O B:VAL107 3.9 13.7 1.0 O B:PRO56 4.0 11.9 1.0 NE2 B:HIS112 4.1 11.8 1.0 NE2 B:HIS57 4.1 10.1 1.0 CD2 B:HIS112 4.2 12.9 1.0 CD2 B:HIS57 4.2 10.8 1.0 CB B:VAL107 4.3 13.4 1.0 CG B:MET118 4.4 10.0 1.0 CA B:CYS105 4.6 10.8 1.0 C B:VAL107 4.7 13.8 1.0 N B:HIS57 4.8 11.5 1.0 C B:PRO56 4.8 12.1 1.0 N B:VAL107 4.8 12.6 1.0 N B:THR58 4.8 10.2 1.0 CA B:VAL107 4.9 13.4 1.0 CA B:HIS112 4.9 12.2 1.0 CB B:MET118 4.9 9.3 1.0 C B:HIS57 4.9 10.8 1.0

Copper binding site 9 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu1002 b:13.6 occ:0.90 CU2 B:C2O1002 0.0 13.6 0.9 ND1 B:HIS62 2.0 10.8 1.0 NE2 B:HIS104 2.1 10.8 1.0 NE2 C:HIS254 2.1 12.9 1.0 O1 B:C2O1002 2.6 15.1 0.9 CE1 B:HIS62 2.9 11.3 1.0 CD2 B:HIS104 3.0 10.3 1.0 CG B:HIS62 3.0 10.1 1.0 CE1 B:HIS104 3.0 11.2 1.0 CD2 C:HIS254 3.1 13.3 1.0 CE1 C:HIS254 3.1 13.4 1.0 CB B:HIS62 3.4 10.3 1.0 CZ2 B:TRP102 3.5 8.8 1.0 CE2 B:TRP102 3.9 8.9 1.0 CU C:CU1003 3.9 17.9 0.7 NE1 B:TRP102 4.0 8.8 1.0 NE2 B:HIS62 4.1 10.9 1.0 CD2 B:HIS60 4.1 10.3 1.0 CD2 B:HIS62 4.1 11.0 1.0 ND1 B:HIS104 4.1 9.6 1.0 CG B:HIS104 4.2 9.7 1.0 ND1 C:HIS254 4.2 12.7 1.0 CG C:HIS254 4.3 12.2 1.0 CH2 B:TRP102 4.3 9.1 1.0 CD2 C:HIS204 4.3 9.8 1.0 NE2 C:HIS204 4.4 9.4 1.0 NE2 B:HIS60 4.4 9.7 1.0 CA B:HIS62 4.7 10.0 1.0 CD2 B:TRP102 4.9 8.3 1.0 CU3 B:C2O1002 5.0 13.5 0.9

Copper binding site 10 out of 12 in the Crystal Structure of the Novel Two-Domain Type Laccase From A Metagenome


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 the Novel Two-Domain Type Laccase From A Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu1002 b:13.5 occ:0.90 CU3 B:C2O1002 0.0 13.5 0.9 NE2 C:HIS252 2.0 13.4 1.0 NE2 C:HIS206 2.0 9.9 1.0 NE2 B:HIS106 2.1 12.6 1.0 O1 B:C2O1002 2.4 15.1 0.9 CE1 C:HIS206 2.8 10.2 1.0 CD2 C:HIS252 3.0 12.9 1.0 CE1 C:HIS252 3.0 13.7 1.0 CE1 B:HIS106 3.0 12.7 1.0 CD2 B:HIS106 3.1 12.4 1.0 CD2 C:HIS206 3.1 9.9 1.0 CG2 C:ILE250 3.9 10.4 1.0 CD2 C:HIS204 3.9 9.8 1.0 ND1 C:HIS206 4.0 8.9 1.0 ND1 C:HIS252 4.1 13.4 1.0 CG C:HIS252 4.1 12.1 1.0 CU C:CU1003 4.1 17.9 0.7 CG C:HIS206 4.2 8.8 1.0 ND1 B:HIS106 4.2 12.6 1.0 CG B:HIS106 4.3 11.8 1.0 CD2 B:HIS60 4.4 10.3 1.0 NE2 B:HIS60 4.5 9.7 1.0 NE2 C:HIS204 4.6 9.4 1.0 CD2 C:HIS254 5.0 13.3 1.0 CE1 B:HIS104 5.0 11.2 1.0 CU2 B:C2O1002 5.0 13.6 0.9

H.Komori, K.Miyazaki, Y.Higuchi. X-Ray Structure of A Two-Domain Type Laccase: A Missing Link in the Evolution of Multi-Copper Proteins Febs Lett. V. 583 1189 2009.
ISSN: ISSN 0014-5793
PubMed: 19285076
DOI: 10.1016/J.FEBSLET.2009.03.008