Copper in PDB 3t6x: Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)

The structure of Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose), PDB code: 3t6x was solved by M.Ferraroni, F.Briganti, I.Matera, M.Kolomytseva, L.Golovleva, A.Scozzafava, A.M.Chernykh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.510, 140.040, 172.980, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.6

Pages:

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

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) (pdb code 3t6x). 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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose), PDB code: 3t6x:
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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:18.8 occ:1.00 ND1 A:HIS397 2.0 23.1 1.0 SG A:CYS453 2.0 19.2 1.0 ND1 A:HIS458 2.2 19.0 1.0 CE1 A:HIS397 2.9 22.6 1.0 CG A:HIS397 3.1 21.7 1.0 CG A:HIS458 3.2 18.0 1.0 CE1 A:HIS458 3.2 19.0 1.0 CB A:CYS453 3.3 16.3 1.0 CB A:HIS458 3.4 19.6 1.0 CB A:HIS397 3.5 18.6 1.0 CD1 A:ILE455 3.6 13.5 1.0 CD2 A:PHE463 3.8 21.9 1.0 CB A:ILE455 3.8 17.3 1.0 NE2 A:HIS397 4.0 23.5 1.0 CE2 A:PHE463 4.1 23.0 1.0 CA A:HIS397 4.1 18.0 1.0 CG1 A:ILE455 4.1 15.6 1.0 CD2 A:HIS397 4.2 22.6 1.0 NE2 A:HIS458 4.3 19.5 1.0 CD2 A:HIS458 4.3 17.1 1.0 CD A:PRO398 4.5 16.7 1.0 CA A:CYS453 4.6 17.3 1.0 N A:ILE455 4.6 17.7 1.0 CG2 A:ILE455 4.7 17.1 1.0 CA A:ILE455 4.8 17.4 1.0 CE1 A:PHE341 4.8 28.7 1.0 N A:GLY395 4.9 24.8 1.0 CZ A:PHE341 4.9 28.6 1.0 CA A:HIS458 5.0 20.1 1.0 O A:ILE455 5.0 17.2 1.0

Copper binding site 2 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:18.5 occ:1.00 O2 A:PER512 1.9 33.1 1.0 NE2 A:HIS454 2.0 16.1 1.0 O1 A:PER512 2.1 30.1 1.0 ND1 A:HIS67 2.1 8.9 1.0 NE2 A:HIS110 2.3 11.1 1.0 CD2 A:HIS454 2.9 16.7 1.0 CE1 A:HIS110 2.9 14.1 1.0 CE1 A:HIS67 3.0 11.2 1.0 CE1 A:HIS454 3.1 15.5 1.0 CG A:HIS67 3.2 13.2 1.0 CD2 A:HIS110 3.4 13.5 1.0 CB A:HIS67 3.6 12.6 1.0 CU A:CU504 3.7 16.0 1.0 CD2 A:HIS65 3.9 18.4 1.0 CU A:CU503 4.0 14.1 1.0 CD2 A:HIS400 4.0 15.8 1.0 CG A:HIS454 4.1 17.4 1.0 NE2 A:HIS400 4.1 18.6 1.0 CZ2 A:TRP108 4.1 7.6 1.0 ND1 A:HIS454 4.1 17.3 1.0 ND1 A:HIS110 4.2 14.0 1.0 NE2 A:HIS67 4.2 11.9 1.0 O A:HOH675 4.2 24.7 1.0 CD2 A:HIS67 4.3 12.4 1.0 NE2 A:HIS65 4.4 18.8 1.0 CG A:HIS110 4.4 13.3 1.0 CB A:ALA244 4.5 12.5 1.0 CE2 A:TRP108 4.5 8.4 1.0 CA A:HIS67 4.6 13.1 1.0 NE1 A:TRP108 4.7 5.4 1.0 CG A:HIS400 4.7 15.3 1.0 CH2 A:TRP108 4.8 8.9 1.0 CE1 A:HIS400 4.9 17.0 1.0 CE1 A:HIS452 4.9 14.9 1.0

Copper binding site 3 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:14.1 occ:1.00 NE2 A:HIS402 2.0 15.4 1.0 NE2 A:HIS452 2.1 15.5 1.0 O1 A:PER512 2.1 30.1 1.0 NE2 A:HIS112 2.1 9.5 1.0 O2 A:PER512 2.4 33.1 1.0 CE1 A:HIS402 2.9 16.7 1.0 CE1 A:HIS452 2.9 14.9 1.0 CD2 A:HIS112 3.0 9.2 1.0 CD2 A:HIS402 3.1 17.0 1.0 CE1 A:HIS112 3.2 11.0 1.0 CD2 A:HIS452 3.2 13.8 1.0 CD2 A:HIS400 3.7 15.8 1.0 O A:HOH675 3.8 24.7 1.0 CU A:CU504 3.9 16.0 1.0 CU A:CU502 4.0 18.5 1.0 ND1 A:HIS402 4.0 16.7 1.0 ND1 A:HIS452 4.1 14.1 1.0 CG A:HIS402 4.2 17.0 1.0 CG A:HIS112 4.2 12.5 1.0 CD2 A:HIS65 4.3 18.4 1.0 ND1 A:HIS112 4.3 11.4 1.0 NE2 A:HIS400 4.3 18.6 1.0 CG A:HIS452 4.3 14.1 1.0 NE2 A:HIS65 4.4 18.8 1.0 CD2 A:PHE450 4.5 14.2 1.0 CE1 A:HIS110 4.5 14.1 1.0 NE2 A:HIS454 4.7 16.1 1.0 CG A:HIS65 4.8 17.4 1.0 CD2 A:HIS454 4.8 16.7 1.0 CB A:PHE450 4.9 16.5 1.0 CG A:HIS400 4.9 15.3 1.0 NE2 A:HIS110 5.0 11.1 1.0 CE1 A:HIS65 5.0 18.9 1.0

Copper binding site 4 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu504 b:16.0 occ:1.00 NE2 A:HIS400 1.9 18.6 1.0 NE2 A:HIS65 2.0 18.8 1.0 O A:HOH1106 2.2 17.2 1.0 O2 A:PER512 2.5 33.1 1.0 CD2 A:HIS400 2.9 15.8 1.0 CD2 A:HIS65 2.9 18.4 1.0 CE1 A:HIS65 2.9 18.9 1.0 CE1 A:HIS400 2.9 17.0 1.0 CD2 A:HIS402 3.4 17.0 1.0 NE2 A:HIS402 3.4 15.4 1.0 ND1 A:HIS67 3.5 8.9 1.0 CG A:HIS402 3.7 17.0 1.0 CU A:CU502 3.7 18.5 1.0 CA A:HIS67 3.8 13.1 1.0 CE1 A:HIS402 3.8 16.7 1.0 CG A:HIS67 3.8 13.2 1.0 N A:GLY68 3.9 13.7 1.0 CU A:CU503 3.9 14.1 1.0 O1 A:PER512 3.9 30.1 1.0 ND1 A:HIS402 3.9 16.7 1.0 ND1 A:HIS65 4.0 18.9 1.0 CG A:HIS65 4.0 17.4 1.0 CE1 A:HIS67 4.0 11.2 1.0 ND1 A:HIS400 4.0 16.4 1.0 CG A:HIS400 4.0 15.3 1.0 CB A:HIS67 4.1 12.6 1.0 C A:HIS67 4.3 13.2 1.0 CA A:HIS402 4.4 16.9 1.0 CD2 A:HIS67 4.4 12.4 1.0 NE2 A:HIS67 4.5 11.9 1.0 CB A:HIS402 4.5 16.8 1.0 O A:HOH939 4.6 24.3 1.0 O A:HOH769 4.7 19.8 1.0 N A:HIS402 4.8 16.5 1.0 N A:HIS67 4.9 13.4 1.0 O A:TRP66 4.9 13.8 1.0 CA A:GLY68 5.0 14.4 1.0

Copper binding site 5 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu501 b:17.7 occ:1.00 ND1 B:HIS458 2.0 18.7 1.0 SG B:CYS453 2.0 19.7 1.0 CD2 B:HIS397 2.1 22.5 1.0 CG B:HIS458 3.0 18.9 1.0 CG B:HIS397 3.0 23.0 1.0 CE1 B:HIS458 3.0 15.7 1.0 NE2 B:HIS397 3.1 23.4 1.0 CB B:CYS453 3.3 19.4 1.0 CB B:HIS458 3.3 21.4 1.0 CB B:HIS397 3.5 22.6 1.0 CD2 B:PHE463 3.7 21.1 1.0 CD1 B:ILE455 3.7 18.5 1.0 CB B:ILE455 3.8 21.3 1.0 CG1 B:ILE455 3.9 21.3 1.0 CE2 B:PHE463 4.0 21.6 1.0 CA B:HIS397 4.1 22.6 1.0 NE2 B:HIS458 4.1 16.6 1.0 CD2 B:HIS458 4.2 15.1 1.0 ND1 B:HIS397 4.2 23.7 1.0 CE1 B:HIS397 4.2 22.2 1.0 CA B:CYS453 4.6 19.3 1.0 CG2 B:ILE455 4.7 21.2 1.0 CD B:PRO398 4.8 21.2 1.0 N B:ILE455 4.8 20.9 1.0 CE1 B:PHE341 4.8 23.6 1.0 CZ B:PHE341 4.9 22.5 1.0 CA B:HIS458 4.9 22.1 1.0 CG B:PHE463 4.9 22.4 1.0 CA B:ILE455 4.9 21.4 1.0 O B:GLY394 4.9 29.4 1.0

Copper binding site 6 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu502 b:21.6 occ:1.00 ND1 B:HIS67 2.0 14.8 1.0 NE2 B:HIS454 2.0 16.3 1.0 O1 B:PER514 2.2 36.1 1.0 O2 B:PER514 2.2 37.2 1.0 NE2 B:HIS110 2.2 19.8 1.0 CE1 B:HIS67 2.9 15.1 1.0 CE1 B:HIS110 2.9 19.3 1.0 CE1 B:HIS454 3.0 18.5 1.0 CD2 B:HIS454 3.0 18.6 1.0 CG B:HIS67 3.1 14.0 1.0 CD2 B:HIS110 3.4 20.1 1.0 CB B:HIS67 3.5 14.8 1.0 CU B:CU504 3.8 20.9 1.0 CD2 B:HIS65 3.9 15.4 1.0 CD2 B:HIS400 4.0 17.9 1.0 NE2 B:HIS67 4.0 17.2 1.0 CU B:CU503 4.1 18.8 1.0 NE2 B:HIS400 4.1 17.3 1.0 ND1 B:HIS454 4.1 17.9 1.0 ND1 B:HIS110 4.1 19.1 1.0 CG B:HIS454 4.1 19.1 1.0 CZ2 B:TRP108 4.1 13.4 1.0 CD2 B:HIS67 4.2 13.8 1.0 O B:HOH996 4.2 35.4 1.0 CG B:HIS110 4.4 18.4 1.0 NE2 B:HIS65 4.4 13.6 1.0 CE2 B:TRP108 4.5 12.3 1.0 CB B:ALA244 4.5 13.7 1.0 CA B:HIS67 4.6 15.3 1.0 NE1 B:TRP108 4.6 13.6 1.0 CG B:HIS400 4.8 17.3 1.0 CH2 B:TRP108 4.9 10.6 1.0 CE1 B:HIS400 5.0 16.6 1.0 CE1 B:HIS452 5.0 21.8 1.0

Copper binding site 7 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu503 b:18.8 occ:1.00 O1 B:PER514 2.0 36.1 1.0 NE2 B:HIS402 2.0 18.0 1.0 NE2 B:HIS112 2.0 21.2 1.0 NE2 B:HIS452 2.1 20.7 1.0 O2 B:PER514 2.3 37.2 1.0 CE1 B:HIS402 2.9 20.0 1.0 CE1 B:HIS452 3.0 21.8 1.0 CE1 B:HIS112 3.0 19.7 1.0 CD2 B:HIS112 3.0 20.1 1.0 CD2 B:HIS452 3.1 20.8 1.0 CD2 B:HIS402 3.1 19.2 1.0 O B:HOH996 3.6 35.4 1.0 CD2 B:HIS400 3.9 17.9 1.0 CU B:CU504 4.0 20.9 1.0 ND1 B:HIS402 4.1 19.6 1.0 CU B:CU502 4.1 21.6 1.0 ND1 B:HIS452 4.1 21.5 1.0 ND1 B:HIS112 4.1 20.5 1.0 CD2 B:HIS65 4.2 15.4 1.0 CG B:HIS112 4.2 19.4 1.0 CG B:HIS402 4.2 19.6 1.0 CG B:HIS452 4.2 20.6 1.0 NE2 B:HIS65 4.4 13.6 1.0 NE2 B:HIS400 4.4 17.3 1.0 CD2 B:PHE450 4.5 24.1 1.0 CE1 B:HIS110 4.5 19.3 1.0 NE2 B:HIS454 4.6 16.3 1.0 CG B:HIS65 4.8 15.5 1.0 CD2 B:HIS454 4.8 18.6 1.0 CB B:PHE450 4.9 22.5 1.0

Copper binding site 8 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu504 b:20.9 occ:1.00 NE2 B:HIS65 2.0 13.6 1.0 NE2 B:HIS400 2.0 17.3 1.0 O B:HOH1037 2.1 20.6 1.0 O2 B:PER514 2.4 37.2 1.0 CD2 B:HIS65 2.9 15.4 1.0 CE1 B:HIS400 3.0 16.6 1.0 CD2 B:HIS400 3.0 17.9 1.0 CE1 B:HIS65 3.1 16.4 1.0 ND1 B:HIS67 3.4 14.8 1.0 CD2 B:HIS402 3.4 19.2 1.0 NE2 B:HIS402 3.5 18.0 1.0 CA B:HIS67 3.6 15.3 1.0 CG B:HIS67 3.6 14.0 1.0 CU B:CU502 3.8 21.6 1.0 N B:GLY68 3.8 15.5 1.0 O1 B:PER514 3.8 36.1 1.0 CG B:HIS402 3.8 19.6 1.0 CE1 B:HIS67 3.9 15.1 1.0 CB B:HIS67 3.9 14.8 1.0 CE1 B:HIS402 4.0 20.0 1.0 CU B:CU503 4.0 18.8 1.0 CG B:HIS65 4.1 15.5 1.0 ND1 B:HIS65 4.1 16.0 1.0 ND1 B:HIS400 4.1 16.8 1.0 CG B:HIS400 4.2 17.3 1.0 ND1 B:HIS402 4.2 19.6 1.0 C B:HIS67 4.2 15.5 1.0 CD2 B:HIS67 4.3 13.8 1.0 NE2 B:HIS67 4.4 17.2 1.0 CA B:HIS402 4.4 20.8 1.0 O B:HOH665 4.5 17.3 1.0 O B:HOH723 4.5 18.4 1.0 CB B:HIS402 4.6 20.5 1.0 N B:HIS67 4.7 15.8 1.0 N B:HIS402 4.8 20.2 1.0 CA B:GLY68 4.9 15.6 1.0 O B:LEU401 4.9 19.6 1.0 O B:TRP66 4.9 16.1 1.0

Copper binding site 9 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu501 b:22.0 occ:1.00 ND1 C:HIS397 2.1 26.6 1.0 SG C:CYS453 2.1 19.5 1.0 ND1 C:HIS458 2.1 25.4 1.0 CG C:HIS397 3.0 27.6 1.0 CE1 C:HIS397 3.1 28.2 1.0 CG C:HIS458 3.1 22.9 1.0 CE1 C:HIS458 3.1 23.9 1.0 CB C:CYS453 3.3 18.9 1.0 CB C:HIS397 3.3 25.8 1.0 CB C:HIS458 3.4 22.6 1.0 CD1 C:ILE455 3.8 22.2 1.0 CD2 C:PHE463 3.8 22.8 1.0 CA C:HIS397 3.9 25.8 1.0 CB C:ILE455 3.9 20.4 1.0 CG1 C:ILE455 4.1 20.0 1.0 NE2 C:HIS397 4.1 27.3 1.0 CD2 C:HIS397 4.1 27.5 1.0 CE2 C:PHE463 4.2 20.8 1.0 NE2 C:HIS458 4.2 22.7 1.0 CD2 C:HIS458 4.3 23.1 1.0 O C:GLY394 4.5 32.7 1.0 CD C:PRO398 4.6 23.5 1.0 CA C:CYS453 4.7 19.3 1.0 N C:ILE455 4.7 19.9 1.0 CG2 C:ILE455 4.8 21.2 1.0 N C:HIS397 4.8 26.1 1.0 CA C:ILE455 4.9 20.4 1.0 O C:ILE455 4.9 21.1 1.0 C C:HIS397 4.9 24.8 1.0 CA C:HIS458 4.9 22.2 1.0

Copper binding site 10 out of 12 in the Crystal Structure of Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose)


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 Steccherinum Ochraceum Laccase Obtained By Multi- Crystals Composite Data Collection Technique (20% Dose) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu502 b:20.4 occ:1.00 O1 C:PER510 2.0 20.6 1.0 NE2 C:HIS454 2.1 12.8 1.0 ND1 C:HIS67 2.2 19.3 1.0 O2 C:PER510 2.2 18.9 1.0 NE2 C:HIS110 2.3 13.5 1.0 CE1 C:HIS67 3.1 16.9 1.0 CE1 C:HIS110 3.1 11.9 1.0 CE1 C:HIS454 3.1 16.7 1.0 CD2 C:HIS454 3.1 15.5 1.0 CG C:HIS67 3.2 17.4 1.0 CD2 C:HIS110 3.4 11.8 1.0 CB C:HIS67 3.6 16.4 1.0 CD2 C:HIS65 3.7 18.4 1.0 CU C:CU504 3.8 19.3 1.0 CD2 C:HIS400 4.0 14.0 1.0 CU C:CU503 4.1 15.6 1.0 NE2 C:HIS400 4.1 15.8 1.0 CZ2 C:TRP108 4.1 13.7 1.0 NE2 C:HIS65 4.1 18.7 1.0 NE2 C:HIS67 4.2 18.9 1.0 ND1 C:HIS454 4.2 17.1 1.0 CG C:HIS454 4.3 17.1 1.0 ND1 C:HIS110 4.3 11.9 1.0 CD2 C:HIS67 4.3 17.8 1.0 CG C:HIS110 4.5 13.7 1.0 O C:HOH804 4.5 23.6 1.0 CE2 C:TRP108 4.5 13.4 1.0 NE1 C:TRP108 4.5 13.9 1.0 CB C:ALA244 4.6 15.0 1.0 CA C:HIS67 4.6 16.6 1.0 CG C:HIS400 4.8 17.5 1.0 CH2 C:TRP108 4.8 13.3 1.0 CE1 C:HIS400 4.9 15.1 1.0 CG C:HIS65 5.0 16.9 1.0 CE1 C:HIS452 5.0 15.0 1.0

M.Ferraroni, I.Matera, A.Chernykh, M.Kolomytseva, L.A.Golovleva, A.Scozzafava, F.Briganti. Reaction Intermediates and Redox State Changes in A Blue Laccase From Steccherinum Ochraceum Observed By Crystallographic High/Low X-Ray Dose Experiments. J.Inorg.Biochem. V. 111 203 2012.
ISSN: ISSN 0162-0134
PubMed: 22341982
DOI: 10.1016/J.JINORGBIO.2012.01.011