Atomistry » Copper » PDB 3f00-3ie9 » 3fu8
Atomistry »
  Copper »
    PDB 3f00-3ie9 »
      3fu8 »

Copper in PDB 3fu8: Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol

Enzymatic activity of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol

All present enzymatic activity of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol:
1.10.3.2;

Protein crystallography data

The structure of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol, PDB code: 3fu8 was solved by J.P.Kallio, N.Hakulinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.78 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.710, 62.370, 125.140, 90.00, 96.36, 90.00
R / Rfree (%) 20.3 / 25.6

Other elements in 3fu8:

The structure of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol (pdb code 3fu8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol, PDB code: 3fu8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 1 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:14.2
occ:1.00
 ND1 A:HIS508 2.0 14.7 1.0
ND1 A:HIS431 2.0 11.5 1.0
SG A:CYS503 2.1 13.0 1.0
CE1 A:HIS431 3.0 15.1 1.0
CG A:HIS508 3.0 12.2 1.0
CE1 A:HIS508 3.0 15.0 1.0
CG A:HIS431 3.1 10.3 1.0
CB A:CYS503 3.2 10.8 1.0
CB A:HIS508 3.3 10.5 1.0
CB A:HIS431 3.5 10.3 1.0
CD1 A:LEU513 3.6 12.5 1.0
CD1 A:ILE505 3.8 9.2 1.0
CA A:HIS431 4.0 9.1 1.0
NE2 A:HIS508 4.1 14.7 1.0
NE2 A:HIS431 4.1 13.1 1.0
CD2 A:HIS508 4.1 12.8 1.0
CB A:ILE505 4.1 9.0 1.0
CD2 A:HIS431 4.2 10.7 1.0
CD A:PRO432 4.3 9.2 1.0
CG1 A:ILE505 4.4 9.5 1.0
O A:PRO430 4.4 11.1 1.0
CA A:CYS503 4.6 9.9 1.0
CA A:HIS508 4.8 11.7 1.0
N A:ILE505 4.9 9.2 1.0
CG A:LEU513 4.9 13.3 1.0
C A:HIS431 5.0 9.2 1.0
N A:PRO432 5.0 9.0 1.0
CG2 A:ILE505 5.0 8.7 1.0

Copper binding site 2 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 2 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:16.9
occ:1.00
 NE2 A:HIS436 2.0 16.2 1.0
NE2 A:HIS502 2.0 14.0 1.0
NE2 A:HIS140 2.2 13.7 1.0
O A:HOH1176 2.3 19.6 1.0
CE1 A:HIS436 2.8 10.7 1.0
CD2 A:HIS502 3.0 12.8 1.0
CE1 A:HIS502 3.0 15.0 1.0
CE1 A:HIS140 3.1 15.3 1.0
CD2 A:HIS436 3.2 10.6 1.0
CD2 A:HIS140 3.2 16.7 1.0
ND1 A:HIS436 4.0 12.8 1.0
CD2 A:HIS434 4.0 12.1 1.0
CU A:CU604 4.1 17.0 1.0
CD2 A:HIS93 4.1 11.9 1.0
ND1 A:HIS502 4.1 16.3 1.0
CG A:HIS502 4.1 12.4 1.0
O A:HOH1137 4.2 26.5 1.0
CG A:HIS436 4.2 11.1 1.0
ND1 A:HIS140 4.2 17.8 1.0
NE2 A:HIS93 4.2 14.2 1.0
CG A:HIS140 4.3 14.2 1.0
CD1 A:LEU500 4.4 12.5 1.0
O A:HOH1118 4.6 68.3 1.0
CB A:LEU500 4.6 10.4 1.0
NE2 A:HIS434 4.6 14.7 1.0
CG A:HIS93 4.8 10.7 1.0
O A:HOH1161 4.8 56.9 1.0
CU A:CU603 4.9 13.9 1.0
CE1 A:HIS93 5.0 14.9 1.0
CE1 A:HIS138 5.0 11.2 1.0

Copper binding site 3 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 3 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:13.9
occ:1.00
 ND1 A:HIS95 2.0 8.2 1.0
NE2 A:HIS138 2.1 12.6 1.0
NE2 A:HIS504 2.1 12.6 1.0
O A:HOH1176 2.6 19.6 1.0
CE1 A:HIS95 3.0 12.7 1.0
CD2 A:HIS138 3.0 9.6 1.0
CG A:HIS95 3.0 10.3 1.0
CD2 A:HIS504 3.1 7.7 1.0
CE1 A:HIS504 3.1 9.9 1.0
CE1 A:HIS138 3.1 11.2 1.0
CB A:HIS95 3.4 11.3 1.0
CZ2 A:TRP136 3.5 5.8 1.0
CE2 A:TRP136 3.9 11.7 1.0
CD2 A:HIS93 4.0 11.9 1.0
CU A:CU604 4.0 17.0 1.0
NE2 A:HIS95 4.1 11.2 1.0
CD2 A:HIS95 4.2 13.7 1.0
NE1 A:TRP136 4.2 10.7 1.0
CG A:HIS138 4.2 8.4 1.0
CH2 A:TRP136 4.2 12.7 1.0
ND1 A:HIS138 4.2 10.2 1.0
ND1 A:HIS504 4.2 7.6 1.0
CG A:HIS504 4.3 8.8 1.0
NE2 A:HIS434 4.3 14.7 1.0
CD2 A:HIS434 4.3 12.1 1.0
NE2 A:HIS93 4.5 14.2 1.0
O A:HOH1137 4.6 26.5 1.0
CA A:HIS95 4.7 11.6 1.0
CD2 A:TRP136 4.9 9.0 1.0
CU A:CU602 4.9 16.9 1.0

Copper binding site 4 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 4 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:17.0
occ:1.00
 NE2 A:HIS93 1.9 14.2 1.0
NE2 A:HIS434 2.0 14.7 1.0
CD2 A:HIS93 2.8 11.9 1.0
CD2 A:HIS434 2.8 12.1 1.0
CL A:CL610 2.8 22.9 1.0
CE1 A:HIS93 2.9 14.9 1.0
CE1 A:HIS434 3.0 15.7 1.0
NE2 A:HIS436 3.3 16.2 1.0
O A:HOH1176 3.3 19.6 1.0
CD2 A:HIS436 3.3 10.6 1.0
ND1 A:HIS95 3.7 8.2 1.0
CG A:HIS95 3.7 10.3 1.0
CE1 A:HIS436 3.8 10.7 1.0
CG A:HIS436 3.9 11.1 1.0
CA A:HIS95 3.9 11.6 1.0
CB A:HIS95 3.9 11.3 1.0
CG A:HIS93 4.0 10.7 1.0
ND1 A:HIS93 4.0 11.7 1.0
CG A:HIS434 4.0 12.4 1.0
CU A:CU603 4.0 13.9 1.0
CU A:CU602 4.1 16.9 1.0
ND1 A:HIS434 4.1 11.9 1.0
ND1 A:HIS436 4.1 12.8 1.0
CE1 A:HIS95 4.2 12.7 1.0
CD2 A:HIS95 4.3 13.7 1.0
NE2 A:HIS95 4.6 11.2 1.0
N A:GLY96 4.6 14.1 1.0
CA A:HIS436 4.6 10.2 1.0
CB A:HIS436 4.8 10.6 1.0
C A:HIS95 4.8 12.6 1.0
N A:HIS95 4.8 11.6 1.0
O A:LEU435 4.8 9.4 1.0
N A:HIS436 5.0 10.8 1.0
O A:TRP94 5.0 12.4 1.0
O A:HOH672 5.0 16.6 1.0

Copper binding site 5 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 5 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:14.5
occ:1.00
 SG B:CYS503 2.1 12.1 1.0
ND1 B:HIS431 2.1 14.7 1.0
ND1 B:HIS508 2.1 10.5 1.0
CG B:HIS508 3.0 11.1 1.0
CE1 B:HIS431 3.1 15.9 1.0
CG B:HIS431 3.1 13.4 1.0
CE1 B:HIS508 3.1 11.5 1.0
CB B:CYS503 3.2 12.4 1.0
CB B:HIS508 3.2 9.2 1.0
CB B:HIS431 3.4 13.8 1.0
CD1 B:ILE505 3.7 9.2 1.0
CD1 B:LEU513 3.8 14.3 1.0
CA B:HIS431 4.0 12.4 1.0
CB B:ILE505 4.2 11.2 1.0
NE2 B:HIS431 4.2 15.0 1.0
CD2 B:HIS508 4.2 12.1 1.0
CD2 B:HIS431 4.2 13.9 1.0
NE2 B:HIS508 4.2 12.4 1.0
CD B:PRO432 4.3 12.3 1.0
CG1 B:ILE505 4.3 10.8 1.0
O B:PRO430 4.5 14.7 1.0
CA B:CYS503 4.5 12.2 1.0
CA B:HIS508 4.8 10.9 1.0
N B:ILE505 4.9 10.4 1.0
C B:HIS431 4.9 12.9 1.0
N B:PRO432 4.9 12.3 1.0
N B:HIS431 5.0 12.7 1.0

Copper binding site 6 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 6 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:17.4
occ:1.00
 NE2 B:HIS436 2.0 11.4 1.0
NE2 B:HIS502 2.0 14.8 1.0
NE2 B:HIS140 2.2 16.0 1.0
O B:HOH717 2.2 16.9 1.0
CE1 B:HIS436 2.9 14.5 1.0
CD2 B:HIS502 2.9 13.1 1.0
CE1 B:HIS502 3.0 14.7 1.0
CD2 B:HIS436 3.1 10.5 1.0
CD2 B:HIS140 3.2 17.9 1.0
CE1 B:HIS140 3.2 18.2 1.0
CD2 B:HIS434 4.0 10.8 1.0
ND1 B:HIS436 4.0 11.2 1.0
CG B:HIS502 4.1 12.1 1.0
CU B:CU604 4.1 17.2 1.0
ND1 B:HIS502 4.1 13.5 1.0
CD2 B:HIS93 4.1 14.2 1.0
CG B:HIS436 4.2 10.5 1.0
NE2 B:HIS93 4.2 13.8 1.0
CD1 B:LEU500 4.3 9.7 1.0
ND1 B:HIS140 4.3 17.9 1.0
CG B:HIS140 4.3 15.5 1.0
O B:HOH1019 4.4 20.2 1.0
NE2 B:HIS434 4.5 9.9 1.0
CB B:LEU500 4.6 8.8 1.0
CG B:HIS93 4.9 12.6 1.0
CU B:CU603 4.9 13.5 1.0
CE1 B:HIS138 5.0 11.1 1.0
CE1 B:HIS93 5.0 13.7 1.0
O B:HOH1355 5.0 48.1 1.0

Copper binding site 7 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 7 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:13.5
occ:1.00
 NE2 B:HIS138 2.0 12.2 1.0
ND1 B:HIS95 2.0 14.6 1.0
NE2 B:HIS504 2.1 12.2 1.0
O B:HOH717 2.7 16.9 1.0
CD2 B:HIS138 3.0 11.3 1.0
CE1 B:HIS138 3.0 11.1 1.0
CE1 B:HIS504 3.0 12.6 1.0
CE1 B:HIS95 3.0 15.8 1.0
CG B:HIS95 3.0 12.4 1.0
CD2 B:HIS504 3.2 11.5 1.0
CB B:HIS95 3.4 11.2 1.0
CZ2 B:TRP136 3.5 7.1 1.0
CE2 B:TRP136 4.0 11.6 1.0
CD2 B:HIS93 4.0 14.2 1.0
ND1 B:HIS138 4.1 11.2 1.0
CU B:CU604 4.1 17.2 1.0
CG B:HIS138 4.1 11.3 1.0
CH2 B:TRP136 4.1 12.2 1.0
NE2 B:HIS95 4.1 13.7 1.0
ND1 B:HIS504 4.1 10.5 1.0
CD2 B:HIS95 4.2 15.9 1.0
CG B:HIS504 4.2 12.1 1.0
NE1 B:TRP136 4.3 13.1 1.0
CD2 B:HIS434 4.3 10.8 1.0
NE2 B:HIS434 4.4 9.9 1.0
NE2 B:HIS93 4.6 13.8 1.0
CA B:HIS95 4.6 12.4 1.0
O B:HOH1019 4.8 20.2 1.0
CD2 B:TRP136 4.9 11.4 1.0
CU B:CU602 4.9 17.4 1.0
CZ3 B:TRP136 5.0 11.9 1.0

Copper binding site 8 out of 8 in 3fu8

Go back to Copper Binding Sites List in 3fu8
Copper binding site 8 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:17.2
occ:1.00
 NE2 B:HIS434 2.0 9.9 1.0
NE2 B:HIS93 2.0 13.8 1.0
CL B:CL610 2.9 24.2 1.0
CD2 B:HIS93 2.9 14.2 1.0
CD2 B:HIS434 2.9 10.8 1.0
CE1 B:HIS434 2.9 12.8 1.0
CE1 B:HIS93 3.0 13.7 1.0
O B:HOH717 3.3 16.9 1.0
CD2 B:HIS436 3.5 10.5 1.0
NE2 B:HIS436 3.5 11.4 1.0
ND1 B:HIS95 3.7 14.6 1.0
CG B:HIS95 3.8 12.4 1.0
CA B:HIS95 3.8 12.4 1.0
CG B:HIS436 3.9 10.5 1.0
CE1 B:HIS436 3.9 14.5 1.0
CB B:HIS95 4.0 11.2 1.0
ND1 B:HIS434 4.0 11.2 1.0
CG B:HIS434 4.1 13.1 1.0
CG B:HIS93 4.1 12.6 1.0
CU B:CU603 4.1 13.5 1.0
ND1 B:HIS93 4.1 11.6 1.0
CU B:CU602 4.1 17.4 1.0
ND1 B:HIS436 4.1 11.2 1.0
CE1 B:HIS95 4.3 15.8 1.0
CD2 B:HIS95 4.3 15.9 1.0
N B:GLY96 4.4 15.2 1.0
NE2 B:HIS95 4.6 13.7 1.0
CA B:HIS436 4.6 9.7 1.0
C B:HIS95 4.6 14.3 1.0
N B:HIS95 4.7 12.8 1.0
CB B:HIS436 4.8 10.4 1.0
O B:TRP94 4.8 12.7 1.0
O B:LEU435 4.9 9.1 1.0
N B:HIS436 5.0 10.5 1.0

Reference:

J.P.Kallio, S.Auer, J.Janis, M.Andberg, K.Kruus, J.Rouvinen, A.Koivula, N.Hakulinen. Structure-Function Studies of A Melanocarpus Albomyces Laccase Suggest A Pathway For Oxidation of Phenolic Compounds. J.Mol.Biol. V. 392 895 2009.
ISSN: ISSN 0022-2836
PubMed: 19563811
DOI: 10.1016/J.JMB.2009.06.053
Page generated: Wed Jul 31 00:56:06 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy