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Copper in PDB 1bt1: Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State

Enzymatic activity of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State

All present enzymatic activity of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State:
1.10.3.1;

Protein crystallography data

The structure of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State, PDB code: 1bt1 was solved by T.Klabunde, C.Eicken, J.C.Sacchettini, B.Krebs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.820, 164.750, 52.160, 90.00, 97.50, 90.00
R / Rfree (%) 16.8 / 25.6

Copper Binding Sites:

The binding sites of Copper atom in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State (pdb code 1bt1). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State, PDB code: 1bt1:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1bt1

Go back to Copper Binding Sites List in 1bt1
Copper binding site 1 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu500

b:17.2
occ:1.00
CU2 A:C2O500 0.0 17.2 1.0
O1 A:C2O500 1.9 10.5 1.0
NE2 A:HIS88 2.0 9.1 1.0
NE2 A:HIS109 2.2 16.8 1.0
NE2 A:HIS118 2.3 15.6 1.0
CE1 A:HIS88 3.0 3.6 1.0
CU3 A:C2O500 3.0 12.0 1.0
CD2 A:HIS109 3.0 14.0 1.0
CD2 A:HIS88 3.1 5.5 1.0
CE1 A:HIS118 3.1 15.6 1.0
CD2 A:HIS118 3.2 15.6 1.0
CE1 A:HIS109 3.4 11.4 1.0
SG A:CYS92 3.9 15.4 1.0
ND1 A:HIS88 4.1 4.6 1.0
CG A:HIS88 4.2 2.4 1.0
ND1 A:HIS118 4.2 12.6 1.0
CG A:HIS109 4.3 9.8 1.0
NE2 A:HIS274 4.3 8.3 1.0
CE1 A:HIS274 4.3 11.8 1.0
CG A:HIS118 4.3 12.4 1.0
ND1 A:HIS109 4.4 5.9 1.0
CZ A:PHE270 4.4 2.3 1.0
CE2 A:PHE270 4.5 6.7 1.0
NE2 A:HIS240 4.7 6.8 1.0
CE1 A:PHE114 4.7 7.2 1.0
CD1 A:PHE261 4.8 13.6 1.0
CE1 A:HIS240 4.9 8.9 1.0
CE1 A:PHE261 4.9 16.6 1.0
CG A:PHE261 5.0 17.3 1.0

Copper binding site 2 out of 4 in 1bt1

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Copper binding site 2 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu500

b:12.0
occ:1.00
CU3 A:C2O500 0.0 12.0 1.0
O1 A:C2O500 1.9 10.5 1.0
NE2 A:HIS240 2.1 6.8 1.0
NE2 A:HIS274 2.2 8.3 1.0
NE2 A:HIS244 2.3 11.1 1.0
CE1 A:HIS274 2.9 11.8 1.0
CE1 A:HIS240 2.9 8.9 1.0
CE1 A:HIS244 3.0 10.6 1.0
CU2 A:C2O500 3.0 17.2 1.0
CD2 A:HIS240 3.2 4.3 1.0
CD2 A:HIS274 3.2 10.0 1.0
CD2 A:HIS244 3.3 10.9 1.0
ND1 A:HIS274 4.0 10.1 1.0
ND1 A:HIS240 4.1 6.0 1.0
ND1 A:HIS244 4.1 8.5 1.0
CG A:HIS274 4.2 9.7 1.0
CG A:HIS240 4.2 5.2 1.0
NE2 A:HIS118 4.3 15.6 1.0
CG A:HIS244 4.3 5.5 1.0
CE2 A:PHE270 4.3 6.7 1.0
NE2 A:HIS88 4.4 9.1 1.0
CE1 A:PHE114 4.5 7.2 1.0
CE1 A:PHE261 4.6 16.6 1.0
CD2 A:HIS118 4.6 15.6 1.0
CE1 A:HIS88 4.7 3.6 1.0
NE2 A:HIS109 4.7 16.8 1.0
CZ A:PHE114 4.8 7.2 1.0
CZ A:PHE270 4.8 2.3 1.0
CD2 A:HIS109 4.8 14.0 1.0
CE1 A:HIS118 5.0 15.6 1.0

Copper binding site 3 out of 4 in 1bt1

Go back to Copper Binding Sites List in 1bt1
Copper binding site 3 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:16.1
occ:1.00
CU2 B:C2O500 0.0 16.1 1.0
O1 B:C2O500 1.9 11.7 1.0
NE2 B:HIS88 2.0 5.5 1.0
NE2 B:HIS109 2.2 15.2 1.0
NE2 B:HIS118 2.3 14.8 1.0
CE1 B:HIS88 2.9 3.4 1.0
CU3 B:C2O500 3.0 16.4 1.0
CD2 B:HIS109 3.0 14.8 1.0
CD2 B:HIS88 3.0 3.8 1.0
CE1 B:HIS118 3.2 13.0 1.0
CD2 B:HIS118 3.3 13.0 1.0
CE1 B:HIS109 3.3 11.2 1.0
SG B:CYS92 3.9 11.3 1.0
ND1 B:HIS88 4.0 5.5 1.0
CG B:HIS88 4.1 6.4 1.0
CG B:HIS109 4.2 10.8 1.0
NE2 B:HIS274 4.2 10.5 1.0
ND1 B:HIS118 4.3 10.5 1.0
ND1 B:HIS109 4.4 10.4 1.0
CE1 B:HIS274 4.4 13.1 1.0
CG B:HIS118 4.4 11.1 1.0
CZ B:PHE270 4.4 2.3 1.0
CE2 B:PHE270 4.5 2.5 1.0
CD1 B:PHE261 4.6 15.4 1.0
CE1 B:PHE261 4.7 17.1 1.0
NE2 B:HIS240 4.7 7.2 1.0
CE1 B:PHE114 4.8 8.0 1.0
CG B:PHE261 4.9 19.3 1.0
NE2 B:HIS244 5.0 10.8 1.0

Copper binding site 4 out of 4 in 1bt1

Go back to Copper Binding Sites List in 1bt1
Copper binding site 4 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes) in the Native Cu(II)-Cu(II) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:16.4
occ:1.00
CU3 B:C2O500 0.0 16.4 1.0
O1 B:C2O500 1.9 11.7 1.0
NE2 B:HIS240 2.1 7.2 1.0
NE2 B:HIS274 2.1 10.5 1.0
NE2 B:HIS244 2.3 10.8 1.0
CE1 B:HIS274 2.9 13.1 1.0
CE1 B:HIS240 2.9 12.0 1.0
CU2 B:C2O500 3.0 16.1 1.0
CE1 B:HIS244 3.1 10.7 1.0
CD2 B:HIS240 3.2 6.7 1.0
CD2 B:HIS274 3.2 11.8 1.0
CD2 B:HIS244 3.4 7.8 1.0
ND1 B:HIS274 4.0 9.7 1.0
ND1 B:HIS240 4.1 6.5 1.0
ND1 B:HIS244 4.2 10.0 1.0
CG B:HIS274 4.2 10.0 1.0
CG B:HIS240 4.2 4.7 1.0
NE2 B:HIS118 4.2 14.8 1.0
NE2 B:HIS88 4.3 5.5 1.0
CG B:HIS244 4.4 7.0 1.0
CE1 B:PHE261 4.4 17.1 1.0
CE2 B:PHE270 4.4 2.5 1.0
CE1 B:PHE114 4.5 8.0 1.0
CD2 B:HIS118 4.6 13.0 1.0
CE1 B:HIS88 4.7 3.4 1.0
NE2 B:HIS109 4.8 15.2 1.0
CZ B:PHE114 4.8 4.8 1.0
CD2 B:HIS109 4.8 14.8 1.0
CZ B:PHE270 4.9 2.3 1.0
CD1 B:PHE261 4.9 15.4 1.0
CZ B:PHE261 5.0 15.9 1.0
CE1 B:HIS118 5.0 13.0 1.0

Reference:

T.Klabunde, C.Eicken, J.C.Sacchettini, B.Krebs. Crystal Structure of A Plant Catechol Oxidase Containing A Dicopper Center. Nat.Struct.Biol. V. 5 1084 1998.
ISSN: ISSN 1072-8368
PubMed: 9846879
DOI: 10.1038/4193
Page generated: Wed Sep 2 21:37:37 2020
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