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Copper in PDB 1bug: Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu)

Enzymatic activity of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu)

All present enzymatic activity of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu):
1.10.3.1;

Protein crystallography data

The structure of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu), PDB code: 1bug 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 (%) 18.1 / 27.3

Copper Binding Sites:

The binding sites of Copper atom in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu) (pdb code 1bug). 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)- Inhibitor Complex with Phenylthiourea (Ptu), PDB code: 1bug:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1bug

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Copper binding site 1 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu)


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)- Inhibitor Complex with Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu500

b:15.7
occ:1.00
NE2 A:HIS88 2.0 2.1 1.0
NE2 A:HIS118 2.2 18.6 1.0
NE2 A:HIS109 2.2 13.2 1.0
S1 A:URS1002 2.3 14.3 1.0
CD2 A:HIS88 2.9 2.0 1.0
CE1 A:HIS88 3.1 2.0 1.0
CD2 A:HIS109 3.1 10.2 1.0
CD2 A:HIS118 3.1 13.0 1.0
CE1 A:HIS118 3.1 15.2 1.0
C7 A:URS1002 3.2 8.8 1.0
N2 A:URS1002 3.2 6.7 1.0
CE1 A:HIS109 3.3 12.5 1.0
SG A:CYS92 4.0 15.8 1.0
CG A:HIS88 4.1 4.6 1.0
ND1 A:HIS88 4.1 2.0 1.0
ND1 A:HIS118 4.2 9.9 1.0
CG A:HIS118 4.2 6.1 1.0
CU A:CU501 4.2 15.7 1.0
CG A:HIS109 4.3 13.9 1.0
CE1 A:HIS274 4.3 6.0 1.0
CZ A:PHE270 4.4 5.7 1.0
ND1 A:HIS109 4.4 9.4 1.0
CE2 A:PHE270 4.5 6.0 1.0
NE2 A:HIS274 4.6 2.0 1.0
N1 A:URS1002 4.6 11.0 1.0
CD2 A:PHE117 4.7 9.6 1.0
CE2 A:PHE117 4.7 4.7 1.0
CE1 A:PHE114 4.9 7.5 1.0

Copper binding site 2 out of 4 in 1bug

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Copper binding site 2 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu)


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)- Inhibitor Complex with Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:15.7
occ:1.00
NE2 A:HIS244 2.0 8.0 1.0
NE2 A:HIS240 2.1 10.2 1.0
NE2 A:HIS274 2.1 2.0 1.0
S1 A:URS1002 2.3 14.3 1.0
N1 A:URS1002 2.6 11.0 1.0
C7 A:URS1002 2.7 8.8 1.0
CE1 A:HIS244 2.8 4.5 1.0
CD2 A:HIS244 3.0 5.8 1.0
CE1 A:HIS240 3.0 10.3 1.0
CE1 A:HIS274 3.1 6.0 1.0
CD2 A:HIS274 3.1 6.4 1.0
CD2 A:HIS240 3.2 2.0 1.0
C3 A:URS1002 3.5 9.3 1.0
CE2 A:PHE270 3.8 6.0 1.0
ND1 A:HIS244 3.9 4.2 1.0
N2 A:URS1002 4.0 6.7 1.0
CG A:HIS244 4.0 6.5 1.0
C4 A:URS1002 4.0 7.2 1.0
ND1 A:HIS240 4.1 8.5 1.0
ND1 A:HIS274 4.2 8.6 1.0
CG A:HIS274 4.2 4.5 1.0
CU A:CU500 4.2 15.7 1.0
CG A:HIS240 4.2 2.8 1.0
CD2 A:PHE270 4.4 7.2 1.0
C2 A:URS1002 4.5 4.2 1.0
CZ A:PHE270 4.7 5.7 1.0
NE2 A:HIS88 4.8 2.1 1.0
ND1 A:HIS273 4.9 4.0 1.0
O A:HIS240 4.9 15.3 1.0
CE1 A:HIS88 5.0 2.0 1.0

Copper binding site 3 out of 4 in 1bug

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Copper binding site 3 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu)


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)- Inhibitor Complex with Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:13.2
occ:1.00
NE2 B:HIS118 2.1 16.7 1.0
NE2 B:HIS88 2.2 3.0 1.0
NE2 B:HIS109 2.2 14.9 1.0
S1 B:URS1002 2.2 11.7 1.0
CE1 B:HIS118 3.0 15.0 1.0
CD2 B:HIS88 3.0 4.0 1.0
CD2 B:HIS118 3.0 14.1 1.0
CD2 B:HIS109 3.0 15.2 1.0
C7 B:URS1002 3.3 11.3 1.0
CE1 B:HIS88 3.3 2.0 1.0
CE1 B:HIS109 3.3 13.6 1.0
N2 B:URS1002 3.4 11.1 1.0
SG B:CYS92 3.9 8.6 1.0
ND1 B:HIS118 4.1 12.7 1.0
CG B:HIS118 4.1 10.7 1.0
CU B:CU501 4.2 15.6 1.0
CG B:HIS88 4.2 2.0 1.0
CG B:HIS109 4.2 13.7 1.0
CE1 B:HIS274 4.3 9.6 1.0
ND1 B:HIS88 4.3 2.0 1.0
ND1 B:HIS109 4.3 11.6 1.0
CZ B:PHE270 4.4 2.0 1.0
NE2 B:HIS274 4.5 2.0 1.0
CE2 B:PHE270 4.6 2.0 1.0
N1 B:URS1002 4.7 11.4 1.0
CD2 B:PHE117 4.7 10.0 1.0
CE2 B:PHE117 4.7 2.0 1.0
CE1 B:PHE114 4.8 9.0 1.0

Copper binding site 4 out of 4 in 1bug

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Copper binding site 4 out of 4 in the Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex with Phenylthiourea (Ptu)


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)- Inhibitor Complex with Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:15.6
occ:1.00
NE2 B:HIS240 2.0 5.8 1.0
NE2 B:HIS244 2.1 2.0 1.0
NE2 B:HIS274 2.1 2.0 1.0
S1 B:URS1002 2.3 11.7 1.0
N1 B:URS1002 2.7 11.4 1.0
C7 B:URS1002 2.8 11.3 1.0
CE1 B:HIS240 2.9 10.9 1.0
CE1 B:HIS244 3.0 2.0 1.0
CD2 B:HIS244 3.0 3.8 1.0
CE1 B:HIS274 3.0 9.6 1.0
CD2 B:HIS240 3.1 2.5 1.0
CD2 B:HIS274 3.2 6.2 1.0
C3 B:URS1002 3.6 7.6 1.0
ND1 B:HIS244 4.0 6.5 1.0
CE2 B:PHE270 4.0 2.0 1.0
N2 B:URS1002 4.0 11.1 1.0
C4 B:URS1002 4.1 7.9 1.0
ND1 B:HIS240 4.1 10.7 1.0
CG B:HIS244 4.1 5.0 1.0
ND1 B:HIS274 4.2 13.1 1.0
CG B:HIS240 4.2 8.2 1.0
CU B:CU500 4.2 13.2 1.0
CG B:HIS274 4.3 4.7 1.0
CD2 B:PHE270 4.6 3.8 1.0
C2 B:URS1002 4.6 9.5 1.0
NE2 B:HIS88 4.8 3.0 1.0
CE1 B:PHE114 4.8 9.0 1.0
CZ B:PHE270 4.8 2.0 1.0
O B:HIS240 4.8 13.4 1.0
ND1 B:HIS273 5.0 3.0 1.0
CE1 B:HIS88 5.0 2.0 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 21:38:03 2020
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