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Copper in PDB 1aso: X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms

Enzymatic activity of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms

All present enzymatic activity of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms:
1.10.3.3;

Protein crystallography data

The structure of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms, PDB code: 1aso was solved by A.Messerschmidt, H.Luecke, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.090, 105.210, 112.660, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / n/a

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms (pdb code 1aso). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms, PDB code: 1aso:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 1aso

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Copper binding site 1 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu554

b:14.4
occ:1.00
 ND1 A:HIS512 2.1 6.0 1.0
ND1 A:HIS445 2.1 9.7 1.0
SG A:CYS507 2.2 7.0 1.0
SD A:MET517 3.0 13.4 1.0
CG A:HIS512 3.0 6.0 1.0
CE1 A:HIS512 3.0 6.0 1.0
CE1 A:HIS445 3.1 9.1 1.0
CG A:HIS445 3.1 9.5 1.0
CB A:CYS507 3.3 7.7 1.0
CB A:HIS512 3.4 6.0 1.0
CB A:HIS445 3.5 6.0 1.0
CE A:MET517 4.0 10.4 1.0
CA A:HIS445 4.1 8.4 1.0
NE2 A:HIS512 4.1 6.0 1.0
CB A:ILE509 4.1 6.8 1.0
NE2 A:HIS445 4.2 11.3 1.0
CD2 A:HIS512 4.2 6.0 1.0
CD2 A:HIS445 4.2 10.9 1.0
CD1 A:ILE509 4.2 6.0 1.0
CG A:MET517 4.4 9.0 1.0
CG1 A:ILE509 4.4 6.0 1.0
O A:HOH639 4.5 6.0 1.0
CA A:CYS507 4.7 9.9 1.0
CG2 A:ILE509 4.8 6.0 1.0
O A:THR444 4.9 15.8 1.0
CA A:HIS512 4.9 6.7 1.0
N A:ILE509 5.0 6.0 1.0

Copper binding site 2 out of 9 in 1aso

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Copper binding site 2 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu555

b:30.9
occ:1.00
 NE2 A:HIS506 2.0 22.1 1.0
NE2 A:HIS450 2.1 17.1 1.0
NE2 A:HIS106 2.2 27.4 1.0
CE1 A:HIS450 2.9 10.3 1.0
CE1 A:HIS506 2.9 18.8 1.0
CD2 A:HIS506 3.0 16.2 1.0
CD2 A:HIS450 3.1 12.0 1.0
CD2 A:HIS106 3.1 25.1 1.0
CE1 A:HIS106 3.1 31.6 1.0
O A:HOH700 3.8 36.4 1.0
CD2 A:HIS448 3.9 7.5 1.0
ND1 A:HIS506 4.0 16.3 1.0
ND1 A:HIS450 4.0 12.0 1.0
CG A:HIS506 4.1 13.2 1.0
CG A:HIS450 4.2 7.6 1.0
ND1 A:HIS106 4.2 27.3 1.0
CG A:HIS106 4.2 24.5 1.0
CU A:CU557 4.4 18.8 1.0
NE2 A:HIS448 4.6 8.3 1.0
CD2 A:HIS60 4.6 8.3 1.0
CB A:ALA504 4.7 7.7 1.0
NE2 A:HIS60 4.7 6.0 1.0
CE1 A:HIS104 4.8 10.4 1.0
CG2 A:THR75 4.9 6.0 1.0

Copper binding site 3 out of 9 in 1aso

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Copper binding site 3 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu556

b:14.1
occ:1.00
 ND1 A:HIS62 1.9 13.2 1.0
NE2 A:HIS104 2.0 12.2 1.0
NE2 A:HIS508 2.1 14.3 1.0
CE1 A:HIS62 2.8 12.9 1.0
CD2 A:HIS104 2.9 12.4 1.0
CE1 A:HIS104 2.9 10.4 1.0
CG A:HIS62 3.0 11.6 1.0
CE1 A:HIS508 3.0 6.0 1.0
CD2 A:HIS508 3.1 9.1 1.0
CB A:HIS62 3.5 9.8 1.0
NE2 A:HIS62 3.9 16.5 1.0
CE2 A:PHE102 4.0 11.5 1.0
ND1 A:HIS104 4.0 6.0 1.0
CG A:HIS104 4.0 10.9 1.0
CD2 A:HIS62 4.1 9.6 1.0
CU A:CU557 4.1 18.8 1.0
ND1 A:HIS508 4.2 6.8 1.0
CZ A:PHE102 4.2 8.9 1.0
CG A:HIS508 4.2 7.9 1.0
CD2 A:HIS60 4.3 8.3 1.0
CD2 A:HIS448 4.4 7.5 1.0
NE2 A:HIS448 4.4 8.3 1.0
CA A:HIS62 4.6 11.3 1.0
NE2 A:HIS60 4.7 6.0 1.0
CG A:HIS448 4.9 6.4 1.0
CE1 A:HIS448 4.9 7.6 1.0
CD2 A:PHE102 5.0 12.1 1.0
CA A:GLY259 5.0 8.4 1.0

Copper binding site 4 out of 9 in 1aso

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Copper binding site 4 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu557

b:18.8
occ:1.00
 NE2 A:HIS60 2.0 6.0 1.0
NE2 A:HIS448 2.1 8.3 1.0
O A:OH558 2.2 8.6 1.0
CE1 A:HIS60 2.9 6.0 1.0
CD2 A:HIS60 2.9 8.3 1.0
CE1 A:HIS448 3.0 7.6 1.0
CD2 A:HIS448 3.0 7.5 1.0
NE2 A:HIS450 3.6 17.1 1.0
CA A:HIS62 3.6 11.3 1.0
CG A:HIS62 3.7 11.6 1.0
CD2 A:HIS450 3.7 12.0 1.0
CE1 A:HIS450 3.8 10.3 1.0
ND1 A:HIS62 3.9 13.2 1.0
CB A:HIS62 3.9 9.8 1.0
ND1 A:HIS60 3.9 6.0 1.0
CG A:HIS450 4.0 7.6 1.0
CG A:HIS60 4.0 7.2 1.0
ND1 A:HIS450 4.0 12.0 1.0
ND1 A:HIS448 4.1 6.0 1.0
CG A:HIS448 4.1 6.4 1.0
N A:GLY63 4.1 13.9 1.0
CD2 A:HIS62 4.1 9.6 1.0
CU A:CU556 4.1 14.1 1.0
C A:HIS62 4.4 12.8 1.0
CU A:CU555 4.4 30.9 1.0
CE1 A:HIS62 4.4 12.9 1.0
N A:HIS62 4.5 12.9 1.0
NE2 A:HIS62 4.5 16.5 1.0
O A:HOH774 4.6 6.0 1.0
O A:TRP61 4.6 10.9 1.0
O A:HOH640 4.7 12.4 1.0
CA A:HIS450 4.7 7.9 1.0
CB A:HIS450 4.8 8.8 1.0
O A:LEU449 4.9 7.8 1.0
C A:TRP61 4.9 13.2 1.0
NE2 A:HIS104 4.9 12.2 1.0

Copper binding site 5 out of 9 in 1aso

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Copper binding site 5 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu559

b:77.8
occ:1.00
 NE2 B:HIS286 2.1 58.5 1.0
NE2 A:HIS286 2.1 52.1 1.0
CE1 A:HIS286 2.9 47.9 1.0
CE1 B:HIS286 3.0 58.5 1.0
CD2 B:HIS286 3.0 54.4 1.0
CD2 A:HIS286 3.0 45.2 1.0
O A:HOH891 3.3 49.3 1.0
O A:HOH619 4.0 50.4 1.0
ND1 A:HIS286 4.0 40.0 1.0
CG A:HIS286 4.0 36.7 1.0
ND1 B:HIS286 4.1 52.5 1.0
CG B:HIS286 4.1 47.4 1.0
O A:PRO287 4.1 20.7 1.0
O B:PRO287 4.4 23.3 1.0
CD A:PRO287 4.5 15.7 1.0

Copper binding site 6 out of 9 in 1aso

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Copper binding site 6 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu554

b:21.2
occ:1.00
 ND1 B:HIS512 2.1 18.4 1.0
ND1 B:HIS445 2.1 21.8 1.0
SG B:CYS507 2.1 18.4 1.0
SD B:MET517 2.9 21.1 1.0
CE1 B:HIS445 3.0 21.1 1.0
CE1 B:HIS512 3.1 17.4 1.0
CG B:HIS512 3.1 17.6 1.0
CG B:HIS445 3.1 20.1 1.0
CB B:CYS507 3.3 18.1 1.0
CB B:HIS512 3.4 20.6 1.0
CE B:MET517 3.5 20.4 1.0
CB B:HIS445 3.5 14.3 1.0
CB B:ILE509 4.1 16.7 1.0
NE2 B:HIS445 4.1 19.9 1.0
NE2 B:HIS512 4.2 18.8 1.0
CA B:HIS445 4.2 17.4 1.0
CD2 B:HIS445 4.3 18.8 1.0
CD1 B:ILE509 4.3 9.4 1.0
CD2 B:HIS512 4.3 18.9 1.0
O B:HOH660 4.4 22.8 1.0
CG1 B:ILE509 4.4 13.4 1.0
CG B:MET517 4.5 13.6 1.0
CA B:CYS507 4.6 18.4 1.0
CG2 B:ILE509 4.8 17.6 1.0
CA B:HIS512 4.9 19.5 1.0
O B:THR444 5.0 18.0 1.0
N B:ILE509 5.0 15.0 1.0

Copper binding site 7 out of 9 in 1aso

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Copper binding site 7 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu555

b:38.4
occ:1.00
 NE2 B:HIS506 2.1 29.6 1.0
NE2 B:HIS450 2.1 26.3 1.0
NE2 B:HIS106 2.1 36.4 1.0
CE1 B:HIS450 2.9 21.0 1.0
CE1 B:HIS506 2.9 26.8 1.0
CD2 B:HIS506 3.0 25.9 1.0
CD2 B:HIS106 3.0 33.8 1.0
CE1 B:HIS106 3.1 39.0 1.0
CD2 B:HIS450 3.1 21.0 1.0
O B:HOH720 3.6 43.2 1.0
CD2 B:HIS448 4.0 20.7 1.0
ND1 B:HIS506 4.0 22.6 1.0
CG B:HIS506 4.0 23.2 1.0
ND1 B:HIS450 4.1 20.2 1.0
CG B:HIS450 4.2 19.3 1.0
ND1 B:HIS106 4.2 36.5 1.0
CG B:HIS106 4.2 33.2 1.0
CU B:CU557 4.5 24.3 1.0
CD2 B:HIS60 4.6 19.9 1.0
NE2 B:HIS448 4.7 19.7 1.0
CB B:ALA504 4.7 14.9 1.0
NE2 B:HIS60 4.8 18.2 1.0
CE1 B:HIS104 4.9 16.2 1.0
CG2 B:THR75 4.9 21.3 1.0

Copper binding site 8 out of 9 in 1aso

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Copper binding site 8 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu556

b:33.1
occ:1.00
 NE2 B:HIS104 2.0 17.6 1.0
ND1 B:HIS62 2.1 21.5 1.0
NE2 B:HIS508 2.1 19.2 1.0
CE1 B:HIS104 2.9 16.2 1.0
CE1 B:HIS62 2.9 19.8 1.0
CD2 B:HIS104 2.9 16.8 1.0
CE1 B:HIS508 3.1 13.4 1.0
CD2 B:HIS508 3.1 17.9 1.0
CG B:HIS62 3.1 22.7 1.0
CB B:HIS62 3.6 17.8 1.0
CE2 B:PHE102 4.0 18.8 1.0
ND1 B:HIS104 4.0 14.6 1.0
CU B:CU557 4.0 24.3 1.0
CG B:HIS104 4.0 14.6 1.0
NE2 B:HIS62 4.1 15.7 1.0
ND1 B:HIS508 4.2 14.8 1.0
CG B:HIS508 4.2 16.6 1.0
CD2 B:HIS60 4.2 19.9 1.0
CD2 B:HIS62 4.2 15.4 1.0
CD2 B:HIS448 4.2 20.7 1.0
CZ B:PHE102 4.3 10.2 1.0
NE2 B:HIS448 4.4 19.7 1.0
NE2 B:HIS60 4.6 18.2 1.0
O B:HOH720 4.7 43.2 1.0
CA B:HIS62 4.7 20.3 1.0
CG B:HIS448 4.8 19.1 1.0
CA B:GLY259 4.9 14.4 1.0
CD2 B:PHE102 5.0 13.1 1.0
CE1 B:HIS448 5.0 13.4 1.0

Copper binding site 9 out of 9 in 1aso

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Copper binding site 9 out of 9 in the X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini: Reduced-, Peroxide-, and Azide-Forms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu557

b:24.3
occ:1.00
 NE2 B:HIS448 2.0 19.7 1.0
NE2 B:HIS60 2.0 18.2 1.0
O B:OH558 2.2 21.4 1.0
CD2 B:HIS448 2.9 20.7 1.0
CE1 B:HIS448 2.9 13.4 1.0
CD2 B:HIS60 2.9 19.9 1.0
CE1 B:HIS60 2.9 23.0 1.0
ND1 B:HIS62 3.4 21.5 1.0
NE2 B:HIS450 3.5 26.3 1.0
CD2 B:HIS450 3.6 21.0 1.0
CE1 B:HIS450 3.7 21.0 1.0
CA B:HIS62 3.7 20.3 1.0
CG B:HIS62 3.7 22.7 1.0
ND1 B:HIS450 3.9 20.2 1.0
CG B:HIS450 3.9 19.3 1.0
ND1 B:HIS448 4.0 17.0 1.0
CG B:HIS448 4.0 19.1 1.0
ND1 B:HIS60 4.0 16.5 1.0
CB B:HIS62 4.0 17.8 1.0
CG B:HIS60 4.0 18.2 1.0
CE1 B:HIS62 4.0 19.8 1.0
CU B:CU556 4.0 33.1 1.0
N B:GLY63 4.1 20.1 1.0
O B:HOH661 4.3 26.4 1.0
C B:HIS62 4.5 21.0 1.0
CU B:CU555 4.5 38.4 1.0
CD2 B:HIS62 4.6 15.4 1.0
N B:HIS62 4.6 17.3 1.0
NE2 B:HIS62 4.7 15.7 1.0
O B:TRP61 4.7 17.7 1.0
CA B:HIS450 4.8 19.4 1.0
CB B:HIS450 4.8 18.4 1.0
O B:HOH793 4.9 29.6 1.0
NE2 B:HIS104 4.9 17.6 1.0
O B:LEU449 5.0 19.3 1.0
C B:TRP61 5.0 18.9 1.0

Reference:

A.Messerschmidt, H.Luecke, R.Huber. X-Ray Structures and Mechanistic Implications of Three Functional Derivatives of Ascorbate Oxidase From Zucchini. Reduced, Peroxide and Azide Forms. J.Mol.Biol. V. 230 997 1993.
ISSN: ISSN 0022-2836
PubMed: 8478945
DOI: 10.1006/JMBI.1993.1215
Page generated: Tue Jul 30 21:31:47 2024

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