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Copper in PDB 1asp: 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: 1asp 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 / 2.59
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.330, 105.320, 112.840, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 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 1asp). 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: 1asp:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 1asp

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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:12.1
occ:0.97
ND1 A:HIS512 2.1 6.0 1.0
ND1 A:HIS445 2.1 9.3 1.0
SG A:CYS507 2.1 6.0 1.0
SD A:MET517 3.0 6.8 1.0
CG A:HIS512 3.1 6.2 1.0
CE1 A:HIS512 3.1 6.0 1.0
CE1 A:HIS445 3.1 9.6 1.0
CG A:HIS445 3.1 15.6 1.0
CB A:CYS507 3.2 6.0 1.0
CB A:HIS512 3.4 6.0 1.0
CB A:HIS445 3.5 8.4 1.0
CE A:MET517 4.0 9.0 1.0
CA A:HIS445 4.1 6.1 1.0
NE2 A:HIS512 4.2 6.0 1.0
NE2 A:HIS445 4.2 9.2 1.0
CB A:ILE509 4.3 7.3 1.0
CD2 A:HIS512 4.3 6.0 1.0
CD2 A:HIS445 4.3 14.9 1.0
CG A:MET517 4.4 6.0 1.0
CD1 A:ILE509 4.4 12.8 1.0
CA A:CYS507 4.5 6.0 1.0
O A:HOH641 4.6 6.0 1.0
CG1 A:ILE509 4.6 6.0 1.0
CA A:HIS512 4.9 6.0 1.0
O A:THR444 4.9 6.5 1.0
CG2 A:ILE509 4.9 6.0 1.0
CB A:MET517 4.9 6.0 1.0

Copper binding site 2 out of 9 in 1asp

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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:33.9
occ:0.49
O1 A:PEO560 1.9 22.0 1.0
NE2 A:HIS450 2.0 22.9 1.0
NE2 A:HIS506 2.0 33.4 1.0
NE2 A:HIS106 2.1 38.3 1.0
CE1 A:HIS450 2.8 17.0 1.0
CE1 A:HIS506 3.0 34.8 1.0
O2 A:PEO560 3.0 35.8 1.0
CD2 A:HIS450 3.0 12.5 1.0
CE1 A:HIS106 3.1 42.7 1.0
CD2 A:HIS506 3.1 26.7 1.0
CD2 A:HIS106 3.1 39.4 1.0
ND1 A:HIS450 3.9 15.6 1.0
CG A:HIS450 4.1 8.7 1.0
ND1 A:HIS506 4.1 35.7 1.0
CD2 A:HIS448 4.1 6.8 1.0
CG A:HIS506 4.1 25.5 1.0
ND1 A:HIS106 4.3 41.6 1.0
CG A:HIS106 4.3 43.0 1.0
CU A:CU557 4.4 15.7 0.8
O A:HOH812 4.6 25.4 1.0
CD2 A:HIS60 4.6 7.8 1.0
NE2 A:HIS60 4.7 6.0 1.0
NE2 A:HIS448 4.7 6.5 1.0
CE1 A:HIS104 4.8 16.0 1.0
CU A:CU556 4.8 19.9 0.8
CG2 A:THR75 4.9 6.0 1.0
CB A:ALA504 4.9 7.3 1.0

Copper binding site 3 out of 9 in 1asp

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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:19.9
occ:0.82
ND1 A:HIS62 2.0 11.0 1.0
NE2 A:HIS104 2.1 17.3 1.0
NE2 A:HIS508 2.2 14.6 1.0
CE1 A:HIS62 2.8 9.3 1.0
CG A:HIS62 3.0 15.4 1.0
CE1 A:HIS104 3.0 16.0 1.0
CD2 A:HIS104 3.1 16.6 1.0
CD2 A:HIS508 3.1 12.8 1.0
CE1 A:HIS508 3.1 15.5 1.0
O2 A:PEO560 3.5 35.8 1.0
CB A:HIS62 3.6 11.6 1.0
CU A:CU557 3.7 15.7 0.8
O1 A:PEO560 3.9 22.0 1.0
NE2 A:HIS62 3.9 10.4 1.0
CD2 A:HIS60 4.0 7.8 1.0
CD2 A:HIS62 4.1 10.1 1.0
CD2 A:HIS448 4.1 6.8 1.0
ND1 A:HIS104 4.1 14.2 1.0
NE2 A:HIS448 4.2 6.5 1.0
CG A:HIS104 4.2 17.0 1.0
ND1 A:HIS508 4.2 15.2 1.0
CG A:HIS508 4.3 11.7 1.0
NE2 A:HIS60 4.3 6.0 1.0
CE2 A:PHE102 4.5 14.4 1.0
CG A:HIS448 4.6 6.4 1.0
CA A:HIS62 4.6 8.9 1.0
CE1 A:HIS448 4.6 7.2 1.0
CZ A:PHE102 4.7 6.0 1.0
CU A:CU555 4.8 33.9 0.5
ND1 A:HIS448 4.9 7.8 1.0

Copper binding site 4 out of 9 in 1asp

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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:15.7
occ:0.80
NE2 A:HIS60 2.0 6.0 1.0
NE2 A:HIS448 2.1 6.5 1.0
O A:OH558 2.1 6.0 1.0
CE1 A:HIS60 2.8 7.0 1.0
CD2 A:HIS60 2.9 7.8 1.0
CD2 A:HIS448 3.0 6.8 1.0
CE1 A:HIS448 3.0 7.2 1.0
NE2 A:HIS450 3.2 22.9 1.0
CD2 A:HIS450 3.3 12.5 1.0
CA A:HIS62 3.7 8.9 1.0
CE1 A:HIS450 3.7 17.0 1.0
CU A:CU556 3.7 19.9 0.8
CG A:HIS62 3.8 15.4 1.0
CG A:HIS450 3.8 8.7 1.0
ND1 A:HIS60 3.9 6.0 1.0
ND1 A:HIS62 4.0 11.0 1.0
CG A:HIS60 4.0 8.8 1.0
ND1 A:HIS448 4.0 7.8 1.0
CB A:HIS62 4.0 11.6 1.0
ND1 A:HIS450 4.0 15.6 1.0
CG A:HIS448 4.1 6.4 1.0
CD2 A:HIS62 4.2 10.1 1.0
N A:GLY63 4.3 11.9 1.0
O A:HOH772 4.4 14.6 1.0
CU A:CU555 4.4 33.9 0.5
CE1 A:HIS62 4.4 9.3 1.0
O A:HOH642 4.5 6.0 1.0
C A:HIS62 4.5 9.9 1.0
NE2 A:HIS62 4.6 10.4 1.0
N A:HIS62 4.6 11.3 1.0
O A:TRP61 4.7 9.5 1.0
CA A:HIS450 4.7 6.0 1.0
CB A:HIS450 4.8 6.6 1.0
O A:LEU449 4.8 13.3 1.0
NE2 A:HIS104 4.9 17.3 1.0
C A:TRP61 4.9 9.2 1.0

Copper binding site 5 out of 9 in 1asp

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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:47.2
occ:0.63
NE2 B:HIS286 2.0 46.9 1.0
NE2 A:HIS286 2.1 41.0 1.0
CE1 A:HIS286 2.9 40.1 1.0
CE1 B:HIS286 2.9 48.2 1.0
CD2 B:HIS286 2.9 44.2 1.0
CD2 A:HIS286 3.0 33.4 1.0
O A:HOH888 3.3 59.5 1.0
ND1 A:HIS286 3.9 37.2 1.0
CG A:HIS286 4.0 29.6 1.0
ND1 B:HIS286 4.0 44.2 1.0
CG B:HIS286 4.0 42.6 1.0
O B:PRO287 4.1 33.0 1.0
O A:PRO287 4.1 27.1 1.0
O B:HOH638 4.3 59.1 1.0
O A:HOH621 4.5 66.0 1.0
CD A:PRO287 4.8 23.6 1.0
CD B:PRO287 4.9 26.7 1.0

Copper binding site 6 out of 9 in 1asp

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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:18.2
occ:0.94
ND1 B:HIS512 2.1 19.4 1.0
SG B:CYS507 2.1 16.2 1.0
ND1 B:HIS445 2.1 16.7 1.0
SD B:MET517 2.8 16.2 1.0
CE1 B:HIS445 3.1 14.0 1.0
CE1 B:HIS512 3.1 17.0 1.0
CG B:HIS445 3.1 20.3 1.0
CG B:HIS512 3.1 19.6 1.0
CB B:CYS507 3.3 13.9 1.0
CB B:HIS512 3.4 22.1 1.0
CB B:HIS445 3.5 19.3 1.0
CE B:MET517 3.7 21.4 1.0
CA B:HIS445 4.1 19.1 1.0
NE2 B:HIS445 4.1 10.5 1.0
NE2 B:HIS512 4.2 14.6 1.0
CD2 B:HIS445 4.2 19.8 1.0
CD2 B:HIS512 4.3 19.0 1.0
CB B:ILE509 4.3 16.5 1.0
CG B:MET517 4.4 18.4 1.0
CD1 B:ILE509 4.5 15.2 1.0
O B:HOH658 4.5 17.8 1.0
CA B:CYS507 4.6 15.3 1.0
CG1 B:ILE509 4.8 16.4 1.0
O B:THR444 4.9 23.9 1.0
CA B:HIS512 4.9 21.0 1.0
CB B:MET517 4.9 15.0 1.0

Copper binding site 7 out of 9 in 1asp

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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:43.1
occ:0.47
O1 B:PEO559 2.0 39.6 1.0
NE2 B:HIS506 2.0 38.5 1.0
NE2 B:HIS450 2.0 36.5 1.0
NE2 B:HIS106 2.2 52.4 1.0
CE1 B:HIS450 2.9 36.0 1.0
O2 B:PEO559 2.9 56.7 1.0
CE1 B:HIS506 2.9 36.6 1.0
CD2 B:HIS506 3.0 35.9 1.0
CD2 B:HIS450 3.0 31.5 1.0
CD2 B:HIS106 3.1 52.8 1.0
CE1 B:HIS106 3.2 57.7 1.0
ND1 B:HIS506 3.9 39.5 1.0
ND1 B:HIS450 4.0 30.8 1.0
CG B:HIS506 4.0 33.8 1.0
CG B:HIS450 4.1 29.6 1.0
CD2 B:HIS448 4.1 19.4 1.0
CG B:HIS106 4.3 51.7 1.0
ND1 B:HIS106 4.3 54.7 1.0
CU B:CU557 4.5 29.6 0.8
CD2 B:HIS60 4.7 32.2 1.0
NE2 B:HIS448 4.7 21.1 1.0
O B:HOH718 4.8 24.0 1.0
CU B:CU556 4.8 27.2 0.8
CB B:ALA504 4.8 18.1 1.0
NE2 B:HIS60 4.9 30.8 1.0
CE1 B:HIS104 4.9 18.7 1.0

Copper binding site 8 out of 9 in 1asp

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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:27.2
occ:0.79
NE2 B:HIS104 2.1 19.3 1.0
ND1 B:HIS62 2.1 25.1 1.0
NE2 B:HIS508 2.2 23.4 1.0
CE1 B:HIS62 3.0 24.8 1.0
CE1 B:HIS104 3.0 18.7 1.0
CD2 B:HIS104 3.0 22.5 1.0
CD2 B:HIS508 3.1 22.8 1.0
CE1 B:HIS508 3.1 25.5 1.0
O2 B:PEO559 3.1 56.7 1.0
CG B:HIS62 3.2 20.9 1.0
CB B:HIS62 3.7 17.0 1.0
CU B:CU557 3.7 29.6 0.8
CD2 B:HIS448 4.0 19.4 1.0
O1 B:PEO559 4.0 39.6 1.0
NE2 B:HIS448 4.0 21.1 1.0
CD2 B:HIS60 4.1 32.2 1.0
ND1 B:HIS104 4.1 18.1 1.0
NE2 B:HIS62 4.1 26.8 1.0
CG B:HIS104 4.1 20.4 1.0
ND1 B:HIS508 4.2 21.8 1.0
CG B:HIS508 4.2 23.4 1.0
CD2 B:HIS62 4.3 23.1 1.0
CE2 B:PHE102 4.4 14.2 1.0
NE2 B:HIS60 4.4 30.8 1.0
CZ B:PHE102 4.6 15.9 1.0
CG B:HIS448 4.6 22.3 1.0
CE1 B:HIS448 4.7 19.3 1.0
CA B:HIS62 4.7 19.0 1.0
CU B:CU555 4.8 43.1 0.5
ND1 B:HIS448 5.0 22.9 1.0

Copper binding site 9 out of 9 in 1asp

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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:29.6
occ:0.75
NE2 B:HIS448 2.0 21.1 1.0
NE2 B:HIS60 2.0 30.8 1.0
O B:OH558 2.1 29.4 1.0
CD2 B:HIS448 2.9 19.4 1.0
CE1 B:HIS448 2.9 19.3 1.0
CE1 B:HIS60 2.9 33.7 1.0
CD2 B:HIS60 2.9 32.2 1.0
NE2 B:HIS450 3.4 36.5 1.0
ND1 B:HIS62 3.5 25.1 1.0
CA B:HIS62 3.6 19.0 1.0
CD2 B:HIS450 3.6 31.5 1.0
CE1 B:HIS450 3.6 36.0 1.0
CG B:HIS62 3.7 20.9 1.0
CU B:CU556 3.7 27.2 0.8
CB B:HIS62 3.9 17.0 1.0
CG B:HIS450 3.9 29.6 1.0
ND1 B:HIS450 3.9 30.8 1.0
ND1 B:HIS448 4.0 22.9 1.0
CG B:HIS448 4.0 22.3 1.0
ND1 B:HIS60 4.0 30.2 1.0
CG B:HIS60 4.0 30.4 1.0
N B:GLY63 4.1 19.3 1.0
CE1 B:HIS62 4.2 24.8 1.0
C B:HIS62 4.4 21.2 1.0
O B:HOH659 4.4 21.5 1.0
N B:HIS62 4.5 17.9 1.0
CD2 B:HIS62 4.5 23.1 1.0
CU B:CU555 4.5 43.1 0.5
O B:TRP61 4.7 14.7 1.0
NE2 B:HIS62 4.7 26.8 1.0
CB B:HIS450 4.8 28.5 1.0
NE2 B:HIS104 4.8 19.3 1.0
CA B:HIS450 4.8 23.7 1.0
C B:TRP61 4.9 19.0 1.0
O B:LEU449 5.0 23.9 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: Wed Oct 28 14:13:36 2020
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