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Copper in PDB 1asq: 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: 1asq 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 / 2.32
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.320, 105.280, 113.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 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 1asq). 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: 1asq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 1asq

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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:10.5
occ:0.94
 ND1 A:HIS512 2.0 6.0 1.0
SG A:CYS507 2.1 6.2 1.0
ND1 A:HIS445 2.1 6.5 1.0
SD A:MET517 2.9 6.0 1.0
CE1 A:HIS512 3.0 6.0 1.0
CG A:HIS512 3.0 6.0 1.0
CE1 A:HIS445 3.1 8.2 1.0
CG A:HIS445 3.1 6.0 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 6.0 1.0
CE A:MET517 3.7 6.1 1.0
NE2 A:HIS512 4.1 6.0 1.0
CA A:HIS445 4.2 6.3 1.0
CD2 A:HIS512 4.2 6.0 1.0
NE2 A:HIS445 4.2 6.8 1.0
CD2 A:HIS445 4.3 9.6 1.0
CB A:ILE509 4.3 6.0 1.0
CD1 A:ILE509 4.4 6.8 1.0
CG A:MET517 4.4 6.0 1.0
CG1 A:ILE509 4.6 6.0 1.0
CA A:CYS507 4.6 7.0 1.0
O A:HOH641 4.7 6.0 1.0
O A:THR444 4.8 8.6 1.0
CA A:HIS512 4.8 6.7 1.0
CB A:MET517 5.0 6.0 1.0
CG2 A:ILE509 5.0 6.1 1.0

Copper binding site 2 out of 9 in 1asq

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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:22.4
occ:0.88
 N1 A:AZI560 1.9 21.4 1.0
NE2 A:HIS506 2.1 17.5 1.0
NE2 A:HIS106 2.1 19.1 1.0
NE2 A:HIS450 2.1 13.1 1.0
N1 A:AZI559 2.2 26.9 0.8
N2 A:AZI560 2.6 29.5 1.0
CE1 A:HIS506 2.9 10.4 1.0
CE1 A:HIS450 2.9 8.6 1.0
N2 A:AZI559 3.0 34.8 0.8
CD2 A:HIS106 3.0 14.7 1.0
CD2 A:HIS506 3.0 12.4 1.0
CE1 A:HIS106 3.1 17.6 1.0
CD2 A:HIS450 3.1 11.5 1.0
N3 A:AZI560 3.5 19.0 1.0
N3 A:AZI559 4.0 25.1 0.8
ND1 A:HIS506 4.0 14.4 1.0
ND1 A:HIS450 4.1 10.9 1.0
CG A:HIS506 4.1 12.8 1.0
CG A:HIS106 4.2 15.7 1.0
ND1 A:HIS106 4.2 17.9 1.0
CG A:HIS450 4.2 6.5 1.0
CD2 A:HIS448 4.4 9.4 1.0
O A:HOH702 4.6 30.3 1.0
CG2 A:THR75 4.7 6.0 1.0
CU A:CU557 4.7 15.0 0.8
CD2 A:LEU513 4.8 7.5 1.0
CD2 A:HIS60 4.9 6.1 1.0
NE2 A:HIS60 5.0 6.0 1.0

Copper binding site 3 out of 9 in 1asq

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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:14.7
occ:0.86
 ND1 A:HIS62 2.0 10.0 1.0
NE2 A:HIS104 2.1 11.2 1.0
NE2 A:HIS508 2.2 12.6 1.0
CE1 A:HIS62 2.9 11.5 1.0
CE1 A:HIS104 3.0 9.0 1.0
CG A:HIS62 3.0 10.0 1.0
CD2 A:HIS104 3.1 11.5 1.0
CD2 A:HIS508 3.1 10.6 1.0
CE1 A:HIS508 3.1 9.4 1.0
N1 A:AZI560 3.4 21.4 1.0
CB A:HIS62 3.6 7.5 1.0
N2 A:AZI560 3.6 29.5 1.0
CU A:CU557 3.7 15.0 0.8
CD2 A:HIS60 3.9 6.1 1.0
NE2 A:HIS62 4.0 10.7 1.0
CD2 A:HIS448 4.1 9.4 1.0
CD2 A:HIS62 4.1 6.0 1.0
ND1 A:HIS104 4.1 9.9 1.0
NE2 A:HIS448 4.2 8.2 1.0
CG A:HIS104 4.2 11.4 1.0
ND1 A:HIS508 4.2 8.9 1.0
NE2 A:HIS60 4.2 6.0 1.0
CG A:HIS508 4.2 8.5 1.0
N3 A:AZI560 4.3 19.0 1.0
CE2 A:PHE102 4.4 9.7 1.0
CG A:HIS448 4.6 6.0 1.0
CA A:HIS62 4.7 6.5 1.0
CZ A:PHE102 4.7 8.8 1.0
CE1 A:HIS448 4.7 9.5 1.0
ND1 A:HIS448 5.0 8.2 1.0

Copper binding site 4 out of 9 in 1asq

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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:15.0
occ:0.80
 NE2 A:HIS60 2.0 6.0 1.0
O A:OH558 2.0 11.2 1.0
NE2 A:HIS448 2.1 8.2 1.0
CE1 A:HIS60 2.8 6.0 1.0
CD2 A:HIS60 2.9 6.1 1.0
CD2 A:HIS448 3.0 9.4 1.0
CE1 A:HIS448 3.0 9.5 1.0
NE2 A:HIS450 3.4 13.1 1.0
CE1 A:HIS450 3.6 8.6 1.0
CU A:CU556 3.7 14.7 0.9
CD2 A:HIS450 3.7 11.5 1.0
CG A:HIS62 3.7 10.0 1.0
CA A:HIS62 3.7 6.5 1.0
ND1 A:HIS62 3.8 10.0 1.0
ND1 A:HIS60 3.9 6.0 1.0
CG A:HIS60 4.0 6.0 1.0
CB A:HIS62 4.0 7.5 1.0
ND1 A:HIS450 4.0 10.9 1.0
ND1 A:HIS448 4.0 8.2 1.0
CG A:HIS450 4.0 6.5 1.0
CG A:HIS448 4.0 6.0 1.0
N1 A:AZI560 4.0 21.4 1.0
CD2 A:HIS62 4.2 6.0 1.0
O A:HOH775 4.3 20.0 1.0
N A:GLY63 4.3 7.8 1.0
CE1 A:HIS62 4.3 11.5 1.0
C A:HIS62 4.6 7.9 1.0
NE2 A:HIS62 4.6 10.7 1.0
N A:HIS62 4.6 6.0 1.0
CU A:CU555 4.7 22.4 0.9
O A:HOH642 4.7 7.8 1.0
O A:TRP61 4.8 6.0 1.0
CA A:HIS450 4.9 11.3 1.0
NE2 A:HIS104 4.9 11.2 1.0
CB A:HIS450 5.0 9.7 1.0

Copper binding site 5 out of 9 in 1asq

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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:Cu561

b:78.1
occ:1.00
 NE2 B:HIS286 2.1 53.6 1.0
NE2 A:HIS286 2.2 50.5 1.0
CE1 A:HIS286 3.0 47.6 1.0
CE1 B:HIS286 3.0 51.0 1.0
CD2 B:HIS286 3.0 44.8 1.0
CD2 A:HIS286 3.1 40.5 1.0
O A:HOH892 3.2 67.0 1.0
ND1 A:HIS286 4.0 39.3 1.0
O A:HOH621 4.0 62.0 1.0
ND1 B:HIS286 4.1 42.8 1.0
CG A:HIS286 4.1 31.6 1.0
CG B:HIS286 4.1 38.7 1.0
O A:PRO287 4.2 18.1 1.0
O B:PRO287 4.2 22.8 1.0
O B:HOH639 4.4 73.4 1.0
CD A:PRO287 4.7 15.7 1.0

Copper binding site 6 out of 9 in 1asq

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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:19.7
occ:0.91
 ND1 B:HIS512 2.1 19.3 1.0
SG B:CYS507 2.1 16.3 1.0
ND1 B:HIS445 2.1 17.1 1.0
SD B:MET517 2.8 18.8 1.0
CE1 B:HIS445 3.0 13.3 1.0
CE1 B:HIS512 3.1 19.9 1.0
CG B:HIS445 3.1 15.6 1.0
CG B:HIS512 3.1 20.4 1.0
CB B:CYS507 3.3 18.9 1.0
CB B:HIS512 3.4 20.5 1.0
CB B:HIS445 3.5 11.2 1.0
CE B:MET517 3.7 22.6 1.0
CA B:HIS445 4.1 15.7 1.0
NE2 B:HIS445 4.1 12.8 1.0
NE2 B:HIS512 4.2 20.2 1.0
CD2 B:HIS445 4.2 12.1 1.0
CD1 B:ILE509 4.3 11.4 1.0
CD2 B:HIS512 4.3 21.2 1.0
CB B:ILE509 4.3 13.4 1.0
CG B:MET517 4.4 17.3 1.0
O B:HOH660 4.5 8.9 1.0
CA B:CYS507 4.6 20.6 1.0
CG1 B:ILE509 4.7 13.3 1.0
O B:THR444 4.9 16.8 1.0
CA B:HIS512 4.9 18.5 1.0
CB B:MET517 5.0 20.7 1.0
CG2 B:ILE509 5.0 11.3 1.0

Copper binding site 7 out of 9 in 1asq

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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:31.9
occ:0.76
 N1 B:AZI560 2.0 32.6 0.9
NE2 B:HIS450 2.1 28.7 1.0
N1 B:AZI559 2.1 37.0 0.8
NE2 B:HIS506 2.1 28.2 1.0
NE2 B:HIS106 2.1 33.4 1.0
N2 B:AZI560 2.6 39.3 0.9
CE1 B:HIS450 2.9 26.0 1.0
N2 B:AZI559 2.9 41.4 0.8
CE1 B:HIS506 3.0 25.6 1.0
CD2 B:HIS506 3.0 27.5 1.0
CD2 B:HIS450 3.1 21.3 1.0
CD2 B:HIS106 3.1 31.8 1.0
CE1 B:HIS106 3.1 33.9 1.0
N3 B:AZI560 3.6 27.8 0.9
N3 B:AZI559 3.9 35.5 0.8
ND1 B:HIS450 4.0 24.1 1.0
ND1 B:HIS506 4.0 25.5 1.0
CG B:HIS506 4.1 25.0 1.0
CG B:HIS450 4.1 22.4 1.0
ND1 B:HIS106 4.2 29.6 1.0
CG B:HIS106 4.2 31.1 1.0
CD2 B:HIS448 4.4 27.8 1.0
CU B:CU557 4.6 26.7 0.7
CG2 B:THR75 4.7 15.7 1.0
CD2 B:HIS60 4.8 27.2 1.0
CB B:ALA504 4.9 23.2 1.0
NE2 B:HIS448 4.9 28.6 1.0
NE2 B:HIS60 4.9 25.5 1.0

Copper binding site 8 out of 9 in 1asq

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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:28.1
occ:0.83
 NE2 B:HIS104 2.0 22.1 1.0
ND1 B:HIS62 2.1 27.8 1.0
NE2 B:HIS508 2.1 25.5 1.0
CE1 B:HIS104 2.9 18.4 1.0
CD2 B:HIS104 3.0 21.1 1.0
CE1 B:HIS62 3.0 25.9 1.0
CE1 B:HIS508 3.1 22.7 1.0
CD2 B:HIS508 3.1 24.4 1.0
N1 B:AZI560 3.1 32.6 0.9
CG B:HIS62 3.1 26.0 1.0
N2 B:AZI560 3.4 39.3 0.9
CU B:CU557 3.6 26.7 0.7
CB B:HIS62 3.6 22.5 1.0
CD2 B:HIS448 3.9 27.8 1.0
NE2 B:HIS448 4.0 28.6 1.0
N3 B:AZI560 4.0 27.8 0.9
CD2 B:HIS60 4.0 27.2 1.0
ND1 B:HIS104 4.1 19.7 1.0
CG B:HIS104 4.1 17.7 1.0
NE2 B:HIS62 4.1 27.1 1.0
ND1 B:HIS508 4.2 24.7 1.0
CG B:HIS508 4.2 24.9 1.0
CD2 B:HIS62 4.3 25.6 1.0
NE2 B:HIS60 4.3 25.5 1.0
CE2 B:PHE102 4.4 18.0 1.0
CE1 B:HIS448 4.7 26.8 1.0
CG B:HIS448 4.7 28.1 1.0
CA B:HIS62 4.7 21.8 1.0
CZ B:PHE102 4.7 18.5 1.0

Copper binding site 9 out of 9 in 1asq

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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:26.7
occ:0.68
 NE2 B:HIS60 2.0 25.5 1.0
NE2 B:HIS448 2.0 28.6 1.0
O B:OH558 2.1 27.8 1.0
CE1 B:HIS60 2.9 25.8 1.0
CD2 B:HIS60 2.9 27.2 1.0
CD2 B:HIS448 3.0 27.8 1.0
CE1 B:HIS448 3.0 26.8 1.0
NE2 B:HIS450 3.5 28.7 1.0
ND1 B:HIS62 3.5 27.8 1.0
CE1 B:HIS450 3.5 26.0 1.0
CU B:CU556 3.6 28.1 0.8
CA B:HIS62 3.6 21.8 1.0
CG B:HIS62 3.7 26.0 1.0
CD2 B:HIS450 3.8 21.3 1.0
CB B:HIS62 3.9 22.5 1.0
N1 B:AZI560 3.9 32.6 0.9
ND1 B:HIS450 3.9 24.1 1.0
ND1 B:HIS60 3.9 22.9 1.0
CG B:HIS60 4.0 25.4 1.0
CG B:HIS450 4.0 22.4 1.0
ND1 B:HIS448 4.1 28.6 1.0
CG B:HIS448 4.1 28.1 1.0
CE1 B:HIS62 4.2 25.9 1.0
N B:GLY63 4.2 24.2 1.0
O B:HOH661 4.5 24.4 1.0
C B:HIS62 4.5 24.0 1.0
CD2 B:HIS62 4.5 25.6 1.0
N B:HIS62 4.5 21.1 1.0
CU B:CU555 4.6 31.9 0.8
NE2 B:HIS104 4.7 22.1 1.0
NE2 B:HIS62 4.7 27.1 1.0
O B:TRP61 4.8 19.8 1.0
CA B:HIS450 5.0 22.3 1.0
N2 B:AZI560 5.0 39.3 0.9

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 21:32:58 2024

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