Atomistry » Copper » PDB 1a2v-1baw » 1asp
Atomistry »
  Copper »
    PDB 1a2v-1baw »
      1asp »

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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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

Go back to Copper Binding Sites List in 1asp
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: Tue Jul 30 21:32:57 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy