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Platinum in PDB 1w07: Arabidopsis Thaliana Acyl-Coa Oxidase 1

Enzymatic activity of Arabidopsis Thaliana Acyl-Coa Oxidase 1

All present enzymatic activity of Arabidopsis Thaliana Acyl-Coa Oxidase 1:
1.3.3.6;

Protein crystallography data

The structure of Arabidopsis Thaliana Acyl-Coa Oxidase 1, PDB code: 1w07 was solved by A.Henriksen, L.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.201, 117.001, 131.047, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.9

Other elements in 1w07:

The structure of Arabidopsis Thaliana Acyl-Coa Oxidase 1 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Arabidopsis Thaliana Acyl-Coa Oxidase 1 (pdb code 1w07). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the Arabidopsis Thaliana Acyl-Coa Oxidase 1, PDB code: 1w07:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 1w07

Go back to Platinum Binding Sites List in 1w07
Platinum binding site 1 out of 6 in the Arabidopsis Thaliana Acyl-Coa Oxidase 1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Arabidopsis Thaliana Acyl-Coa Oxidase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1663

b:58.9
occ:1.00
 SD A:MET256 2.5 35.8 1.0
O A:HOH2113 2.5 30.2 1.0
CE A:MET256 2.9 40.0 1.0
O A:HOH2054 3.2 30.4 1.0
CG A:MET256 3.6 36.8 1.0
CB A:MET256 3.7 35.1 1.0
O A:HOH2183 3.7 50.8 1.0
NH1 A:ARG251 4.0 37.6 1.0
CB A:LYS260 4.3 41.5 1.0
O A:VAL261 4.9 37.0 1.0

Platinum binding site 2 out of 6 in 1w07

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Platinum binding site 2 out of 6 in the Arabidopsis Thaliana Acyl-Coa Oxidase 1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Arabidopsis Thaliana Acyl-Coa Oxidase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1664

b:41.9
occ:1.00
 O A:HOH2011 2.2 17.5 1.0
NE2 A:HIS6 2.3 26.6 1.0
O A:HOH2003 2.5 18.6 1.0
OE1 A:GLU2 2.6 31.6 0.5
OE2 A:GLU2 2.8 34.8 0.5
CD2 A:HIS6 3.0 23.1 1.0
OE2 A:GLU2 3.1 35.0 0.5
CD A:GLU2 3.2 35.3 0.5
CE1 A:HIS6 3.4 31.3 1.0
OD1 A:ASN624 3.5 28.6 1.0
O A:HOH2001 3.6 30.3 1.0
CD A:GLU2 3.8 34.7 0.5
O A:HOH2005 4.0 22.8 1.0
CG A:ASN624 4.1 26.7 1.0
O A:HOH2342 4.1 25.9 1.0
CG A:HIS6 4.3 26.1 1.0
ND1 A:HIS6 4.4 29.9 1.0
OE1 A:GLU2 4.6 35.3 0.5
ND2 A:ASN624 4.6 24.7 1.0
CG A:GLU2 4.7 32.9 0.5
CG A:GLU2 4.7 31.3 0.5
CB A:ASN624 4.8 24.7 1.0

Platinum binding site 3 out of 6 in 1w07

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Platinum binding site 3 out of 6 in the Arabidopsis Thaliana Acyl-Coa Oxidase 1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Arabidopsis Thaliana Acyl-Coa Oxidase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1665

b:0.8
occ:1.00
 SD A:MET281 2.9 46.4 1.0
ND1 A:HIS374 2.9 46.8 1.0
CB A:MET281 2.9 52.2 1.0
CG A:MET281 3.5 49.3 1.0
CE1 A:HIS374 3.7 42.6 1.0
CG A:HIS374 3.7 45.9 1.0
CE A:MET281 3.7 46.3 1.0
NH1 A:ARG285 3.9 41.1 1.0
O A:MET281 4.0 55.1 1.0
CB A:HIS374 4.0 41.9 1.0
CA A:MET281 4.3 53.6 1.0
CA A:HIS374 4.3 41.7 1.0
C A:MET281 4.4 54.3 1.0
CZ A:ARG285 4.5 43.9 1.0
NE2 A:HIS374 4.7 45.6 1.0
CD2 A:HIS374 4.8 45.4 1.0
NH2 A:ARG285 4.8 42.7 1.0
O A:HIS374 5.0 40.1 1.0

Platinum binding site 4 out of 6 in 1w07

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Platinum binding site 4 out of 6 in the Arabidopsis Thaliana Acyl-Coa Oxidase 1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Arabidopsis Thaliana Acyl-Coa Oxidase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1662

b:63.1
occ:1.00
 SD B:MET256 2.7 38.2 1.0
CE B:MET256 2.9 35.2 1.0
O B:HOH2189 3.0 37.4 1.0
CG B:MET256 3.6 33.7 1.0
CB B:MET256 3.6 34.1 1.0
NH1 B:ARG251 4.1 38.3 1.0
CG B:LYS260 4.5 43.4 1.0
CB B:LYS260 4.9 44.0 1.0

Platinum binding site 5 out of 6 in 1w07

Go back to Platinum Binding Sites List in 1w07
Platinum binding site 5 out of 6 in the Arabidopsis Thaliana Acyl-Coa Oxidase 1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Arabidopsis Thaliana Acyl-Coa Oxidase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1663

b:0.3
occ:1.00
 NE2 B:HIS6 2.4 35.0 1.0
CE1 B:HIS6 3.0 26.6 1.0
CD2 B:HIS6 3.6 29.8 1.0
ND1 B:HIS6 4.2 29.1 1.0
CB B:ILE4 4.3 31.7 1.0
OD1 B:ASN624 4.5 23.0 1.0
O B:HOH2357 4.5 33.4 1.0
CG B:HIS6 4.5 26.6 1.0
CG1 B:ILE4 4.5 36.5 1.0
CG2 B:ILE4 4.6 32.6 1.0

Platinum binding site 6 out of 6 in 1w07

Go back to Platinum Binding Sites List in 1w07
Platinum binding site 6 out of 6 in the Arabidopsis Thaliana Acyl-Coa Oxidase 1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Arabidopsis Thaliana Acyl-Coa Oxidase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1664

b:88.5
occ:1.00
 NE2 B:HIS374 2.1 1.4 1.0
CD2 B:HIS374 2.9 24.6 1.0
CE1 B:HIS374 2.9 26.5 1.0
SD B:MET281 3.2 55.0 1.0
NH1 B:ARG285 3.4 35.9 1.0
CZ B:ARG285 3.6 36.1 1.0
CB B:MET281 3.6 46.0 1.0
NH2 B:ARG285 3.7 34.9 1.0
CE B:MET281 3.8 44.4 1.0
ND1 B:HIS374 4.0 31.9 1.0
CG B:HIS374 4.0 28.9 1.0
CG B:MET281 4.0 44.9 1.0
NE B:ARG285 4.2 39.0 1.0
O B:HOH2194 4.6 41.6 1.0
CD1 B:TYR278 4.8 46.6 1.0
CD B:ARG285 4.8 37.4 1.0
CA B:MET281 5.0 47.9 1.0

Reference:

L.Pedersen, A.Henriksen. Acyl-Coa Oxidase 1 From Arabidopsis Thaliana. Structure of A Key Enzyme in Plant Lipid Metabolism J.Mol.Biol. V. 345 487 2005.
ISSN: ISSN 0022-2836
PubMed: 15581893
DOI: 10.1016/J.JMB.2004.10.062
Page generated: Thu Oct 10 10:41:03 2024

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