Copper in PDB 6hqi: Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum

All present enzymatic activity of Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum:
1.10.3.1;

The structure of Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum, PDB code: 6hqi was solved by I.Kampatsikas, A.Bijelic, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.23 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.620, 54.100, 69.820, 90.00, 104.60, 90.00
R / Rfree (%)	19.1 / 22.9

The binding sites of Copper atom in the Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum (pdb code 6hqi). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum, PDB code: 6hqi:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:10.2 occ:0.09 NE2 A:HIS241 1.8 28.7 1.0 NE2 A:HIS245 2.0 32.7 1.0 NE2 A:HIS283 2.4 25.6 1.0 O A:O603 2.5 32.4 1.0 CE1 A:HIS241 2.8 27.8 1.0 CD2 A:HIS241 2.8 26.8 1.0 CD2 A:HIS245 3.0 31.6 1.0 CE1 A:HIS245 3.0 33.1 1.0 CE1 A:HIS283 3.0 26.0 1.0 CD2 A:HIS283 3.4 24.5 1.0 ND1 A:HIS241 3.8 27.0 1.0 CG A:HIS241 3.9 26.4 1.0 CD2 A:HIS282 4.0 23.3 1.0 NE2 A:HIS282 4.0 22.5 1.0 CE1 A:PHE279 4.1 28.6 1.0 ND1 A:HIS245 4.1 32.5 1.0 ND1 A:HIS283 4.1 24.9 1.0 CG A:HIS245 4.1 31.0 1.0 CU A:CU602 4.2 30.3 0.3 CG A:HIS283 4.3 23.5 1.0 CD1 A:PHE279 4.7 27.8 1.0 CE1 A:HIS93 4.7 49.7 1.0 NE2 A:HIS93 4.7 49.6 1.0 CZ A:PHE279 4.8 29.2 1.0

Copper binding site 2 out of 2 in the Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Holo-Form of Polyphenol Oxidase From Solanum Lycopersicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:30.3 occ:0.31 NE2 A:HIS93 1.4 49.6 1.0 O A:O603 1.8 32.4 1.0 NE2 A:HIS111 2.1 47.1 1.0 NE2 A:HIS120 2.3 28.6 1.0 CE1 A:HIS93 2.4 49.7 1.0 CD2 A:HIS93 2.5 48.5 1.0 CE1 A:HIS111 2.9 47.9 1.0 CE1 A:HIS120 3.1 29.1 1.0 CD2 A:HIS111 3.2 47.6 1.0 CD2 A:HIS120 3.4 27.5 1.0 ND1 A:HIS93 3.5 49.2 1.0 CG A:HIS93 3.6 48.5 1.0 NE2 A:HIS283 3.8 25.6 1.0 CE1 A:PHE270 3.9 58.0 1.0 CE1 A:HIS283 4.0 26.0 1.0 ND1 A:HIS111 4.1 48.7 1.0 CU A:CU601 4.2 10.2 0.1 ND1 A:HIS120 4.2 28.0 1.0 CG A:HIS111 4.3 47.9 1.0 CG A:HIS120 4.4 26.6 1.0 CZ A:PHE279 4.5 29.2 1.0 CE1 A:PHE116 4.6 27.3 1.0 CZ A:PHE270 4.6 59.2 1.0 CE1 A:PHE279 4.7 28.6 1.0 NE2 A:HIS241 4.8 28.7 1.0 CD1 A:PHE270 4.8 57.0 1.0 CE1 A:HIS241 4.9 27.8 1.0 CD2 A:HIS283 5.0 24.5 1.0

I.Kampatsikas, A.Bijelic, A.Rompel. Biochemical and Structural Characterization of Tomato Polyphenol Oxidases Provide Novel Insights Into Their Substrate Specificity. Sci Rep V. 9 4022 2019.
ISSN: ESSN 2045-2322
PubMed: 30858490
DOI: 10.1038/S41598-019-39687-0