Copper in PDB 8po9: Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella

Protein crystallography data

The structure of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella, PDB code: 8po9 was solved by R.Illanes-Vicioso, E.Ruiz-Lopez, M.Sola, F.Bertocchini, E.A.Palomo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.26 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.75, 196.58, 224.12, 90, 90, 90
R / Rfree (%) 17.1 / 21.8

Other elements in 8po9:

The structure of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 22 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella (pdb code 8po9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella, PDB code: 8po9:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8po9

Go back to Copper Binding Sites List in 8po9
Copper binding site 1 out of 6 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu901

b:34.3
occ:0.91
 O A:HOH1135 2.1 35.1 1.0
OD1 A:ASP318 2.1 31.7 1.0
O A:HOH1090 2.1 42.4 1.0
O A:GLN299 2.2 38.0 1.0
OE1 A:GLU219 2.2 40.1 1.0
OE2 A:GLU219 2.4 35.1 1.0
CD A:GLU219 2.6 33.2 1.0
CG A:ASP318 2.8 33.4 1.0
OD2 A:ASP318 2.9 38.0 1.0
O A:HOH1022 2.9 49.2 1.0
C A:GLN299 3.2 33.1 1.0
OD2 A:ASP220 3.7 40.4 1.0
CA A:GLN299 4.0 34.4 1.0
CG A:GLU219 4.1 33.1 1.0
N A:THR300 4.2 30.1 1.0
CB A:ASP318 4.3 33.9 1.0
CB A:GLN299 4.3 34.0 1.0
CA A:THR300 4.4 29.2 1.0
CG A:ASP220 4.5 35.6 1.0
OD1 A:ASP220 4.5 35.0 1.0
N A:SER301 4.5 27.8 1.0
OD1 A:ASP319 4.7 36.5 1.0
CA A:ASP318 5.0 30.2 1.0

Copper binding site 2 out of 6 in 8po9

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Copper binding site 2 out of 6 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu901

b:39.3
occ:0.95
 O B:HOH1059 2.1 35.9 1.0
OD1 B:ASP318 2.1 35.4 1.0
O B:HOH1187 2.1 46.2 1.0
O B:GLN299 2.1 38.1 1.0
OE1 B:GLU219 2.2 36.9 1.0
OE2 B:GLU219 2.4 36.3 1.0
CD B:GLU219 2.6 34.4 1.0
CG B:ASP318 2.8 36.3 1.0
OD2 B:ASP318 2.9 43.2 1.0
C B:GLN299 3.2 30.9 1.0
O B:HOH1079 3.3 46.4 1.0
OD2 B:ASP220 3.7 39.4 1.0
CA B:GLN299 4.0 34.2 1.0
CG B:GLU219 4.1 34.3 1.0
O B:HOH1072 4.2 47.1 1.0
N B:THR300 4.2 28.6 1.0
CB B:ASP318 4.3 32.9 1.0
CB B:GLN299 4.3 35.1 1.0
CA B:THR300 4.4 27.8 1.0
N B:SER301 4.5 26.3 1.0
CG B:ASP220 4.5 35.3 1.0
OD1 B:ASP220 4.5 36.3 1.0
OD1 B:ASP319 4.8 34.9 1.0
CA B:ASP318 4.9 30.9 1.0
C B:THR300 5.0 30.4 1.0
OG B:SER301 5.0 30.7 1.0

Copper binding site 3 out of 6 in 8po9

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Copper binding site 3 out of 6 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu901

b:35.8
occ:0.92
 O C:HOH1054 2.1 38.6 1.0
OD1 C:ASP318 2.1 34.2 1.0
O C:HOH1100 2.1 52.4 1.0
OE1 C:GLU219 2.2 45.7 1.0
O C:GLN299 2.2 38.1 1.0
OE2 C:GLU219 2.4 39.5 1.0
CD C:GLU219 2.6 36.6 1.0
OD2 C:ASP318 2.7 45.1 1.0
CG C:ASP318 2.7 40.0 1.0
C C:GLN299 3.3 34.7 1.0
OD2 C:ASP220 3.5 42.0 1.0
CG C:GLU219 4.0 33.8 1.0
CA C:GLN299 4.0 35.6 1.0
N C:THR300 4.2 29.9 1.0
CB C:ASP318 4.2 36.4 1.0
CG C:ASP220 4.3 36.5 1.0
CB C:GLN299 4.3 36.3 1.0
CA C:THR300 4.5 31.2 1.0
OD1 C:ASP220 4.5 41.2 1.0
N C:SER301 4.5 30.2 1.0
CA C:ASP318 4.9 33.2 1.0
OG C:SER301 5.0 34.3 1.0

Copper binding site 4 out of 6 in 8po9

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Copper binding site 4 out of 6 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu901

b:39.0
occ:0.99
 O D:HOH1069 2.1 68.4 1.0
OD1 D:ASP318 2.1 37.1 1.0
O D:HOH1128 2.1 43.3 1.0
OE1 D:GLU219 2.2 47.4 1.0
O D:GLN299 2.2 39.8 1.0
OE2 D:GLU219 2.4 40.8 1.0
CD D:GLU219 2.6 40.5 1.0
OD2 D:ASP318 2.7 41.9 1.0
CG D:ASP318 2.8 41.5 1.0
C D:GLN299 3.3 32.9 1.0
O D:HOH1073 3.3 57.8 1.0
OD2 D:ASP220 3.6 42.1 1.0
CA D:GLN299 4.0 34.2 1.0
CG D:GLU219 4.1 32.4 1.0
N D:THR300 4.2 30.1 1.0
CB D:GLN299 4.3 42.2 1.0
OD1 D:ASP220 4.3 43.0 1.0
CB D:ASP318 4.3 32.9 1.0
CG D:ASP220 4.3 42.9 1.0
O D:HOH1131 4.4 49.5 1.0
CA D:THR300 4.5 33.0 1.0
N D:SER301 4.7 30.5 1.0
OD1 D:ASP319 4.9 41.1 1.0
O D:HOH1004 4.9 42.8 1.0

Copper binding site 5 out of 6 in 8po9

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Copper binding site 5 out of 6 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu901

b:37.0
occ:0.98
 O E:HOH1107 2.1 48.2 1.0
O E:HOH1145 2.1 40.8 1.0
OD1 E:ASP318 2.1 30.1 1.0
O E:GLN299 2.2 36.1 1.0
OE1 E:GLU219 2.2 42.4 1.0
OE2 E:GLU219 2.3 33.5 1.0
CD E:GLU219 2.6 37.0 1.0
CG E:ASP318 2.8 35.2 1.0
OD2 E:ASP318 2.9 42.5 1.0
C E:GLN299 3.2 31.2 1.0
O E:HOH1004 3.3 46.3 1.0
OD2 E:ASP220 3.5 36.3 1.0
CA E:GLN299 4.0 29.5 1.0
CG E:GLU219 4.0 35.5 1.0
N E:THR300 4.2 31.5 1.0
O E:HOH1087 4.3 50.8 1.0
CG E:ASP220 4.3 39.6 1.0
CB E:ASP318 4.3 32.8 1.0
CB E:GLN299 4.4 33.6 1.0
OD1 E:ASP220 4.4 38.4 1.0
CA E:THR300 4.4 32.6 1.0
N E:SER301 4.5 26.8 1.0
OD1 E:ASP319 4.8 39.3 1.0
O E:HOH1047 4.9 40.6 1.0
C E:THR300 5.0 29.2 1.0
CA E:ASP318 5.0 29.5 1.0

Copper binding site 6 out of 6 in 8po9

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Copper binding site 6 out of 6 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu901

b:39.7
occ:1.00
 O F:HOH1017 2.1 37.0 1.0
OD1 F:ASP318 2.1 32.7 1.0
O F:HOH1126 2.1 40.0 1.0
OE1 F:GLU219 2.2 37.3 1.0
O F:GLN299 2.2 37.7 1.0
OE2 F:GLU219 2.3 36.3 1.0
CD F:GLU219 2.6 35.4 1.0
OD2 F:ASP318 2.8 40.9 1.0
CG F:ASP318 2.8 37.3 1.0
C F:GLN299 3.2 31.9 1.0
O F:HOH1011 3.4 41.8 1.0
OD2 F:ASP220 3.6 39.8 1.0
CA F:GLN299 4.0 35.6 1.0
CG F:GLU219 4.0 32.3 1.0
N F:THR300 4.2 28.2 1.0
CB F:ASP318 4.3 37.8 1.0
CB F:GLN299 4.3 33.0 1.0
CG F:ASP220 4.4 35.5 1.0
OD1 F:ASP220 4.5 36.9 1.0
CA F:THR300 4.5 30.0 1.0
N F:SER301 4.5 28.8 1.0
CA F:ASP318 4.9 34.5 1.0
OD1 F:ASP319 4.9 41.8 1.0
OG F:SER301 5.0 30.6 1.0

Reference:

M.Spinola-Amilibia, R.Illanes-Vicioso, E.Ruiz-L Formula See Text Pez, P.Colomer-Vidal, F.V.Rodriguez, R.Peces Perez, C.F.Arias, T.Torroba, M.Sol Formula See Text, E.Arias-Palomo, F.Bertocchini. Plastic Degradation By Insect Hexamerins: Near-Atomic Resolution Structures of the Polyethylene-Degrading Proteins From the Wax Worm Saliva. Sci Adv V. 9 I6813 2023.
ISSN: ESSN 2375-2548
PubMed: 37729416
DOI: 10.1126/SCIADV.ADI6813
Page generated: Wed Jul 31 10:08:03 2024

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