Magnesium 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:

Copper (Cu) 6 atoms
Chlorine (Cl) 22 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella, PDB code: 8po9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8po9

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Magnesium binding site 1 out of 5 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg902

b:54.8
occ:1.00
 O A:TYR409 2.1 57.1 1.0
O A:SER406 2.2 51.6 1.0
O A:MET412 2.5 49.7 1.0
OD1 A:ASN413 2.5 40.6 1.0
C A:TYR409 3.2 58.1 1.0
C A:SER406 3.3 56.4 1.0
CG A:ASN413 3.3 40.2 1.0
C A:MET412 3.5 43.3 1.0
O A:HOH1017 3.8 40.5 1.0
ND2 A:ASN413 3.9 39.1 1.0
N A:MET412 4.0 51.9 1.0
CA A:GLU410 4.0 53.8 1.0
C A:GLU410 4.1 49.9 1.0
O A:GLU410 4.1 52.3 1.0
N A:GLU410 4.1 50.1 1.0
O A:HOH1001 4.1 38.1 1.0
N A:TYR409 4.1 64.5 1.0
CA A:SER406 4.1 49.3 1.0
CA A:TYR409 4.2 58.2 1.0
N A:ASN413 4.3 42.5 1.0
N A:ILE407 4.3 61.9 1.0
CA A:ASN413 4.3 39.9 1.0
CA A:MET412 4.4 47.0 1.0
CB A:ASN413 4.4 36.0 1.0
OG A:SER406 4.4 44.7 1.0
CA A:ILE407 4.4 63.6 1.0
C A:ILE407 4.5 65.9 1.0
O A:ILE407 4.5 74.2 1.0
O A:SER405 4.6 54.9 1.0
CB A:TYR409 4.7 53.7 1.0
N A:ASN411 4.7 52.2 1.0
CB A:SER406 4.9 45.4 1.0
C A:ASN411 4.9 58.9 1.0
N A:ASN408 5.0 68.8 1.0

Magnesium binding site 2 out of 5 in 8po9

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Magnesium binding site 2 out of 5 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg902

b:49.6
occ:1.00
 O B:TYR409 2.0 48.0 1.0
O B:SER406 2.5 48.5 1.0
OD1 B:ASN413 2.5 39.1 1.0
O B:MET412 2.6 44.8 1.0
O B:HOH1267 2.8 50.0 1.0
CG B:ASN413 3.1 38.7 1.0
C B:TYR409 3.2 52.5 1.0
ND2 B:ASN413 3.3 36.0 1.0
C B:MET412 3.4 41.0 1.0
O B:HOH1003 3.6 39.7 1.0
C B:SER406 3.6 47.7 1.0
O B:GLU410 3.8 47.6 1.0
N B:MET412 3.9 50.5 1.0
C B:GLU410 4.0 50.2 1.0
N B:GLU410 4.0 50.2 1.0
CA B:GLU410 4.0 51.0 1.0
N B:ASN413 4.1 37.3 1.0
CA B:TYR409 4.2 56.3 1.0
N B:TYR409 4.2 55.8 1.0
CB B:ASN413 4.2 36.5 1.0
CA B:MET412 4.2 45.7 1.0
CA B:ASN413 4.2 36.7 1.0
CA B:SER406 4.4 39.9 1.0
O B:ILE407 4.5 56.8 1.0
N B:ILE407 4.6 52.4 1.0
C B:ILE407 4.6 53.3 1.0
O B:HOH1018 4.6 39.0 1.0
N B:ASN411 4.7 51.1 1.0
OG B:SER406 4.7 39.5 1.0
CB B:TYR409 4.7 46.8 1.0
CA B:ILE407 4.7 52.2 1.0
O B:SER405 4.8 49.4 1.0
C B:ASN411 4.8 57.8 1.0

Magnesium binding site 3 out of 5 in 8po9

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Magnesium binding site 3 out of 5 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg902

b:57.1
occ:1.00
 O C:TYR409 2.2 61.9 1.0
O C:SER406 2.3 59.4 1.0
OD1 C:ASN413 2.4 46.9 1.0
O C:MET412 2.5 51.4 1.0
O C:HOH1155 2.6 54.4 1.0
CG C:ASN413 2.9 44.6 1.0
ND2 C:ASN413 3.2 48.7 1.0
C C:MET412 3.3 48.3 1.0
C C:TYR409 3.4 63.7 1.0
C C:SER406 3.5 58.5 1.0
O C:HOH1003 3.5 44.3 1.0
O C:GLU410 3.8 65.1 1.0
N C:MET412 3.9 64.1 1.0
N C:ASN413 4.0 44.1 1.0
C C:GLU410 4.0 66.2 1.0
CB C:ASN413 4.1 42.5 1.0
CA C:ASN413 4.1 42.7 1.0
CA C:GLU410 4.1 68.2 1.0
CA C:MET412 4.2 56.7 1.0
N C:GLU410 4.2 60.5 1.0
CA C:SER406 4.3 54.5 1.0
N C:TYR409 4.4 60.9 1.0
CA C:TYR409 4.4 62.8 1.0
N C:ILE407 4.5 63.3 1.0
CA C:ILE407 4.6 67.0 1.0
C C:ILE407 4.7 62.2 1.0
OG C:SER406 4.7 44.6 1.0
O C:ILE407 4.7 66.2 1.0
N C:ASN411 4.7 63.8 1.0
C C:ASN411 4.8 68.7 1.0
O C:SER405 4.9 57.2 1.0
CB C:TYR409 4.9 54.1 1.0
CG C:MET412 5.0 57.1 1.0

Magnesium binding site 4 out of 5 in 8po9

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Magnesium binding site 4 out of 5 in the Polyethylene Oxidation Hexamerin Pease Cibeles (XP_026756460) From Galleria Mellonella


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
E:Mg902

b:48.9
occ:1.00
 O E:SER406 2.1 49.0 1.0
O E:TYR409 2.2 44.8 1.0
OD1 E:ASN413 2.3 34.9 1.0
O E:HOH1209 2.6 42.2 1.0
O E:MET412 2.8 38.2 1.0
CG E:ASN413 3.2 36.3 1.0
C E:SER406 3.3 47.5 1.0
C E:TYR409 3.3 50.0 1.0
C E:MET412 3.7 35.9 1.0
ND2 E:ASN413 3.8 32.8 1.0
CA E:SER406 4.1 39.7 1.0
CA E:GLU410 4.1 43.5 1.0
N E:TYR409 4.1 46.6 1.0
N E:GLU410 4.1 40.5 1.0
N E:ILE407 4.2 55.2 1.0
O E:GLU410 4.2 49.3 1.0
CA E:TYR409 4.2 47.8 1.0
C E:GLU410 4.3 48.2 1.0
CB E:ASN413 4.3 34.3 1.0
CA E:ILE407 4.3 54.0 1.0
CA E:ASN413 4.3 34.0 1.0
C E:ILE407 4.3 52.1 1.0
N E:ASN413 4.3 34.1 1.0
N E:MET412 4.3 51.0 1.0
O E:ILE407 4.4 56.2 1.0
OG E:SER406 4.5 40.6 1.0
CA E:MET412 4.6 43.6 1.0
O E:SER405 4.7 46.1 1.0
CB E:TYR409 4.8 43.0 1.0
N E:ASN408 4.9 48.8 1.0
CB E:SER406 4.9 38.1 1.0

Magnesium binding site 5 out of 5 in 8po9

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
F:Mg902

b:56.0
occ:1.00
 O F:TYR409 2.1 55.6 1.0
O F:SER406 2.3 60.6 1.0
OD1 F:ASN413 2.5 47.5 1.0
O F:HOH1221 2.8 55.4 1.0
O F:MET412 2.9 56.0 1.0
C F:TYR409 3.2 53.4 1.0
CG F:ASN413 3.3 45.0 1.0
O F:HOH1006 3.4 44.5 1.0
C F:SER406 3.5 61.7 1.0
O F:GLU410 3.6 53.7 1.0
ND2 F:ASN413 3.7 45.4 1.0
C F:MET412 3.8 54.5 1.0
CA F:GLU410 3.8 56.7 1.0
C F:GLU410 3.8 52.5 1.0
N F:GLU410 4.0 53.7 1.0
N F:MET412 4.2 60.0 1.0
N F:TYR409 4.2 57.4 1.0
O F:ILE407 4.3 73.4 1.0
CA F:TYR409 4.3 54.1 1.0
CA F:ILE407 4.3 72.1 1.0
C F:ILE407 4.3 73.0 1.0
N F:ILE407 4.4 71.1 1.0
CA F:SER406 4.4 59.3 1.0
CB F:ASN413 4.5 43.9 1.0
N F:ASN413 4.5 46.7 1.0
CA F:ASN413 4.5 45.5 1.0
CA F:MET412 4.6 56.8 1.0
N F:ASN411 4.7 51.0 1.0
OG F:SER406 4.7 49.0 1.0
CB F:TYR409 4.9 54.1 1.0
O F:SER405 4.9 63.0 1.0
C F:ASN411 5.0 59.9 1.0
N F:ASN408 5.0 68.4 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: Fri Oct 4 16:07:42 2024

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