Magnesium in PDB 8gr7: COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium

The structure of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium, PDB code: 8gr7 was solved by S.C.Chen, C.H.Hsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.98 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.203, 45.224, 79.324, 85.06, 78.05, 79.95
R / Rfree (%)	16.2 / 20.6

The binding sites of Magnesium atom in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium (pdb code 8gr7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium, PDB code: 8gr7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:38.6 occ:1.00 OD1 A:ASP87 2.2 36.8 1.0 O11 A:PPV404 2.4 42.0 1.0 O12 A:PPV404 2.4 36.8 1.0 O A:HOH506 2.5 38.6 1.0 CG A:ASP87 3.2 35.1 1.0 OPP A:PPV404 3.3 42.4 1.0 P1 A:PPV404 3.3 40.6 1.0 P2 A:PPV404 3.4 36.7 1.0 MG A:MG402 3.5 66.8 1.0 OD2 A:ASP87 3.5 38.5 1.0 OD2 A:ASP91 3.7 53.5 1.0 NH1 A:ARG311 3.9 31.7 1.0 O31 A:PPV404 4.0 36.7 1.0 O22 A:PPV404 4.2 26.7 1.0 OD1 A:ASP91 4.3 49.3 1.0 CG A:ASP91 4.4 48.2 1.0 CE A:MET229 4.5 50.4 1.0 OE1 A:GLU88 4.5 43.2 1.0 O32 A:PPV404 4.5 41.8 1.0 OE2 A:GLU230 4.6 24.8 1.0 CB A:ASP87 4.6 18.7 1.0 O21 A:PPV404 4.6 36.3 1.0 O A:HOH512 4.7 47.6 1.0 O A:HOH518 4.8 38.4 1.0

Magnesium binding site 2 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:66.8 occ:1.00 OE1 A:GLU157 2.4 27.1 1.0 O11 A:PPV404 2.5 42.0 1.0 O A:HOH512 2.8 47.6 1.0 O A:HOH518 3.0 38.4 1.0 CD A:GLU157 3.2 21.5 1.0 O A:HOH506 3.3 38.6 1.0 OE2 A:GLU157 3.3 22.6 1.0 MG A:MG401 3.5 38.6 1.0 P1 A:PPV404 3.8 40.6 1.0 OD2 A:ASP87 3.8 38.5 1.0 ND2 A:ASN238 3.9 14.2 1.0 O A:HOH624 4.0 24.7 1.0 O31 A:PPV404 4.0 36.7 1.0 OD1 A:ASP91 4.0 49.3 1.0 O A:HOH528 4.1 19.9 1.0 O A:HOH542 4.2 32.8 1.0 O21 A:PPV404 4.5 36.3 1.0 OD1 A:ASP87 4.5 36.8 1.0 CG A:ASP87 4.6 35.1 1.0 CG A:GLU157 4.6 19.3 1.0 NH1 A:ARG176 4.7 22.5 1.0 CG A:ASN238 4.8 14.2 1.0 CB A:ASN238 4.9 17.0 1.0 CG A:ASP91 5.0 48.2 1.0

Magnesium binding site 3 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:28.7 occ:1.00 O A:HOH513 2.1 21.1 1.0 O22 A:PPV404 2.1 26.7 1.0 O31 A:PPV404 2.2 36.7 1.0 OE2 A:GLU230 2.2 24.8 1.0 OG A:SER226 2.3 16.0 1.0 OD1 A:ASN222 2.5 24.3 1.0 CB A:SER226 3.2 14.4 1.0 CD A:GLU230 3.2 25.2 1.0 P2 A:PPV404 3.4 36.7 1.0 P1 A:PPV404 3.4 40.6 1.0 CG A:ASN222 3.5 23.5 1.0 O A:HOH506 3.5 38.6 1.0 NH2 A:ARG176 3.6 25.2 1.0 OPP A:PPV404 3.6 42.4 1.0 OE1 A:GLU230 3.7 25.8 1.0 O A:HOH518 3.7 38.4 1.0 ND2 A:ASN222 3.9 20.7 1.0 O A:ASN222 3.9 12.9 1.0 OD1 A:ASP223 4.1 19.0 1.0 O12 A:PPV404 4.1 36.8 1.0 O11 A:PPV404 4.4 42.0 1.0 O21 A:PPV404 4.4 36.3 1.0 C A:ASN222 4.4 9.0 1.0 CG A:GLU230 4.5 20.6 1.0 O32 A:PPV404 4.5 41.8 1.0 CZ A:ARG176 4.5 25.1 1.0 CA A:SER226 4.6 8.7 1.0 CA A:ASP223 4.6 10.3 1.0 CB A:ASN222 4.8 16.5 1.0 N A:ASP223 4.8 8.1 1.0 ND2 A:ASN239 4.8 14.0 1.0 NH1 A:ARG176 4.9 22.5 1.0 CE A:MET229 4.9 50.4 1.0

Magnesium binding site 4 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:23.9 occ:1.00 O A:SER180 2.5 10.6 1.0 O4 A:PEG405 2.6 30.1 1.0 C1 A:PEG405 2.9 27.6 1.0 C3 A:PEG405 3.0 29.8 1.0 O2 A:PEG405 3.0 37.0 1.0 O A:HOH669 3.1 40.0 1.0 O1 A:PEG405 3.2 36.0 1.0 O21 A:PPV404 3.3 36.3 1.0 C4 A:PEG405 3.3 30.4 1.0 C A:SER180 3.5 15.7 1.0 C2 A:PEG405 3.5 27.9 1.0 OPP A:PPV404 3.9 42.4 1.0 CA A:SER180 4.0 17.4 1.0 P1 A:PPV404 4.3 40.6 1.0 CB A:SER180 4.6 13.0 1.0 N A:ALA181 4.6 10.4 1.0 CB A:ALA181 4.6 13.6 1.0

Magnesium binding site 5 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:41.2 occ:1.00 O32 B:PPV404 2.1 36.0 1.0 OD2 B:ASP87 2.2 33.6 1.0 O B:HOH522 2.2 39.3 1.0 O31 B:PPV404 2.4 29.7 1.0 CG B:ASP87 3.2 32.0 1.0 MG B:MG402 3.2 68.6 1.0 P2 B:PPV404 3.3 34.7 1.0 OD2 B:ASP91 3.4 40.4 1.0 OD1 B:ASP87 3.4 31.1 1.0 P1 B:PPV404 3.4 32.5 1.0 OPP B:PPV404 3.5 30.7 1.0 NH2 B:ARG311 3.8 34.6 1.0 O12 B:PPV404 4.0 28.8 1.0 O11 B:PPV404 4.2 28.7 1.0 CG B:ASP91 4.3 39.0 1.0 OD1 B:ASP91 4.4 37.1 1.0 O B:HOH517 4.4 33.7 1.0 O22 B:PPV404 4.5 30.5 1.0 CB B:ASP87 4.5 24.5 1.0 OE2 B:GLU230 4.5 22.5 1.0 O21 B:PPV404 4.6 38.8 1.0 O B:HOH531 4.9 34.4 1.0

Magnesium binding site 6 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:68.6 occ:1.00 O B:HOH531 2.2 34.4 1.0 O32 B:PPV404 2.4 36.0 1.0 O B:HOH522 2.7 39.3 1.0 OE1 B:GLU157 2.9 25.5 1.0 O12 B:PPV404 3.2 28.8 1.0 MG B:MG401 3.2 41.2 1.0 P2 B:PPV404 3.4 34.7 1.0 O B:HOH517 3.4 33.7 1.0 ND2 B:ASN238 4.0 13.7 1.0 OE2 B:GLU230 4.0 22.5 1.0 CD B:GLU157 4.0 27.7 1.0 O22 B:PPV404 4.2 30.5 1.0 OE2 B:GLU157 4.3 24.0 1.0 O B:HOH612 4.4 19.7 1.0 OD1 B:ASP87 4.5 31.1 1.0 OD1 B:ASP91 4.6 37.1 1.0 CD B:GLU230 4.6 26.8 1.0 OPP B:PPV404 4.7 30.7 1.0 CB B:ASN238 4.7 11.0 1.0 NH1 B:ARG176 4.7 22.7 1.0 OD2 B:ASP91 4.7 40.4 1.0 MG B:MG403 4.8 26.7 1.0 OD2 B:ASP87 4.8 33.6 1.0 O B:HOH533 4.8 22.8 1.0 O31 B:PPV404 4.8 29.7 1.0 CG B:ASN238 4.8 20.2 1.0 O B:ASN238 4.9 19.2 1.0

Magnesium binding site 7 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:26.7 occ:1.00 O11 B:PPV404 1.9 28.7 1.0 O B:HOH533 2.2 22.8 1.0 O12 B:PPV404 2.3 28.8 1.0 OE2 B:GLU230 2.3 22.5 1.0 OD1 B:ASN222 2.3 18.7 1.0 OG B:SER226 2.4 18.8 1.0 CB B:SER226 3.1 18.3 1.0 P1 B:PPV404 3.2 32.5 1.0 CD B:GLU230 3.3 26.8 1.0 CG B:ASN222 3.3 21.3 1.0 P2 B:PPV404 3.4 34.7 1.0 OPP B:PPV404 3.5 30.7 1.0 NH2 B:ARG176 3.7 27.4 1.0 ND2 B:ASN222 3.7 15.9 1.0 OE1 B:GLU230 3.7 21.2 1.0 O B:HOH522 3.8 39.3 1.0 O B:HOH531 3.8 34.4 1.0 O B:ASN222 3.9 16.4 1.0 O31 B:PPV404 4.1 29.7 1.0 OD1 B:ASP223 4.2 15.1 1.0 O21 B:PPV404 4.3 38.8 1.0 O32 B:PPV404 4.3 36.0 1.0 C B:ASN222 4.4 11.6 1.0 O22 B:PPV404 4.5 30.5 1.0 CG B:GLU230 4.5 20.5 1.0 CZ B:ARG176 4.6 31.6 1.0 CA B:SER226 4.6 11.1 1.0 CA B:ASP223 4.6 11.7 1.0 CB B:ASN222 4.6 17.0 1.0 N B:ASP223 4.7 10.2 1.0 MG B:MG402 4.8 68.6 1.0 ND2 B:ASN239 4.9 14.2 1.0 O B:HOH501 4.9 31.3 1.0 NH1 B:ARG176 5.0 22.7 1.0

Magnesium binding site 8 out of 8 in the COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of COP4 From Antrodia Cinnamomea in Complex with Pyrophosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:28.7 occ:1.00 O B:HOH501 2.3 31.3 1.0 O B:HOH508 2.4 43.7 1.0 O B:SER180 2.5 14.5 1.0 O4 B:PEG405 2.9 40.3 1.0 O2 B:PEG405 2.9 30.4 1.0 O1 B:PEG405 3.0 27.4 1.0 C4 B:PEG405 3.1 33.2 1.0 C3 B:PEG405 3.1 30.5 1.0 C2 B:PEG405 3.1 28.3 1.0 O B:HOH659 3.1 35.0 1.0 C1 B:PEG405 3.2 24.5 1.0 O22 B:PPV404 3.3 30.5 1.0 C B:SER180 3.6 19.7 1.0 OPP B:PPV404 3.9 30.7 1.0 CA B:SER180 4.2 12.8 1.0 P2 B:PPV404 4.3 34.7 1.0 CB B:ALA181 4.5 10.8 1.0 N B:ALA181 4.6 10.5 1.0 CB B:SER180 4.7 18.2 1.0

S.C.Chen, B.C.Jiang, Y.J.Lu, C.H.Chang, T.H.Wu, S.W.Lin, H.W.Yin, T.H.Lee, C.H.Hsu. Characterization and Crystal Structures of A Cubebol-Producing Sesquiterpene Synthase From Antrodia Cinnamomea. J.Agric.Food Chem. 2023.
ISSN: ESSN 1520-5118
PubMed: 37566786
DOI: 10.1021/ACS.JAFC.3C00570