Magnesium in PDB 8h4p: Class I Sesquiterpene Synthase

The structure of Class I Sesquiterpene Synthase, PDB code: 8h4p was solved by A.N.Li, T.T.Lou, M.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.79 / 1.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.704, 59.416, 83.548, 90, 98.33, 90
R / Rfree (%)	17.1 / 19.8

The binding sites of Magnesium atom in the Class I Sesquiterpene Synthase (pdb code 8h4p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Class I Sesquiterpene Synthase, PDB code: 8h4p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Class I Sesquiterpene Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Class I Sesquiterpene Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:5.7 occ:1.00 OE2 A:GLU251 2.0 6.2 1.0 O22 A:PPV401 2.0 6.3 1.0 O31 A:PPV401 2.0 5.4 1.0 O A:HOH630 2.1 6.6 1.0 OG A:SER247 2.1 6.8 1.0 OD1 A:ASN243 2.1 5.5 1.0 CD A:GLU251 3.0 7.3 1.0 CG A:ASN243 3.1 5.8 1.0 CB A:SER247 3.2 6.7 1.0 P1 A:PPV401 3.2 6.0 1.0 P2 A:PPV401 3.3 5.8 1.0 OPP A:PPV401 3.4 5.7 1.0 ND2 A:ASN243 3.5 5.7 1.0 OE1 A:GLU251 3.5 7.6 1.0 O A:HOH646 3.8 6.7 1.0 O21 A:PPV401 3.9 5.9 1.0 O A:ASN243 4.0 7.0 1.0 O A:HOH616 4.1 7.0 1.0 O12 A:PPV401 4.2 5.6 1.0 CG A:GLU251 4.3 6.8 1.0 O32 A:PPV401 4.3 6.6 1.0 NH2 A:ARG203 4.3 6.4 1.0 C A:ASN243 4.3 6.0 1.0 CB A:ASN243 4.4 5.6 1.0 O11 A:PPV401 4.5 6.0 1.0 CA A:SER247 4.5 6.8 1.0 OD1 A:ASP244 4.7 7.0 1.0 N A:ASP244 4.8 5.9 1.0 MG A:MG405 4.8 6.0 1.0 C A:SER247 4.8 7.2 1.0 CA A:ASP244 4.9 6.9 1.0 CE A:LYS250 4.9 7.3 1.0 O A:SER247 4.9 7.3 1.0 CA A:ASN243 5.0 6.1 1.0 O A:HOH606 5.0 8.5 1.0

Magnesium binding site 2 out of 6 in the Class I Sesquiterpene Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Class I Sesquiterpene Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:5.8 occ:1.00 OD1 A:ASP114 2.0 6.3 1.0 O A:HOH669 2.1 5.7 1.0 O12 A:PPV401 2.1 5.6 1.0 O A:HOH517 2.1 7.3 1.0 O A:HOH695 2.1 7.2 1.0 O A:HOH508 2.3 5.8 1.0 CG A:ASP114 2.9 6.0 1.0 MG A:MG405 3.1 6.0 1.0 OD2 A:ASP114 3.3 6.2 1.0 P2 A:PPV401 3.3 5.8 1.0 O32 A:PPV401 3.6 6.6 1.0 O A:HOH742 4.1 15.0 1.0 O A:HOH616 4.1 7.0 1.0 O A:HOH646 4.2 6.7 1.0 OD2 A:ASP206 4.2 8.3 1.0 O22 A:PPV401 4.2 6.3 1.0 O A:ASP114 4.3 5.5 1.0 CB A:ASP114 4.3 6.0 1.0 CG A:ASP206 4.4 8.4 1.0 CB A:ASP206 4.4 7.0 1.0 OPP A:PPV401 4.4 5.7 1.0 OE2 A:GLU256 4.4 11.5 1.0 O A:ASP206 4.5 7.2 1.0 O A:HOH618 4.6 16.1 1.0 OG1 A:THR176 4.6 6.2 1.0 CA A:ASP114 4.7 5.4 1.0 O21 A:PPV401 4.8 5.9 1.0 C10 A:BTM402 4.8 13.8 1.0 O A:HOH587 4.8 6.2 1.0 CD1 A:LEU172 4.9 5.5 1.0 OD1 A:ASP206 4.9 7.7 1.0 NH1 A:ARG203 4.9 6.2 1.0 C9 A:BTM402 4.9 14.3 1.0 C A:ASP114 5.0 5.4 1.0

Magnesium binding site 3 out of 6 in the Class I Sesquiterpene Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Class I Sesquiterpene Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:6.0 occ:1.00 OD2 A:ASP114 2.0 6.2 1.0 O21 A:PPV401 2.0 5.9 1.0 O12 A:PPV401 2.1 5.6 1.0 O A:HOH587 2.1 6.2 1.0 O A:HOH616 2.1 7.0 1.0 O A:HOH508 2.2 5.8 1.0 CG A:ASP114 2.9 6.0 1.0 MG A:MG404 3.1 5.8 1.0 P2 A:PPV401 3.2 5.8 1.0 OD1 A:ASP114 3.3 6.3 1.0 P1 A:PPV401 3.3 6.0 1.0 OPP A:PPV401 3.4 5.7 1.0 NH2 A:ARG320 3.7 7.8 1.0 NZ A:LYS250 3.8 7.3 1.0 O22 A:PPV401 3.8 6.3 1.0 OE2 A:GLU256 3.9 11.5 1.0 OE1 A:GLU256 4.0 8.7 1.0 O A:HOH695 4.1 7.2 1.0 O31 A:PPV401 4.2 5.4 1.0 O A:ASP114 4.2 5.5 1.0 OE2 A:GLU251 4.3 6.2 1.0 CD A:GLU256 4.3 9.9 1.0 CB A:ASP114 4.3 6.0 1.0 O11 A:PPV401 4.3 6.0 1.0 OD1 A:ASP115 4.4 8.8 1.0 O32 A:PPV401 4.4 6.6 1.0 O A:HOH646 4.5 6.7 1.0 O A:HOH753 4.7 9.2 1.0 O A:HOH517 4.7 7.3 1.0 C A:ASP114 4.8 5.4 1.0 MG A:MG403 4.8 5.7 1.0 O A:HOH669 4.8 5.7 1.0 O A:HOH709 4.9 9.6 1.0 CZ A:ARG320 4.9 7.9 1.0 CE A:LYS250 5.0 7.3 1.0

Magnesium binding site 4 out of 6 in the Class I Sesquiterpene Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Class I Sesquiterpene Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:6.3 occ:1.00 OD2 B:ASP114 2.0 6.9 1.0 O12 B:PPV401 2.0 6.0 1.0 O11 B:PPV401 2.1 5.9 1.0 O B:HOH585 2.1 6.0 1.0 O B:HOH581 2.1 7.6 1.0 O B:HOH507 2.2 5.3 1.0 CG B:ASP114 3.0 6.7 1.0 MG B:MG404 3.1 6.2 1.0 P1 B:PPV401 3.2 6.0 1.0 P2 B:PPV401 3.3 6.2 1.0 OD1 B:ASP114 3.3 6.8 1.0 OPP B:PPV401 3.4 5.7 1.0 NH2 B:ARG320 3.8 8.6 1.0 O31 B:PPV401 3.8 6.4 1.0 NZ B:LYS250 3.8 7.5 1.0 OE2 B:GLU256 3.9 12.7 1.0 OE1 B:GLU256 4.0 9.6 1.0 O B:HOH734 4.1 7.0 1.0 O22 B:PPV401 4.2 5.7 1.0 OE2 B:GLU251 4.2 7.6 1.0 O B:ASP114 4.2 6.2 1.0 CD B:GLU256 4.3 11.3 1.0 O32 B:PPV401 4.3 6.3 1.0 CB B:ASP114 4.3 6.6 1.0 OD1 B:ASP115 4.5 9.2 1.0 O21 B:PPV401 4.5 6.8 1.0 O B:HOH657 4.5 6.8 1.0 O B:HOH741 4.6 9.8 1.0 O B:HOH510 4.7 7.6 1.0 MG B:MG405 4.8 6.0 1.0 C B:ASP114 4.8 6.0 1.0 O B:HOH694 4.8 9.7 1.0 O B:HOH655 4.8 5.8 1.0 CZ B:ARG320 4.9 9.0 1.0 CE B:LYS250 4.9 7.7 1.0

Magnesium binding site 5 out of 6 in the Class I Sesquiterpene Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Class I Sesquiterpene Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:6.2 occ:1.00 OD1 B:ASP114 2.0 6.8 1.0 O B:HOH655 2.1 5.8 1.0 O11 B:PPV401 2.1 5.9 1.0 O B:HOH734 2.1 7.0 1.0 O B:HOH510 2.1 7.6 1.0 O B:HOH507 2.3 5.3 1.0 CG B:ASP114 3.0 6.7 1.0 MG B:MG403 3.1 6.3 1.0 P1 B:PPV401 3.3 6.0 1.0 OD2 B:ASP114 3.3 6.9 1.0 O21 B:PPV401 3.6 6.8 1.0 O B:HOH748 4.1 16.1 1.0 O B:HOH581 4.2 7.6 1.0 O B:HOH657 4.2 6.8 1.0 OD2 B:ASP206 4.2 9.2 1.0 O31 B:PPV401 4.3 6.4 1.0 O B:ASP114 4.3 6.2 1.0 CB B:ASP114 4.3 6.6 1.0 CG B:ASP206 4.3 8.3 1.0 OPP B:PPV401 4.4 5.7 1.0 OE2 B:GLU256 4.4 12.7 1.0 CB B:ASP206 4.4 7.6 1.0 O B:ASP206 4.5 7.2 1.0 O B:HOH642 4.5 17.1 1.0 OG1 B:THR176 4.6 6.8 1.0 CA B:ASP114 4.7 6.1 1.0 O12 B:PPV401 4.8 6.0 1.0 O B:HOH585 4.8 6.0 1.0 C12 B:BTM402 4.8 15.4 1.0 CD1 B:LEU172 4.8 6.1 1.0 OD1 B:ASP206 4.9 8.6 1.0 NH1 B:ARG203 4.9 6.6 1.0 C13 B:BTM402 4.9 16.2 1.0 C B:ASP114 5.0 6.0 1.0

Magnesium binding site 6 out of 6 in the Class I Sesquiterpene Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Class I Sesquiterpene Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:6.0 occ:1.00 O31 B:PPV401 2.0 6.4 1.0 O22 B:PPV401 2.1 5.7 1.0 OE2 B:GLU251 2.1 7.6 1.0 O B:HOH611 2.1 6.6 1.0 OD1 B:ASN243 2.1 5.3 1.0 OG B:SER247 2.1 6.6 1.0 CD B:GLU251 3.0 7.5 1.0 CG B:ASN243 3.1 5.8 1.0 CB B:SER247 3.2 7.1 1.0 P2 B:PPV401 3.2 6.2 1.0 P1 B:PPV401 3.2 6.0 1.0 OPP B:PPV401 3.4 5.7 1.0 ND2 B:ASN243 3.5 5.8 1.0 OE1 B:GLU251 3.5 7.5 1.0 O B:HOH657 3.8 6.8 1.0 O12 B:PPV401 3.9 6.0 1.0 O B:ASN243 4.0 7.1 1.0 O B:HOH581 4.1 7.6 1.0 O11 B:PPV401 4.2 5.9 1.0 NH2 B:ARG203 4.2 6.4 1.0 CG B:GLU251 4.3 7.6 1.0 O21 B:PPV401 4.3 6.8 1.0 C B:ASN243 4.4 6.3 1.0 CB B:ASN243 4.4 5.6 1.0 O32 B:PPV401 4.5 6.3 1.0 CA B:SER247 4.5 7.0 1.0 OD1 B:ASP244 4.6 7.4 1.0 N B:ASP244 4.7 6.3 1.0 MG B:MG403 4.8 6.3 1.0 CA B:ASP244 4.8 6.9 1.0 C B:SER247 4.8 7.3 1.0 CE B:LYS250 4.9 7.7 1.0 O B:SER247 4.9 7.3 1.0 CA B:ASN243 5.0 6.5 1.0 NH1 B:ARG203 5.0 6.6 1.0 O B:HOH599 5.0 7.8 1.0 CZ B:ARG203 5.0 6.4 1.0

T.Lou, A.Li, H.Xu, J.Pan, B.Xing, R.Wu, J.S.Dickschat, D.Yang, M.Ma. Structural Insights Into Three Sesquiterpene Synthases For the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion By Structure-Based Mutagenesis. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 37018048
DOI: 10.1021/JACS.3C00278