Magnesium in PDB 6wkc: Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions

All present enzymatic activity of Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions:
4.2.3.7;

The structure of Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions, PDB code: 6wkc was solved by R.Prem Kumar, J.O.Matos, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.659, 73.745, 81.224, 90.00, 100.19, 90.00
R / Rfree (%)	16.7 / 19.3

The binding sites of Magnesium atom in the Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions (pdb code 6wkc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions, PDB code: 6wkc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:22.5 occ:1.00 OD1 A:ASP81 2.0 20.3 1.0 O A:HOH601 2.1 21.1 1.0 O A:HOH649 2.1 18.6 1.0 O A:HOH538 2.1 24.8 1.0 O A:HOH973 2.1 27.6 1.0 O A:HOH763 2.2 23.0 1.0 CG A:ASP81 3.2 20.3 1.0 NH1 A:ARG44 3.8 31.9 1.0 OD2 A:ASP84 4.0 24.2 1.0 OD2 A:ASP81 4.0 23.1 1.0 CA A:ASP81 4.1 14.9 1.0 O A:HOH605 4.1 21.6 1.0 O A:PHE77 4.1 13.8 1.0 O A:HOH760 4.2 23.7 1.0 N A:ASP81 4.2 16.2 1.0 CB A:ASP81 4.2 16.6 1.0 O A:HOH934 4.3 40.9 1.0 OD2 A:ASP80 4.3 19.2 1.0 OD1 A:ASP84 4.4 24.1 1.0 O A:HOH1027 4.4 40.4 1.0 CG A:ASP84 4.6 21.7 1.0 C A:ASP80 4.8 14.3 1.0 CZ A:ARG44 4.9 31.9 1.0 O A:HOH1047 4.9 37.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.5 occ:1.00 O A:HOH547 2.0 24.2 1.0 O A:HOH635 2.1 19.1 1.0 O A:HOH527 2.1 23.0 1.0 O A:HOH567 2.1 24.7 1.0 O A:HOH882 2.1 28.0 1.0 O A:HOH1002 2.1 27.3 1.0 O A:HOH887 4.0 39.0 1.0 OD2 A:ASP80 4.0 19.2 1.0 OD1 A:ASP80 4.0 15.1 1.0 O A:HOH705 4.0 27.8 1.0 O A:HOH975 4.0 37.4 1.0 O A:PHE83 4.1 20.8 1.0 O A:HOH907 4.1 38.2 1.0 OD1 A:ASP84 4.2 24.1 1.0 O A:HOH764 4.2 39.4 1.0 O A:HOH790 4.2 30.8 1.0 CG A:ASP80 4.4 17.0 1.0 C A:PHE83 4.5 20.4 1.0 O A:HOH503 4.5 44.8 1.0 O A:ASP80 4.6 14.5 1.0 CB A:PHE83 4.6 16.4 1.0 O A:HOH689 4.8 29.2 1.0 N A:ASP84 4.9 17.3 1.0 CA A:ASP84 4.9 19.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:21.3 occ:1.00 OD1 B:ASP81 2.0 19.1 1.0 O B:HOH517 2.0 26.2 1.0 O B:HOH636 2.1 21.9 1.0 O B:HOH556 2.1 20.0 1.0 O B:HOH995 2.1 22.9 1.0 O B:HOH739 2.3 24.4 1.0 CG B:ASP81 3.2 21.3 1.0 OD2 B:ASP84 3.9 24.6 1.0 NH1 B:ARG44 3.9 27.1 1.0 OD2 B:ASP81 4.0 21.6 1.0 O B:HOH1029 4.1 37.3 1.0 CA B:ASP81 4.1 15.0 1.0 O B:HOH667 4.1 23.5 1.0 O B:PHE77 4.1 14.9 1.0 O B:HOH1034 4.1 41.6 1.0 O B:HOH786 4.2 22.7 1.0 N B:ASP81 4.2 13.8 1.0 CB B:ASP81 4.2 13.9 1.0 OD1 B:ASP84 4.3 24.2 1.0 OD2 B:ASP80 4.4 17.4 1.0 CG B:ASP84 4.5 21.2 1.0 O B:HOH931 4.6 42.8 1.0 C B:ASP80 4.8 15.3 1.0 CZ B:ARG44 4.9 36.2 1.0 O B:HOH602 5.0 43.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pentalenene Synthase Complexed with MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:23.8 occ:1.00 O B:HOH600 2.1 19.5 1.0 O B:HOH515 2.1 20.5 1.0 O B:HOH530 2.1 21.6 1.0 O B:HOH855 2.1 29.9 1.0 O B:HOH1033 2.2 28.5 1.0 O B:HOH522 2.3 26.4 1.0 OD2 B:ASP80 3.9 17.4 1.0 OD1 B:ASP80 4.0 17.0 1.0 OD1 B:ASP84 4.1 24.2 1.0 O B:HOH542 4.1 35.2 1.0 O B:PHE83 4.1 19.9 1.0 O B:HOH828 4.1 28.8 1.0 O B:HOH899 4.1 33.8 1.0 O B:HOH602 4.1 43.6 1.0 O B:HOH665 4.2 32.2 1.0 O B:HOH747 4.2 41.1 1.0 CG B:ASP80 4.3 16.0 1.0 O B:HOH981 4.3 41.8 1.0 C B:PHE83 4.5 20.5 1.0 O B:ASP80 4.5 16.5 1.0 CB B:PHE83 4.6 12.4 1.0 N B:ASP84 4.8 16.7 1.0 CA B:ASP84 4.9 18.0 1.0 O B:HOH784 4.9 40.8 1.0 O B:HOH648 4.9 27.9 1.0 O B:HOH636 5.0 21.9 1.0

J.O.Matos, R.P.Kumar, A.C.Ma, M.Patterson, I.J.Krauss, D.D.Oprian. Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase. Biochemistry V. 59 3271 2020.
ISSN: ISSN 0006-2960
PubMed: 32786410
DOI: 10.1021/ACS.BIOCHEM.0C00518