Magnesium in PDB 8je4: Crystal Structure of Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp)

The structure of Crystal Structure of Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp), PDB code: 8je4 was solved by K.Hamada, A.Oguni, Y.Zhang, M.Satake, Y.Goto, H.Suga, K.Ogata, T.Sengoku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.69 / 2.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.98, 47.88, 89.46, 90, 117.66, 90
R / Rfree (%)	20.7 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp) (pdb code 8je4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp), PDB code: 8je4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp)


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 Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:29.8 occ:1.00 O5 A:PIS401 2.0 31.2 1.0 O6 A:PIS401 2.1 30.2 1.0 O A:HOH539 2.1 27.5 1.0 O A:HOH532 2.1 24.7 1.0 OE1 A:GLU186 2.2 25.0 1.0 O A:HOH528 2.3 23.2 1.0 P1 A:PIS401 3.2 24.3 1.0 CD A:GLU186 3.2 27.2 1.0 O1 A:PIS401 3.2 27.7 1.0 P2 A:PIS401 3.3 32.1 1.0 OE2 A:GLU186 3.5 26.7 1.0 OH A:TYR188 3.6 25.0 1.0 O4 A:PIS401 3.9 31.5 1.0 O A:HOH583 4.1 26.4 1.0 OH A:TYR237 4.1 31.0 1.0 O2 A:PIS401 4.1 31.9 1.0 O3 A:PIS401 4.3 30.1 1.0 OD1 A:ASN231 4.3 31.1 1.0 O A:HOH580 4.5 25.1 1.0 CG A:GLU186 4.6 25.5 1.0 CZ A:TYR188 4.6 27.9 1.0 OD2 A:ASP176 4.7 24.7 1.0 CE2 A:TYR188 4.7 28.6 1.0 S1 A:PIS401 4.8 61.9 1.0 CB A:GLU186 4.9 25.4 1.0 NZ A:LYS137 4.9 27.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp)


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 Limf Prenyltransferase (H239G/W273T Mutant) Bound with the Thiodiphosphate Moiety of Farnesyl S-Thiolodiphosphate (Fspp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:57.5 occ:1.00 O4 B:PIS401 2.3 52.3 1.0 O5 B:PIS401 2.6 57.0 1.0 OE2 B:GLU186 2.7 69.7 1.0 OH B:TYR188 3.2 58.7 1.0 P2 B:PIS401 3.4 59.2 1.0 P1 B:PIS401 3.5 55.2 1.0 O6 B:PIS401 3.5 52.4 1.0 O3 B:PIS401 3.6 50.8 1.0 O1 B:PIS401 3.7 54.1 1.0 OH B:TYR237 3.8 50.1 1.0 CD B:GLU186 3.9 62.6 1.0 CZ B:TYR188 4.2 52.4 1.0 CE2 B:TYR188 4.4 54.2 1.0 OE1 B:GLU186 4.6 56.0 1.0 O2 B:PIS401 4.9 52.6 1.0 OD2 B:ASP176 4.9 42.1 1.0 CG B:GLU186 5.0 49.8 1.0

Y.Zhang, K.Hamada, M.Satake, T.Sengoku, Y.Goto, H.Suga. Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 37877712
DOI: 10.1021/JACS.3C07373