Magnesium in PDB 3p41: Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate

The structure of Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate, PDB code: 3p41 was solved by Y.Patskovsky, R.Toro, J.M.Sauder, S.K.Burley, C.D.Poulter, J.A.Gerlt, S.C.Almo, New York Sgx Research Center For Structural Genomics(Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.76
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.362, 48.362, 208.592, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.3

The structure of Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate (pdb code 3p41). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate, PDB code: 3p41:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate


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 Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg296 b:58.2 occ:1.00 O A:HOH380 2.1 34.5 1.0 OD1 A:ASP223 2.2 38.0 1.0 O A:HOH360 2.3 57.4 1.0 O A:HOH338 2.3 52.8 1.0 O4 A:POP301 2.4 39.1 0.5 O A:HOH375 2.6 41.8 1.0 CG A:ASP223 3.3 37.2 1.0 P2 A:POP301 3.5 44.5 0.5 O6 A:POP301 3.5 48.5 0.5 OD2 A:ASP223 3.8 37.1 1.0 O A:HOH444 3.9 55.6 1.0 NE2 A:GLN219 3.9 34.7 1.0 O A:HOH414 4.2 39.2 1.0 O A:POP301 4.3 48.2 0.5 O A:GLN219 4.4 29.3 1.0 NE2 A:HIS177 4.4 39.5 1.0 N A:ASP223 4.6 36.2 1.0 CB A:ASP223 4.6 30.6 1.0 CE1 A:HIS177 4.7 28.0 1.0 CB A:ASP222 4.7 37.5 1.0 O5 A:POP301 4.7 36.9 0.5 CA A:ASP223 4.7 35.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate


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 Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg297 b:35.5 occ:1.00 O A:HOH384 2.0 33.0 1.0 OD1 A:ASP83 2.1 29.6 1.0 O A:HOH383 2.1 36.9 1.0 O2A A:DMA300 2.2 30.5 1.0 O A:HOH304 2.2 35.2 1.0 OD1 A:ASP89 2.2 40.0 1.0 CG A:ASP83 3.0 31.9 1.0 CG A:ASP89 3.0 26.7 1.0 PA A:DMA300 3.2 38.8 1.0 OD2 A:ASP89 3.2 38.6 1.0 OD2 A:ASP83 3.3 29.0 1.0 MG A:MG298 3.3 34.5 1.0 O1 A:DMA300 3.5 43.7 1.0 O1A A:DMA300 3.8 37.2 1.0 OD2 A:ASP160 4.0 35.0 1.0 OE1 A:GLN157 4.2 24.0 1.0 O A:HOH443 4.3 44.9 1.0 O A:HOH382 4.3 34.7 1.0 C1 A:DMA300 4.4 33.7 1.0 CB A:ASP89 4.4 28.0 1.0 NE2 A:GLN157 4.4 29.5 1.0 CB A:ASP83 4.4 20.4 1.0 O A:HOH365 4.4 41.4 1.0 O2B A:DMA300 4.5 32.4 1.0 O3A A:DMA300 4.6 48.6 1.0 O2 A:POP301 4.7 47.4 0.5 CD A:GLN157 4.7 38.9 1.0 O A:ASP83 4.8 27.7 1.0 CG A:ASP160 4.9 50.1 1.0 CE A:MSE88 4.9 44.2 1.0 NZ A:LYS180 4.9 35.0 1.0 O A:HOH381 4.9 28.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate


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 Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed with Magnesium and Isoprenyl Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg298 b:34.5 occ:1.00 O2B A:DMA300 1.8 32.4 1.0 O A:HOH381 2.0 28.8 1.0 OD1 A:ASP89 2.1 40.0 1.0 OD2 A:ASP83 2.1 29.0 1.0 O2A A:DMA300 2.1 30.5 1.0 O A:HOH382 2.2 34.7 1.0 CG A:ASP83 3.1 31.9 1.0 CG A:ASP89 3.1 26.7 1.0 PB A:DMA300 3.2 41.8 1.0 MG A:MG297 3.3 35.5 1.0 PA A:DMA300 3.4 38.8 1.0 OD1 A:ASP83 3.5 29.6 1.0 CB A:ASP89 3.6 28.0 1.0 O3A A:DMA300 3.7 48.6 1.0 NH1 A:ARG94 3.7 29.1 1.0 O1B A:DMA300 4.0 46.7 1.0 OD2 A:ASP91 4.0 31.1 1.0 O A:HOH443 4.0 44.9 1.0 O3B A:DMA300 4.2 46.1 1.0 OD2 A:ASP89 4.3 38.6 1.0 O A:HOH383 4.3 36.9 1.0 O1 A:DMA300 4.4 43.7 1.0 OD1 A:ASP84 4.4 30.1 1.0 O1A A:DMA300 4.4 37.2 1.0 O A:ASP83 4.5 27.7 1.0 CB A:ASP83 4.5 20.4 1.0 C1 A:DMA300 4.7 33.7 1.0 C A:ASP83 4.7 26.9 1.0 CZ A:ARG94 5.0 36.6 1.0 O A:HOH304 5.0 35.2 1.0

F.H.Wallrapp, J.J.Pan, G.Ramamoorthy, D.E.Almonacid, B.S.Hillerich, R.Seidel, Y.Patskovsky, P.C.Babbitt, S.C.Almo, M.P.Jacobson, C.D.Poulter. Prediction of Function For the Polyprenyl Transferase Subgroup in the Isoprenoid Synthase Superfamily. Proc.Natl.Acad.Sci.Usa V. 110 E1196 2013.
ISSN: ISSN 0027-8424
PubMed: 23493556
DOI: 10.1073/PNAS.1300632110