Magnesium in PDB 8x37: Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp

All present enzymatic activity of Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp:
2.5.1.28;

The structure of Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp, PDB code: 8x37 was solved by R.Imaizumi, H.Matsuura, T.Yanai, K.Takeshita, S.Misawa, H.Yamaguchi, N.Sakai, Y.Miyagi-Inoue, M.Suenaga-Hiromori, K.Kataoka, T.Nakayama, M.Yamamoto, S.Takahashi, S.Yamashita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.26, 50.27, 120.25, 90, 91.33, 90
R / Rfree (%)	22.1 / 27.4

The binding sites of Magnesium atom in the Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp (pdb code 8x37). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp, PDB code: 8x37:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:46.2 occ:1.00 OD1 A:ASP86 1.9 45.8 1.0 O B:HOH501 2.0 40.2 1.0 O4 A:DST401 2.0 57.1 1.0 O A:HOH503 2.0 47.4 1.0 O7 A:DST402 2.1 50.5 1.0 O7 A:DST401 2.4 69.2 1.0 CG A:ASP86 2.9 56.9 1.0 OD2 A:ASP86 3.3 53.5 1.0 P1 A:DST401 3.3 60.2 1.0 P3 A:DST402 3.4 53.6 1.0 P3 A:DST401 3.5 64.0 1.0 NH1 B:ARG297 3.6 75.5 1.0 O2 A:DST401 3.6 56.4 1.0 NH2 A:ARG137 3.9 61.4 1.0 C10 A:DST401 3.9 89.4 1.0 O B:HOH506 4.0 55.0 1.0 S9 A:DST401 4.0 73.9 1.0 O5 A:DST401 4.0 55.3 1.0 O4 A:DST402 4.0 51.3 1.0 S9 A:DST402 4.3 66.8 1.0 O2 A:DST402 4.3 49.7 1.0 NH2 A:ARG90 4.3 51.5 1.0 CB A:ASP86 4.3 51.6 1.0 O6 A:DST401 4.4 61.4 1.0 O8 A:DST402 4.5 62.1 1.0 N A:GLY87 4.5 48.3 1.0 P1 A:DST402 4.6 47.6 1.0 CZ B:ARG297 4.7 66.3 1.0 CA A:ASP86 4.7 47.4 1.0 O8 A:DST401 4.8 78.4 1.0 O6 A:DST402 4.9 42.4 1.0

Magnesium binding site 2 out of 3 in the Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:64.7 occ:1.00 O7 B:DST401 2.0 68.8 1.0 OD1 B:ASP86 2.0 49.2 1.0 O7 B:DST402 2.1 80.0 1.0 O B:HOH502 2.1 50.3 1.0 O6 B:DST401 2.1 64.2 1.0 O B:HOH510 2.2 62.5 1.0 CG B:ASP86 3.1 65.2 1.0 P3 B:DST401 3.1 67.9 1.0 P1 B:DST401 3.1 63.2 1.0 O2 B:DST401 3.3 74.3 1.0 OD2 B:ASP86 3.5 59.2 1.0 P3 B:DST402 3.6 81.8 1.0 O5 B:DST401 3.6 51.5 1.0 C10 B:DST402 4.0 98.1 1.0 S9 B:DST401 4.1 88.5 1.0 O8 B:DST401 4.3 63.4 1.0 O2 B:DST402 4.3 82.1 1.0 O4 B:DST402 4.4 72.8 1.0 CB B:ASP86 4.4 54.7 1.0 NH2 B:ARG90 4.4 68.9 1.0 N B:GLY87 4.4 58.0 1.0 O8 B:DST402 4.4 88.2 1.0 O4 B:DST401 4.5 68.4 1.0 S9 B:DST402 4.6 112.5 1.0 NH1 B:ARG137 4.7 60.8 1.0 CA B:ASP86 4.8 57.5 1.0 NH2 B:ARG89 4.8 65.4 1.0

Magnesium binding site 3 out of 3 in the Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Neryl Diphosphate Synthase From Solanum Lycopersicum Complexed with Dmsapp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:44.6 occ:1.00 N B:TYR205 3.3 42.3 1.0 ND2 B:ASN258 3.3 49.5 1.0 OG1 B:THR132 3.3 70.3 1.0 CB B:TYR205 3.6 42.0 1.0 CB B:TYR204 3.7 43.6 1.0 CB B:THR132 3.8 71.4 1.0 CA B:GLY202 3.8 46.9 1.0 CG2 B:THR132 4.0 78.2 1.0 CA B:TYR205 4.0 38.9 1.0 C B:GLY202 4.2 49.8 1.0 N B:TYR204 4.2 36.9 1.0 C B:TYR204 4.2 45.2 1.0 CA B:TYR204 4.2 41.7 1.0 N B:GLY202 4.4 47.5 1.0 CG B:ASN258 4.4 44.3 1.0 O B:GLY202 4.5 42.9 1.0 OD1 B:ASN258 4.6 42.0 1.0 OE2 B:GLU133 4.6 107.5 1.0 CG B:TYR204 4.7 50.3 1.0 CD2 B:TYR204 4.7 52.3 1.0 N B:GLY203 4.8 42.9 1.0 CD2 A:LEU56 5.0 75.0 1.0

R.Imaizumi, H.Matsuura, T.Yanai, K.Takeshita, S.Misawa, H.Yamaguchi, N.Sakai, Y.Miyagi-Inoue, M.Suenaga-Hiromori, T.Waki, K.Kataoka, T.Nakayama, M.Yamamoto, S.Takahashi, S.Yamashita. Structural-Functional Correlations Between Unique N-Terminal Region and C-Terminal Conserved Motif in Short-Chain Cis-Prenyltransferase From Tomato. Chembiochem 00796 2024.
ISSN: ESSN 1439-7633
PubMed: 38225831
DOI: 10.1002/CBIC.202300796