Magnesium in PDB 8kgb: SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp

All present enzymatic activity of SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp:
2.5.1.28;

The structure of SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp, PDB code: 8kgb was solved by M.Suenaga-Hiromori, T.Ishii, R.Imaizumi, K.Takeshita, T.Yanai, H.Matsuura, N.Sakai, H.Yamaguchi, F.Yanbe, T.Waki, Y.Tozawa, Y.Miyagi-Inoue, M.Yamamoto, K.Kataoka, T.Nakayama, S.Yamashita, S.Takahashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.81 / 2.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.54, 126.71, 72.69, 90, 90.25, 90
R / Rfree (%)	18.8 / 23.5

The binding sites of Magnesium atom in the SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp (pdb code 8kgb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp, PDB code: 8kgb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:45.4 occ:1.00 O2A A:GST401 2.0 47.5 1.0 OD1 A:ASP86 2.1 35.6 1.0 O2B A:GST401 2.1 41.8 1.0 O2A A:IPE402 2.1 41.7 1.0 O A:HOH540 2.2 39.2 1.0 O B:HOH501 2.2 37.9 1.0 CG A:ASP86 3.1 37.5 1.0 PA A:GST401 3.1 48.2 1.0 PB A:GST401 3.2 47.5 1.0 OD2 A:ASP86 3.4 35.3 1.0 O1B A:GST401 3.4 47.3 1.0 O3A A:GST401 3.6 37.0 1.0 PA A:IPE402 3.6 39.3 1.0 NH1 B:ARG301 3.7 68.1 1.0 C1 A:GST401 3.9 49.7 1.0 S1 A:GST401 4.0 44.2 1.0 NH2 A:ARG137 4.1 41.6 1.0 O1B A:IPE402 4.2 38.6 1.0 NH2 A:ARG90 4.2 58.4 1.0 O1 A:IPE402 4.2 42.4 1.0 O B:HOH520 4.3 37.3 1.0 N A:GLY87 4.3 53.3 1.0 CB A:ASP86 4.4 37.1 1.0 O1A A:GST401 4.4 51.3 1.0 O3A A:IPE402 4.5 43.4 1.0 C1 A:IPE402 4.5 51.4 1.0 O3B A:GST401 4.5 47.5 1.0 C2 A:GST401 4.6 48.9 1.0 O1A A:IPE402 4.7 40.4 1.0 CA A:ASP86 4.7 40.3 1.0 CZ B:ARG301 4.9 58.8 1.0 PB A:IPE402 4.9 40.9 1.0

Magnesium binding site 2 out of 4 in the SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:49.5 occ:1.00 O2A B:IPE403 1.9 51.2 1.0 O B:HOH513 2.0 35.1 1.0 O1A B:IPE402 2.1 42.7 1.0 O1B B:IPE403 2.1 58.2 1.0 O B:HOH527 2.1 41.6 1.0 OD1 B:ASP86 2.2 34.6 1.0 PB B:IPE403 3.1 48.5 1.0 CG B:ASP86 3.2 42.1 1.0 PA B:IPE403 3.2 48.9 1.0 O3B B:IPE403 3.4 45.2 1.0 OD2 B:ASP86 3.4 44.8 1.0 O3A B:IPE403 3.5 45.5 1.0 PA B:IPE402 3.5 41.8 1.0 O1 B:IPE403 3.9 42.7 1.0 NH2 B:ARG137 3.9 51.2 1.0 NH2 B:ARG90 4.0 69.4 1.0 O2B B:IPE402 4.1 39.5 1.0 O1 B:IPE402 4.2 44.0 1.0 O B:HOH524 4.2 41.9 1.0 NH1 A:ARG301 4.3 40.4 1.0 O3A B:IPE402 4.3 43.0 1.0 N B:GLY87 4.4 51.1 1.0 O1A B:IPE403 4.4 42.5 1.0 O2B B:IPE403 4.5 50.4 1.0 C2 B:IPE403 4.5 56.0 1.0 CB B:ASP86 4.5 43.0 1.0 O2A B:IPE402 4.6 37.5 1.0 PB B:IPE402 4.8 41.7 1.0 C1 B:IPE403 4.8 48.9 1.0 CA B:ASP86 5.0 43.6 1.0 CA B:GLY87 5.0 54.8 1.0

Magnesium binding site 3 out of 4 in the SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:41.0 occ:1.00 O C:HOH510 1.9 42.5 1.0 O2A C:IPE401 2.0 43.4 1.0 O2A C:GST402 2.0 47.8 1.0 O2B C:GST402 2.1 41.4 1.0 OD1 C:ASP86 2.1 40.7 1.0 O C:HOH504 2.3 36.3 1.0 CG C:ASP86 3.1 39.8 1.0 PA C:GST402 3.1 45.8 1.0 PB C:GST402 3.2 45.1 1.0 OD2 C:ASP86 3.4 44.5 1.0 PA C:IPE401 3.4 40.0 1.0 O1B C:GST402 3.4 47.6 1.0 O3A C:GST402 3.5 37.1 1.0 C1 C:GST402 3.8 52.5 1.0 O1 C:IPE401 4.0 41.0 1.0 NH2 C:ARG137 4.0 41.2 1.0 S1 C:GST402 4.0 46.7 1.0 O3B C:IPE401 4.1 43.6 1.0 NH2 C:ARG90 4.2 61.1 1.0 O D:HOH521 4.2 36.7 1.0 O3A C:IPE401 4.3 41.9 1.0 O1A C:GST402 4.4 52.5 1.0 CB C:ASP86 4.4 35.7 1.0 O1A C:IPE401 4.5 36.7 1.0 N C:GLY87 4.5 43.7 1.0 O3B C:GST402 4.5 44.6 1.0 NH2 D:ARG301 4.5 47.1 1.0 C2 C:GST402 4.5 52.9 1.0 NE D:ARG301 4.7 44.0 1.0 PB C:IPE401 4.8 39.9 1.0 CA C:ASP86 4.8 40.8 1.0

Magnesium binding site 4 out of 4 in the SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SLNDPS1-ATCPT4 Chimera Complexed with Gspp, MG2+, and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:42.3 occ:1.00 O1A D:GST403 2.0 52.8 1.0 O1A D:IPE402 2.1 52.4 1.0 O D:HOH526 2.1 40.2 1.0 O3B D:GST403 2.1 58.7 1.0 O D:HOH501 2.2 43.5 1.0 OD1 D:ASP86 2.2 47.0 1.0 CG D:ASP86 3.1 47.2 1.0 PA D:GST403 3.2 51.4 1.0 OD2 D:ASP86 3.3 42.3 1.0 PB D:GST403 3.3 54.7 1.0 PA D:IPE402 3.5 43.1 1.0 O1B D:GST403 3.6 44.7 1.0 O3A D:GST403 3.6 48.5 1.0 NH1 C:ARG301 3.7 51.6 1.0 O2B D:IPE402 3.9 46.0 1.0 NH2 D:ARG90 4.0 57.2 1.0 NH2 D:ARG137 4.1 52.1 1.0 O D:HOH509 4.2 34.5 1.0 O1 D:IPE402 4.3 46.2 1.0 O3A D:IPE402 4.3 43.8 1.0 S1 D:GST403 4.4 58.3 1.0 O2A D:GST403 4.5 47.0 1.0 CB D:ASP86 4.6 49.0 1.0 N D:GLY87 4.6 58.4 1.0 C1 D:GST403 4.6 60.6 1.0 O2B D:GST403 4.6 49.4 1.0 O2A D:IPE402 4.6 38.9 1.0 PB D:IPE402 4.7 40.5 1.0 CZ C:ARG301 4.9 48.7 1.0 O1B D:IPE402 4.9 40.0 1.0 CZ D:ARG90 5.0 57.2 1.0 CD C:ARG301 5.0 44.7 1.0

M.Suenaga-Hiromori, T.Ishii, R.Imaizumi, K.Takeshita, T.Yanai, H.Matsuura, N.Sakai, T.Mikami, T.Takahashi, C.Minakawa, H.Yamaguchi, F.Yanbe, T.Waki, Y.Tozawa, Y.Miyagi-Inoue, K.Fushihara, M.Yamamoto, K.Kataoka, T.Nakayama, S.Yamashita, S.Takahashi. A Versatile System For Enzymatic Synthesis of Natural and Unnatural Polyisoprenoids on Rubber Particles To Be Published.