Magnesium in PDB 3kra: Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium

All present enzymatic activity of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium:
2.5.1.1;

The structure of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium, PDB code: 3kra was solved by T.-H.Chang, T.-P.Ko, F.-L.Hsieh, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.281, 109.255, 182.504, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.6

The binding sites of Magnesium atom in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium (pdb code 3kra). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium, PDB code: 3kra:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3002 b:38.0 occ:1.00 OD1 A:ASP222 2.0 28.2 1.0 O A:HOH303 2.0 27.7 1.0 O A:HOH305 2.1 40.9 1.0 O A:HOH307 2.2 38.3 1.0 O A:HOH309 2.3 39.0 1.0 O A:HOH308 2.3 42.0 1.0 CG A:ASP222 2.9 28.4 1.0 OD2 A:ASP222 3.3 28.1 1.0 O A:HOH833 3.9 56.1 1.0 O A:HOH414 4.1 41.6 1.0 CB A:ASP222 4.3 26.6 1.0 O A:GLN218 4.4 24.4 1.0 NE2 A:HIS177 4.4 28.0 1.0 O A:HOH917 4.5 55.4 1.0 CE1 A:HIS177 4.5 25.1 1.0 OE1 A:GLN218 4.5 31.5 1.0 CA A:ASP222 4.5 27.7 1.0 N A:ASP222 4.6 26.0 1.0 OD2 A:ASP225 4.9 44.4 1.0

Magnesium binding site 2 out of 3 in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3003 b:58.6 occ:1.00 O A:HOH312 2.0 50.7 1.0 O A:HOH317 2.1 44.7 1.0 OD1 A:ASP91 2.2 37.6 1.0 O A:HOH311 2.3 47.7 1.0 O A:HOH310 2.4 37.7 1.0 OD1 A:ASP89 3.3 46.6 1.0 CG A:ASP91 3.3 37.3 1.0 CG A:ASP89 3.4 45.5 1.0 CB A:ASP89 3.6 39.8 1.0 OD2 A:ASP91 3.7 39.9 1.0 OD2 A:ASP89 3.9 49.3 1.0 OD2 A:ASP83 4.3 31.1 1.0 O A:HOH559 4.3 35.7 1.0 O A:HOH809 4.4 52.5 1.0 O A:HOH318 4.4 45.0 1.0 OD1 A:ASP84 4.5 28.4 1.0 CB A:ASP91 4.6 35.7 1.0 NH1 A:ARG94 4.8 31.5 1.0

Magnesium binding site 3 out of 3 in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg3001 b:69.1 occ:1.00 O D:HOH297 2.0 49.9 1.0 O D:HOH299 2.1 60.7 1.0 O D:HOH298 2.2 48.1 1.0 OD1 D:ASP91 2.2 44.4 1.0 O D:HOH296 2.2 44.6 1.0 OD1 D:ASP89 2.9 49.9 1.0 CG D:ASP91 3.4 42.4 1.0 CG D:ASP89 3.7 44.8 1.0 CB D:ASP89 3.7 41.7 1.0 OD2 D:ASP91 4.0 46.1 1.0 O D:HOH376 4.1 32.1 1.0 OD2 D:ASP83 4.1 33.4 1.0 OD1 D:ASP84 4.3 26.3 1.0 O D:HOH1173 4.4 49.0 1.0 O D:HOH1221 4.4 69.0 1.0 NH1 D:ARG94 4.5 29.2 1.0 CB D:ASP91 4.6 38.4 1.0 OD2 D:ASP89 4.9 47.9 1.0 O D:HOH302 4.9 61.9 1.0

T.-H.Chang, F.-L.Hsieh, T.-P.Ko, K.-H.Teng, P.-H.Liang, A.H.-J.Wang. Structure of A Heterotetrameric Geranyl Pyrophosphate Synthase From Mint (Mentha Piperita) Reveals Intersubunit Regulation Plant Cell V. 22 454 2010.
ISSN: ISSN 1040-4651
PubMed: 20139160
DOI: 10.1105/TPC.109.071738