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Magnesium in PDB 3krp: Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp

Enzymatic activity of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp

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

Protein crystallography data

The structure of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp, PDB code: 3krp was solved by T.-H.Chang, F.-L.Hsieh, T.-P.Ko, 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 / 2.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.260, 109.022, 182.156, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp (pdb code 3krp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp, PDB code: 3krp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3krp

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Magnesium binding site 1 out of 4 in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp


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 and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:61.6
occ:1.00
 O12 A:PPV901 1.8 84.2 1.0
O A:HOH732 2.2 50.0 1.0
OD2 A:ASP89 2.5 59.6 1.0
MG A:MG906 2.5 96.8 1.0
OD1 A:ASP91 2.7 62.7 1.0
OD2 A:ASP83 3.1 47.5 1.0
OD1 A:ASP84 3.2 45.1 1.0
CG A:ASP89 3.2 60.3 1.0
P2 A:PPV901 3.3 83.7 1.0
CB A:ASP89 3.3 58.2 1.0
O21 A:PPV901 3.4 85.6 1.0
CG A:ASP91 3.7 60.0 1.0
O22 A:PPV901 3.8 84.2 1.0
CG A:ASP83 4.0 46.5 1.0
NH1 A:ARG94 4.0 52.5 1.0
OPP A:PPV901 4.2 85.7 1.0
O32 A:PPV901 4.2 83.8 1.0
OD2 A:ASP91 4.2 60.4 1.0
P1 A:PPV901 4.3 86.6 1.0
OD1 A:ASP89 4.3 60.3 1.0
CG A:ASP84 4.4 46.6 1.0
O A:ASP83 4.5 44.9 1.0
OD1 A:ASP83 4.7 49.1 1.0
C A:ASP83 4.7 45.0 1.0
CA A:ASP84 4.7 45.7 1.0
CB A:ASP91 4.7 58.5 1.0
N A:ASP84 4.8 45.8 1.0
O31 A:PPV901 4.8 85.3 1.0
CA A:ASP89 4.8 58.1 1.0
CB A:ASP83 4.8 45.1 1.0
O A:HOH733 5.0 62.7 1.0

Magnesium binding site 2 out of 4 in 3krp

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Magnesium binding site 2 out of 4 in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp


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 and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg906

b:96.8
occ:1.00
 O21 A:PPV901 1.8 85.6 1.0
OD2 A:ASP83 1.8 47.5 1.0
OD2 A:ASP89 2.0 59.6 1.0
CG A:ASP83 2.4 46.5 1.0
CG A:ASP89 2.5 60.3 1.0
OD1 A:ASP83 2.5 49.1 1.0
MG A:MG905 2.5 61.6 1.0
O A:HOH733 2.7 62.7 1.0
OD1 A:ASP89 2.9 60.3 1.0
O12 A:PPV901 3.1 84.2 1.0
P1 A:PPV901 3.2 86.6 1.0
CB A:ASP89 3.4 58.2 1.0
O31 A:PPV901 3.7 85.3 1.0
CB A:ASP83 3.8 45.1 1.0
O A:ASP83 3.9 44.9 1.0
P2 A:PPV901 4.0 83.7 1.0
OPP A:PPV901 4.1 85.7 1.0
C A:ASP83 4.3 45.0 1.0
O11 A:PPV901 4.3 87.2 1.0
O22 A:PPV901 4.3 84.2 1.0
CA A:ASP83 4.5 44.2 1.0
OD1 A:ASP91 4.7 62.7 1.0
O A:HOH732 4.7 50.0 1.0
CA A:ASP89 4.7 58.1 1.0
OE1 A:GLN156 5.0 47.9 1.0

Magnesium binding site 3 out of 4 in 3krp

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Magnesium binding site 3 out of 4 in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp


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 and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:48.5
occ:1.00
 O D:HOH296 2.1 43.5 1.0
O D:HOH570 2.2 46.9 1.0
OD2 D:ASP89 2.2 54.6 1.0
OD1 D:ASP91 2.2 69.4 1.0
OD2 D:ASP83 3.1 51.8 1.0
CG D:ASP89 3.1 54.8 1.0
CG D:ASP91 3.3 69.8 1.0
CB D:ASP89 3.5 54.9 1.0
OD2 D:ASP91 3.8 69.5 1.0
MG D:MG904 4.1 57.5 1.0
O D:HOH302 4.2 50.0 1.0
OD1 D:ASP89 4.2 55.2 1.0
OD1 D:ASP84 4.3 46.8 1.0
CG D:ASP83 4.3 50.2 1.0
O D:HOH301 4.5 51.2 1.0
CB D:ASP91 4.6 67.8 1.0
NH1 D:ARG94 4.6 51.5 1.0
O D:ASP83 4.9 43.8 1.0
OD1 D:ASP83 4.9 49.6 1.0
CA D:ASP89 5.0 55.4 1.0

Magnesium binding site 4 out of 4 in 3krp

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Magnesium binding site 4 out of 4 in the Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mint Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Magnesium and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:57.5
occ:1.00
 OD1 D:ASP84 2.3 46.8 1.0
O D:HOH570 2.8 46.9 1.0
NH1 D:ARG94 2.9 51.5 1.0
OD1 D:ASP91 3.0 69.4 1.0
O D:LEU93 3.0 69.5 1.0
CG D:ASP84 3.0 45.9 1.0
CZ D:ARG94 3.1 51.9 1.0
NE D:ARG94 3.2 55.2 1.0
CB D:ASP91 3.4 67.8 1.0
OD2 D:ASP84 3.4 47.5 1.0
CG D:ASP91 3.6 69.8 1.0
NH2 D:ARG94 4.0 48.9 1.0
O D:LYS235 4.1 82.3 1.0
MG D:MG903 4.1 48.5 1.0
CB D:LYS235 4.2 82.3 1.0
CB D:ASP84 4.2 44.8 1.0
C D:LEU93 4.2 69.4 1.0
CB D:ARG94 4.2 64.8 1.0
CD D:ARG94 4.2 57.7 1.0
CG2 D:THR99 4.5 45.6 1.0
CA D:ARG94 4.6 68.0 1.0
CA D:LYS235 4.7 82.7 1.0
CG D:ARG94 4.7 61.0 1.0
OD2 D:ASP91 4.8 69.5 1.0
CA D:ASP84 4.8 45.5 1.0
N D:ARG94 4.9 68.7 1.0
C D:LYS235 4.9 82.4 1.0
CA D:ASP91 4.9 66.9 1.0
O D:HOH296 5.0 43.5 1.0

Reference:

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
Page generated: Sun Aug 10 23:55:58 2025

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