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Magnesium in PDB 3aq0: Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)

Enzymatic activity of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)

All present enzymatic activity of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant):
2.5.1.30;

Protein crystallography data

The structure of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant), PDB code: 3aq0 was solved by F.-L.Hsieh, T.-H.Chang, 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 / 2.65
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 115.961, 115.961, 385.874, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) (pdb code 3aq0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant), PDB code: 3aq0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3aq0

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Magnesium binding site 1 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:47.0
occ:1.00
 O2A A:FPP1002 2.5 44.6 1.0
O3B A:FPP1002 2.7 42.1 1.0
OD2 A:ASP111 2.7 69.3 1.0
OD2 A:ASP107 2.7 68.9 1.0
CB A:ASP111 3.1 72.0 1.0
CG A:ASP107 3.4 66.8 1.0
CG A:ASP111 3.4 71.0 1.0
OD1 A:ASP107 3.5 68.0 1.0
PA A:FPP1002 3.7 44.7 1.0
PB A:FPP1002 4.2 42.0 1.0
O1 A:FPP1002 4.2 43.8 1.0
O A:ASP107 4.3 68.2 1.0
NH1 A:ARG116 4.3 74.9 1.0
O3A A:FPP1002 4.3 43.8 1.0
MG A:MG1001 4.4 64.0 1.0
OD1 A:ASP108 4.4 74.3 1.0
CB A:ASP107 4.6 64.4 1.0
OD1 A:ASP111 4.6 72.1 1.0
CA A:ASP111 4.6 74.3 1.0
C A:ASP107 4.7 67.4 1.0
O A:ASP111 4.8 79.3 1.0
NH2 A:ARG116 4.9 75.2 1.0

Magnesium binding site 2 out of 8 in 3aq0

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Magnesium binding site 2 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:64.0
occ:1.00
 OD2 A:ASP111 2.4 69.3 1.0
O2A A:FPP1002 3.0 44.6 1.0
OE1 A:GLU169 3.2 71.0 1.0
OD1 A:ASP107 3.2 68.0 1.0
OE2 A:GLU172 3.3 77.8 1.0
CG A:ASP111 3.3 71.0 1.0
O1A A:FPP1002 3.5 45.1 1.0
OE2 A:GLU169 3.5 73.8 1.0
OD1 A:ASP111 3.6 72.1 1.0
PA A:FPP1002 3.6 44.7 1.0
CD A:GLU169 3.7 70.5 1.0
CG A:ASP107 4.0 66.8 1.0
O1 A:FPP1002 4.0 43.8 1.0
OD2 A:ASP107 4.0 68.9 1.0
NZ A:LYS193 4.1 67.1 1.0
CD A:GLU172 4.2 77.3 1.0
MG A:MG1000 4.4 47.0 1.0
C2 A:FPP1002 4.6 40.3 1.0
C1 A:FPP1002 4.7 42.1 1.0
CG A:GLU172 4.7 74.8 1.0
CB A:ASP111 4.7 72.0 1.0
CD A:LYS193 4.9 61.3 1.0
CE A:LYS193 5.0 64.1 1.0

Magnesium binding site 3 out of 8 in 3aq0

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Magnesium binding site 3 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1000

b:53.4
occ:1.00
 OD1 C:ASP107 2.2 59.0 1.0
OD2 C:ASP111 2.3 63.5 1.0
O2A C:FPP1002 2.9 33.5 1.0
CG C:ASP107 3.2 57.3 1.0
CG C:ASP111 3.3 66.3 1.0
OE2 C:GLU169 3.5 65.4 1.0
OD2 C:ASP107 3.5 58.2 1.0
OE1 C:GLU169 3.5 66.1 1.0
OD1 C:ASP111 3.6 67.7 1.0
OE2 C:GLU172 3.7 74.1 1.0
CD C:GLU169 3.8 64.5 1.0
PA C:FPP1002 4.0 34.8 1.0
O1A C:FPP1002 4.4 36.6 1.0
CB C:ASP107 4.5 55.3 1.0
O1 C:FPP1002 4.5 37.4 1.0
CB C:ASP111 4.5 65.7 1.0
C2 C:FPP1002 4.7 40.8 1.0
C1 C:FPP1002 4.8 39.7 1.0
O C:ASP107 4.8 59.4 1.0
CD C:GLU172 4.9 73.3 1.0

Magnesium binding site 4 out of 8 in 3aq0

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Magnesium binding site 4 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:36.4
occ:1.00
 O3B C:FPP1002 2.4 26.4 1.0
OD2 C:ASP107 2.5 58.2 1.0
OD1 C:ASP108 3.1 59.4 1.0
O C:HOH391 3.2 23.6 1.0
OD2 C:ASP111 3.5 63.5 1.0
CG C:ASP107 3.5 57.3 1.0
NH1 C:ARG116 3.6 60.1 1.0
O2A C:FPP1002 3.7 33.5 1.0
CB C:ASP111 3.9 65.7 1.0
PB C:FPP1002 4.0 27.0 1.0
O C:ASP107 4.0 59.4 1.0
OD1 C:ASP107 4.2 59.0 1.0
CG C:ASP111 4.2 66.3 1.0
O C:HOH647 4.2 57.2 1.0
C C:ASP107 4.2 58.5 1.0
CA C:ASP108 4.3 61.1 1.0
CG C:ASP108 4.3 60.5 1.0
N C:ASP108 4.3 58.9 1.0
CB C:ASP107 4.5 55.3 1.0
O1B C:FPP1002 4.5 32.7 1.0
CB C:ALA113 4.5 70.2 1.0
CZ C:ARG116 4.6 61.9 1.0
PA C:FPP1002 4.7 34.8 1.0
O3A C:FPP1002 4.7 31.6 1.0
CB C:ASP108 4.9 61.2 1.0
NH2 C:ARG116 5.0 60.4 1.0

Magnesium binding site 5 out of 8 in 3aq0

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Magnesium binding site 5 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1000

b:62.0
occ:1.00
 O2A E:FPP1002 2.3 43.2 1.0
OD2 E:ASP111 2.4 71.2 1.0
OD1 E:ASP107 2.6 66.8 1.0
PA E:FPP1002 3.2 43.7 1.0
O1A E:FPP1002 3.3 42.5 1.0
CG E:ASP107 3.3 65.7 1.0
OD2 E:ASP107 3.4 66.9 1.0
CG E:ASP111 3.5 73.5 1.0
OE2 E:GLU172 3.6 82.1 1.0
OE1 E:GLU169 3.8 74.0 1.0
O1 E:FPP1002 3.8 44.2 1.0
OD1 E:ASP111 3.9 74.7 1.0
MG E:MG1001 4.1 47.9 1.0
OE2 E:GLU169 4.1 73.5 1.0
CD E:GLU169 4.3 72.2 1.0
C1 E:FPP1002 4.4 45.5 1.0
NZ E:LYS193 4.6 75.8 1.0
O3A E:FPP1002 4.7 42.7 1.0
C2 E:FPP1002 4.7 45.4 1.0
CD E:GLU172 4.7 81.1 1.0
CB E:ASP107 4.8 63.9 1.0
CB E:ASP111 4.8 73.1 1.0
O3B E:FPP1002 5.0 41.6 1.0

Magnesium binding site 6 out of 8 in 3aq0

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Magnesium binding site 6 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:47.9
occ:1.00
 O3B E:FPP1002 2.3 41.6 1.0
OD2 E:ASP107 2.4 66.9 1.0
O2A E:FPP1002 2.7 43.2 1.0
OD2 E:ASP111 3.0 71.2 1.0
CG E:ASP107 3.4 65.7 1.0
PB E:FPP1002 3.8 40.8 1.0
CB E:ASP111 3.8 73.1 1.0
CG E:ASP111 3.8 73.5 1.0
PA E:FPP1002 3.9 43.7 1.0
OD1 E:ASP107 3.9 66.8 1.0
O E:HOH559 4.0 18.9 1.0
MG E:MG1000 4.1 62.0 1.0
O E:ASP107 4.1 67.5 1.0
OD1 E:ASP108 4.1 68.4 1.0
O3A E:FPP1002 4.1 42.7 1.0
NH1 E:ARG116 4.1 69.6 1.0
C E:ASP107 4.5 66.5 1.0
O1B E:FPP1002 4.5 42.5 1.0
CB E:ASP107 4.6 63.9 1.0
C1 E:FPP1002 4.8 45.5 1.0
O2B E:FPP1002 4.8 40.2 1.0
O1 E:FPP1002 4.9 44.2 1.0
N E:ASP108 4.9 67.1 1.0
NH2 E:ARG116 5.0 70.6 1.0

Magnesium binding site 7 out of 8 in 3aq0

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Magnesium binding site 7 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1000

b:42.8
occ:1.00
 OD2 H:ASP111 2.0 73.9 1.0
O2A H:FPP1002 2.6 40.0 1.0
OD1 H:ASP107 3.0 72.4 1.0
CG H:ASP111 3.0 75.5 1.0
OD1 H:ASP111 3.3 76.9 1.0
OE2 H:GLU169 3.5 78.6 1.0
OE1 H:GLU169 3.5 75.8 1.0
PA H:FPP1002 3.5 41.0 1.0
OD2 H:ASP107 3.7 73.7 1.0
CG H:ASP107 3.7 71.2 1.0
O1 H:FPP1002 3.9 43.9 1.0
OE2 H:GLU172 3.9 83.2 1.0
O1A H:FPP1002 3.9 40.5 1.0
CD H:GLU169 3.9 75.0 1.0
MG H:MG1001 4.3 62.0 1.0
CB H:ASP111 4.4 76.5 1.0
NZ H:LYS193 4.5 72.5 1.0
C2 H:FPP1002 4.6 41.2 1.0
CD H:GLU172 4.7 83.0 1.0
C1 H:FPP1002 4.8 42.8 1.0
O3A H:FPP1002 5.0 41.7 1.0

Magnesium binding site 8 out of 8 in 3aq0

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Magnesium binding site 8 out of 8 in the Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ligand-Bound Form of Arabidopsis Medium/Long-Chain Length Prenyl Pyrophosphate Synthase (Surface Polar Residue Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1001

b:62.0
occ:1.00
 O3B H:FPP1002 2.3 42.7 1.0
OD2 H:ASP107 2.9 73.7 1.0
OD2 H:ASP111 3.1 73.9 1.0
O2A H:FPP1002 3.2 40.0 1.0
CB H:ASP111 3.4 76.5 1.0
CG H:ASP107 3.5 71.2 1.0
CG H:ASP111 3.7 75.5 1.0
OD1 H:ASP107 3.8 72.4 1.0
PB H:FPP1002 3.9 42.9 1.0
NH1 H:ARG116 4.0 79.2 1.0
PA H:FPP1002 4.1 41.0 1.0
OD1 H:ASP108 4.1 78.2 1.0
O1 H:FPP1002 4.1 43.9 1.0
MG H:MG1000 4.3 42.8 1.0
O H:ASP107 4.4 72.3 1.0
O3A H:FPP1002 4.4 41.7 1.0
CB H:ASP107 4.6 68.6 1.0
O1B H:FPP1002 4.6 42.8 1.0
NH2 H:ARG116 4.7 79.5 1.0
C H:ASP107 4.7 71.5 1.0
CZ H:ARG116 4.7 80.0 1.0
CA H:ASP111 4.8 78.8 1.0
O2B H:FPP1002 4.9 40.8 1.0
O H:ASP111 4.9 83.7 1.0
OD1 H:ASP111 4.9 76.9 1.0

Reference:

F.-L.Hsieh, T.-H.Chang, T.-P.Ko, A.H.-J.Wang. Structure and Mechanism of An Arabidopsis Medium/Long-Chain-Length Prenyl Pyrophosphate Synthase Plant Physiol. V. 155 1079 2011.
ISSN: ISSN 0032-0889
PubMed: 21220764
DOI: 10.1104/PP.110.168799
Page generated: Sun Aug 10 17:31:48 2025

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