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Magnesium in PDB 3pde: Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium

Enzymatic activity of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium

All present enzymatic activity of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium, PDB code: 3pde was solved by Y.Patskovsky, R.Toro, M.Rutter, J.M.Sauder, S.K.Burley, C.D.Poulter, J.A.Gerlt, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.539, 51.171, 126.567, 95.75, 91.71, 105.31
R / Rfree (%) 17.1 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium (pdb code 3pde). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium, PDB code: 3pde:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3pde

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Magnesium binding site 1 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:29.8
occ:1.00
O A:HOH584 2.1 34.8 1.0
OD1 A:ASP89 2.2 24.9 1.0
O A:HOH965 2.3 39.4 1.0
O2A A:DMA310 2.3 31.1 1.0
OD2 A:ASP95 2.3 39.7 1.0
O A:HOH971 2.4 46.6 1.0
CG A:ASP95 3.1 36.6 1.0
CG A:ASP89 3.1 27.2 1.0
OD1 A:ASP95 3.3 38.4 1.0
OD2 A:ASP89 3.3 30.3 1.0
MG A:MG312 3.4 31.8 1.0
PA A:DMA310 3.4 39.4 1.0
O1 A:DMA310 3.6 45.4 1.0
OD1 A:ASP163 3.9 35.6 0.5
O1A A:DMA310 4.1 42.0 1.0
OD2 A:ASP163 4.1 36.3 0.5
OE1 A:GLN160 4.2 32.6 1.0
NE2 A:GLN160 4.3 25.7 1.0
C1 A:DMA310 4.4 42.1 1.0
CG A:ASP163 4.5 32.9 0.5
CB A:ASP95 4.5 32.4 1.0
CB A:ASP89 4.5 23.2 1.0
O A:HOH970 4.5 36.1 1.0
OD1 A:ASP163 4.6 40.6 0.5
O3B A:DMA310 4.6 41.9 1.0
CD A:GLN160 4.7 38.2 1.0
NZ A:LYS183 4.8 32.6 1.0
O A:ASP89 4.8 23.9 1.0
O3A A:DMA310 4.8 44.3 1.0
CG A:ASP163 5.0 34.0 0.5
O A:HOH878 5.0 26.3 1.0
CG A:MET94 5.0 38.7 1.0

Magnesium binding site 2 out of 8 in 3pde

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Magnesium binding site 2 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:31.8
occ:1.00
O3B A:DMA310 1.9 41.9 1.0
O A:HOH878 2.0 26.3 1.0
OD2 A:ASP89 2.1 30.3 1.0
O A:HOH970 2.2 36.1 1.0
O2A A:DMA310 2.2 31.1 1.0
OD2 A:ASP95 2.2 39.7 1.0
CG A:ASP89 3.1 27.2 1.0
PB A:DMA310 3.2 42.9 1.0
CG A:ASP95 3.3 36.6 1.0
MG A:MG311 3.4 29.8 1.0
PA A:DMA310 3.5 39.4 1.0
OD1 A:ASP89 3.6 24.9 1.0
O3A A:DMA310 3.7 44.3 1.0
CB A:ASP95 3.8 32.4 1.0
O2B A:DMA310 3.8 45.9 1.0
NH2 A:ARG100 3.8 28.2 1.0
OD1 A:ASP97 4.0 54.6 1.0
OD1 A:ASP90 4.3 26.3 1.0
O A:HOH924 4.4 43.2 1.0
O1 A:DMA310 4.4 45.4 1.0
CB A:ASP89 4.4 23.2 1.0
O A:ASP89 4.4 23.9 1.0
O1B A:DMA310 4.4 38.3 1.0
OD1 A:ASP95 4.4 38.4 1.0
C1 A:DMA310 4.6 42.1 1.0
O1A A:DMA310 4.6 42.0 1.0
O A:HOH971 4.7 46.6 1.0
C A:ASP89 4.8 24.0 1.0

Magnesium binding site 3 out of 8 in 3pde

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Magnesium binding site 3 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg310

b:40.8
occ:1.00
O B:HOH636 1.9 35.4 1.0
O B:HOH973 2.2 46.2 1.0
OD2 B:ASP89 2.3 27.8 1.0
OD2 B:ASP95 2.4 33.4 1.0
O1A B:DMA312 2.4 35.6 1.0
CG B:ASP95 3.1 36.2 1.0
OD1 B:ASP95 3.2 44.0 1.0
CG B:ASP89 3.3 27.5 1.0
MG B:MG311 3.3 31.2 1.0
PA B:DMA312 3.5 39.3 1.0
OD1 B:ASP89 3.5 27.2 1.0
OD2 B:ASP163 3.7 39.1 1.0
O1 B:DMA312 3.7 42.4 1.0
O B:HOH1042 3.8 56.5 1.0
C1 B:DMA312 4.1 38.9 1.0
O B:HOH828 4.1 36.4 1.0
O2A B:DMA312 4.1 45.2 1.0
OE1 B:GLN160 4.2 35.8 1.0
CB B:ASP95 4.5 31.6 1.0
NE2 B:GLN160 4.6 29.8 1.0
CB B:ASP89 4.6 17.8 1.0
O B:HOH1126 4.7 54.5 1.0
CG B:ASP163 4.8 46.3 1.0
CD B:GLN160 4.8 33.5 1.0
O3A B:DMA312 4.9 41.7 1.0
O1B B:DMA312 4.9 36.2 1.0
NZ B:LYS183 4.9 40.2 1.0
O B:HOH617 4.9 25.2 1.0
C2 B:DMA312 4.9 41.5 1.0
O B:ASP89 4.9 26.2 1.0

Magnesium binding site 4 out of 8 in 3pde

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Magnesium binding site 4 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg311

b:31.2
occ:1.00
O1B B:DMA312 1.9 36.2 1.0
O1A B:DMA312 2.0 35.6 1.0
O B:HOH617 2.0 25.2 1.0
O B:HOH828 2.1 36.4 1.0
OD1 B:ASP89 2.1 27.2 1.0
OD2 B:ASP95 2.3 33.4 1.0
CG B:ASP89 3.1 27.5 1.0
PB B:DMA312 3.2 40.4 1.0
PA B:DMA312 3.2 39.3 1.0
MG B:MG310 3.3 40.8 1.0
CG B:ASP95 3.4 36.2 1.0
OD2 B:ASP89 3.4 27.8 1.0
O3A B:DMA312 3.5 41.7 1.0
O2B B:DMA312 3.8 43.9 1.0
NH1 B:ARG100 3.8 27.6 1.0
CB B:ASP95 3.9 31.6 1.0
O1 B:DMA312 4.2 42.4 1.0
C1 B:DMA312 4.3 38.9 1.0
O2A B:DMA312 4.3 45.2 1.0
OD2 B:ASP97 4.3 51.1 1.0
OD1 B:ASP90 4.4 28.4 1.0
O3B B:DMA312 4.4 45.4 1.0
CB B:ASP89 4.4 17.8 1.0
OD1 B:ASP95 4.4 44.0 1.0
O B:HOH973 4.5 46.2 1.0
O B:ASP89 4.7 26.2 1.0
C B:ASP89 4.9 21.8 1.0
O B:HOH636 4.9 35.4 1.0
CZ B:ARG100 5.0 27.3 1.0
CG B:ASP97 5.0 49.6 1.0

Magnesium binding site 5 out of 8 in 3pde

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Magnesium binding site 5 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg311

b:28.5
occ:1.00
OD2 C:ASP89 2.0 23.2 1.0
O2B C:DMA310 2.0 32.2 1.0
O C:HOH800 2.0 26.0 1.0
O2A C:DMA310 2.0 31.4 1.0
O C:HOH795 2.2 35.6 1.0
OD2 C:ASP95 2.2 32.4 1.0
CG C:ASP89 3.1 26.0 1.0
PB C:DMA310 3.3 39.8 1.0
MG C:MG312 3.3 33.8 1.0
PA C:DMA310 3.3 38.4 1.0
CG C:ASP95 3.3 34.0 1.0
OD1 C:ASP89 3.5 22.8 1.0
O3A C:DMA310 3.7 40.6 1.0
NH1 C:ARG100 3.8 26.7 1.0
CB C:ASP95 3.8 31.2 1.0
O1B C:DMA310 4.0 40.8 1.0
OD2 C:ASP97 4.1 35.0 1.0
O1 C:DMA310 4.2 34.3 1.0
C1 C:DMA310 4.2 28.9 1.0
CB C:ASP89 4.3 24.5 1.0
OD1 C:ASP95 4.4 38.8 1.0
O C:HOH989 4.4 39.5 1.0
OD1 C:ASP90 4.4 33.9 1.0
O3B C:DMA310 4.5 35.2 1.0
O1A C:DMA310 4.5 41.0 1.0
O C:ASP89 4.6 23.3 1.0
O C:HOH596 4.8 37.0 1.0
C C:ASP89 4.9 25.5 1.0
CZ C:ARG100 5.0 31.0 1.0
O C:HOH440 5.0 29.7 1.0

Magnesium binding site 6 out of 8 in 3pde

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Magnesium binding site 6 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg312

b:33.8
occ:1.00
O C:HOH596 2.0 37.0 1.0
O C:HOH989 2.1 39.5 1.0
OD1 C:ASP89 2.3 22.8 1.0
O2A C:DMA310 2.4 31.4 1.0
OD2 C:ASP95 2.5 32.4 1.0
CG C:ASP89 3.2 26.0 1.0
CG C:ASP95 3.2 34.0 1.0
MG C:MG311 3.3 28.5 1.0
OD2 C:ASP89 3.4 23.2 1.0
OD1 C:ASP95 3.4 38.8 1.0
PA C:DMA310 3.5 38.4 1.0
OD2 C:ASP163 3.6 50.3 1.0
O1 C:DMA310 3.7 34.3 1.0
C1 C:DMA310 4.0 28.9 1.0
OE1 C:GLN160 4.1 32.4 1.0
O1A C:DMA310 4.2 41.0 1.0
NE2 C:GLN160 4.3 33.2 1.0
O C:HOH795 4.5 35.6 1.0
CB C:ASP95 4.6 31.2 1.0
CB C:ASP89 4.6 24.5 1.0
CD C:GLN160 4.7 30.3 1.0
C2 C:DMA310 4.7 37.6 1.0
CG C:ASP163 4.8 44.8 1.0
O2B C:DMA310 4.8 32.2 1.0
NZ C:LYS183 4.8 31.9 1.0
O3A C:DMA310 4.9 40.6 1.0
O C:HOH800 4.9 26.0 1.0
O C:ASP89 5.0 23.3 1.0

Magnesium binding site 7 out of 8 in 3pde

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Magnesium binding site 7 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg310

b:29.4
occ:1.00
O1B D:DMA312 2.0 30.5 1.0
O1A D:DMA312 2.0 33.2 1.0
O D:HOH434 2.1 28.6 1.0
OD1 D:ASP89 2.1 25.0 1.0
OD2 D:ASP95 2.2 33.6 1.0
O D:HOH958 2.2 39.6 1.0
CG D:ASP89 3.1 22.7 1.0
MG D:MG311 3.2 28.3 1.0
PB D:DMA312 3.2 38.7 1.0
PA D:DMA312 3.3 38.2 1.0
CG D:ASP95 3.3 36.3 1.0
OD2 D:ASP89 3.4 21.9 1.0
O3A D:DMA312 3.6 37.4 1.0
CB D:ASP95 3.8 31.9 1.0
NH1 D:ARG100 3.9 22.8 1.0
O2B D:DMA312 3.9 35.4 1.0
O1 D:DMA312 4.2 39.6 1.0
OD2 D:ASP97 4.2 38.0 1.0
OD1 D:ASP95 4.3 36.2 1.0
O D:HOH1081 4.4 49.9 1.0
C1 D:DMA312 4.4 33.0 1.0
O D:HOH753 4.4 35.6 1.0
OD1 D:ASP90 4.4 24.9 1.0
CB D:ASP89 4.4 18.7 1.0
O2A D:DMA312 4.4 38.3 1.0
O3B D:DMA312 4.4 36.2 1.0
O D:ASP89 4.5 22.4 1.0
O D:HOH957 4.8 38.4 1.0
C D:ASP89 4.9 22.9 1.0
O D:HOH822 5.0 43.2 1.0

Magnesium binding site 8 out of 8 in 3pde

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Magnesium binding site 8 out of 8 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Complexed with Isoprenyl Diphosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg311

b:28.3
occ:1.00
O D:HOH957 2.1 38.4 1.0
OD2 D:ASP89 2.2 21.9 1.0
O D:HOH753 2.2 35.6 1.0
O1A D:DMA312 2.3 33.2 1.0
O D:HOH822 2.3 43.2 1.0
OD2 D:ASP95 2.3 33.6 1.0
CG D:ASP95 3.1 36.3 1.0
CG D:ASP89 3.2 22.7 1.0
MG D:MG310 3.2 29.4 1.0
OD1 D:ASP95 3.3 36.2 1.0
PA D:DMA312 3.4 38.2 1.0
OD1 D:ASP89 3.4 25.0 1.0
O1 D:DMA312 3.5 39.6 1.0
OD2 D:ASP163 3.9 40.5 1.0
O2A D:DMA312 4.0 38.3 1.0
O D:HOH714 4.1 51.3 1.0
C1 D:DMA312 4.2 33.0 1.0
OE1 D:GLN160 4.2 31.7 1.0
O D:HOH958 4.2 39.6 1.0
O D:HOH959 4.3 60.1 1.0
NE2 D:GLN160 4.4 35.9 1.0
CB D:ASP95 4.5 31.9 1.0
CB D:ASP89 4.5 18.7 1.0
NZ D:LYS183 4.7 26.8 1.0
O1B D:DMA312 4.7 30.5 1.0
CD D:GLN160 4.7 28.8 1.0
O3A D:DMA312 4.8 37.4 1.0
O D:ASP89 4.8 22.4 1.0
CG D:ASP163 4.8 34.9 1.0
O D:HOH434 4.9 28.6 1.0
C2 D:DMA312 4.9 34.2 1.0

Reference:

F.H.Wallrapp, J.J.Pan, G.Ramamoorthy, D.E.Almonacid, B.S.Hillerich, R.Seidel, Y.Patskovsky, P.C.Babbitt, S.C.Almo, M.P.Jacobson, C.D.Poulter. Prediction of Function For the Polyprenyl Transferase Subgroup in the Isoprenoid Synthase Superfamily. Proc.Natl.Acad.Sci.Usa V. 110 E1196 2013.
ISSN: ISSN 0027-8424
PubMed: 23493556
DOI: 10.1073/PNAS.1300632110
Page generated: Mon Dec 14 08:38:56 2020

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