Atomistry » Magnesium » PDB 3p1g-3pio » 3pde
Atomistry »
  Magnesium »
    PDB 3p1g-3pio »
      3pde »

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

Go back to Magnesium Binding Sites List in 3pde
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

Go back to Magnesium Binding Sites List in 3pde
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

Go back to Magnesium Binding Sites List in 3pde
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

Go back to Magnesium Binding Sites List in 3pde
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

Go back to Magnesium Binding Sites List in 3pde
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

Go back to Magnesium Binding Sites List in 3pde
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

Go back to Magnesium Binding Sites List in 3pde
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

Go back to Magnesium Binding Sites List in 3pde
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: Thu Aug 15 09:10:25 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy