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Magnesium in PDB 2q80: Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp

Enzymatic activity of Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp

All present enzymatic activity of Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp:
2.5.1.1; 2.5.1.10; 2.5.1.29;

Protein crystallography data

The structure of Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp, PDB code: 2q80 was solved by K.L.Kavanagh, J.E.Dunford, G.Bunkoczi, C.Smee, F.Von Delft, C.Arrowsmith, J.Weigelt, A.Edwards, M.Sundstrom, U.Oppermann, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.08 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.248, 141.248, 211.705, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp (pdb code 2q80). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp, PDB code: 2q80:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 2q80

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Magnesium binding site 1 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:46.1
occ:1.00
 O1A A:GRG500 2.0 47.1 1.0
OD1 A:ASP64 2.1 48.3 1.0
OD1 A:ASP68 2.2 49.5 1.0
CG A:ASP64 3.1 47.6 1.0
CG A:ASP68 3.2 48.7 1.0
PA A:GRG500 3.2 47.7 1.0
OD2 A:ASP68 3.4 48.9 1.0
MG A:MG401 3.4 45.8 1.0
OE1 A:GLN126 3.5 55.8 1.0
OD2 A:ASP64 3.5 46.3 1.0
O2A A:GRG500 3.6 48.6 1.0
O1 A:GRG500 3.8 51.2 1.0
C1 A:GRG500 4.1 55.1 1.0
OE2 A:GLU210 4.3 57.2 1.0
NZ A:LYS151 4.3 59.5 1.0
OD2 A:ASP129 4.3 57.4 1.0
CD A:GLN126 4.4 53.8 1.0
NE2 A:GLN126 4.5 53.4 1.0
CB A:ASP64 4.5 48.0 1.0
NZ A:LYS212 4.5 54.9 1.0
O3A A:GRG500 4.5 49.5 1.0
CG A:ASP129 4.5 53.3 1.0
O2B A:GRG500 4.6 52.0 1.0
CB A:ASP68 4.6 48.7 1.0
CE A:LYS212 4.6 55.0 1.0
OD1 A:ASP129 4.7 59.3 1.0
O A:ASP64 5.0 47.3 1.0

Magnesium binding site 2 out of 12 in 2q80

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Magnesium binding site 2 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:45.8
occ:1.00
 O2B A:GRG500 1.9 52.0 1.0
OD2 A:ASP64 2.1 46.3 1.0
OD1 A:ASP68 2.2 49.5 1.0
O1A A:GRG500 2.3 47.1 1.0
CG A:ASP64 3.1 47.6 1.0
CG A:ASP68 3.1 48.7 1.0
PB A:GRG500 3.3 49.7 1.0
OD1 A:ASP64 3.3 48.3 1.0
CB A:ASP68 3.4 48.7 1.0
MG A:MG400 3.4 46.1 1.0
PA A:GRG500 3.6 47.7 1.0
O3A A:GRG500 3.6 49.5 1.0
NZ A:LYS202 3.6 69.2 1.0
OE1 A:GLU210 3.8 56.7 1.0
OG A:SER70 4.1 55.2 1.0
OD2 A:ASP68 4.2 48.9 1.0
O3B A:GRG500 4.2 51.5 1.0
O1B A:GRG500 4.3 51.9 1.0
O A:ASP64 4.3 47.3 1.0
OE2 A:GLU210 4.4 57.2 1.0
NH1 A:ARG73 4.4 56.5 1.0
CB A:ASP64 4.5 48.0 1.0
CD A:GLU210 4.5 54.0 1.0
O2A A:GRG500 4.5 48.6 1.0
C A:ASP64 4.6 48.1 1.0
O1 A:GRG500 4.7 51.2 1.0
CE A:LYS202 4.7 69.5 1.0
C1 A:GRG500 4.7 55.1 1.0
OD1 A:ASP65 4.7 56.5 1.0
CA A:ASP68 4.9 49.4 1.0

Magnesium binding site 3 out of 12 in 2q80

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Magnesium binding site 3 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg400

b:46.9
occ:1.00
 O1A B:GRG500 2.1 47.7 1.0
OD1 B:ASP68 2.1 49.7 1.0
OD1 B:ASP64 2.1 46.5 1.0
CG B:ASP68 3.0 49.8 1.0
CG B:ASP64 3.2 47.6 1.0
OD2 B:ASP68 3.2 49.2 1.0
PA B:GRG500 3.4 51.6 1.0
OD2 B:ASP129 3.4 54.8 1.0
OD2 B:ASP64 3.5 45.8 1.0
MG B:MG401 3.5 46.8 1.0
OE1 B:GLN126 3.7 55.3 1.0
O2A B:GRG500 3.7 50.0 1.0
C1 B:GRG500 4.1 56.5 1.0
O1 B:GRG500 4.1 52.8 1.0
OE2 B:GLU210 4.2 57.3 1.0
NE2 B:GLN126 4.3 53.1 1.0
CD B:GLN126 4.3 54.7 1.0
CB B:ASP68 4.5 49.6 1.0
CG B:ASP129 4.5 53.1 1.0
O2B B:GRG500 4.5 52.3 1.0
NZ B:LYS212 4.5 53.2 1.0
CB B:ASP64 4.6 47.4 1.0
O3A B:GRG500 4.6 51.3 1.0
NZ B:LYS151 4.6 59.7 1.0

Magnesium binding site 4 out of 12 in 2q80

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Magnesium binding site 4 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:46.8
occ:1.00
 O2B B:GRG500 2.1 52.3 1.0
OD1 B:ASP68 2.2 49.7 1.0
OD2 B:ASP64 2.2 45.8 1.0
O1A B:GRG500 2.4 47.7 1.0
CG B:ASP68 3.1 49.8 1.0
CG B:ASP64 3.2 47.6 1.0
CB B:ASP68 3.3 49.6 1.0
PB B:GRG500 3.3 53.0 1.0
O3A B:GRG500 3.4 51.3 1.0
MG B:MG400 3.5 46.9 1.0
PA B:GRG500 3.5 51.6 1.0
OD1 B:ASP64 3.6 46.5 1.0
OE1 B:GLU210 3.7 58.2 1.0
O3B B:GRG500 4.0 51.9 1.0
OG B:SER70 4.1 52.8 1.0
OE2 B:GLU210 4.1 57.3 1.0
OD2 B:ASP68 4.3 49.2 1.0
CD B:GLU210 4.3 54.8 1.0
O B:ASP64 4.4 47.4 1.0
O2A B:GRG500 4.5 50.0 1.0
O1B B:GRG500 4.5 52.8 1.0
CB B:ASP64 4.6 47.4 1.0
NH1 B:ARG73 4.6 56.1 1.0
CE B:LYS202 4.7 67.7 1.0
O1 B:GRG500 4.7 52.8 1.0
NZ B:LYS202 4.7 68.1 1.0
CA B:ASP68 4.8 50.2 1.0
C B:ASP64 4.8 47.8 1.0
OD1 B:ASP65 5.0 55.2 1.0
C1 B:GRG500 5.0 56.5 1.0
NZ B:LYS212 5.0 53.2 1.0

Magnesium binding site 5 out of 12 in 2q80

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Magnesium binding site 5 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg400

b:45.7
occ:1.00
 OD1 C:ASP64 2.1 48.8 1.0
O1A C:GRG500 2.2 47.8 1.0
OD1 C:ASP68 2.2 49.1 1.0
CG C:ASP64 3.1 48.1 1.0
CG C:ASP68 3.1 48.8 1.0
PA C:GRG500 3.1 49.0 1.0
OD2 C:ASP68 3.2 47.9 1.0
O1 C:GRG500 3.3 53.1 1.0
OD2 C:ASP129 3.3 56.5 1.0
OD2 C:ASP64 3.3 46.5 1.0
OE1 C:GLN126 3.4 57.0 1.0
O2A C:GRG500 3.6 49.1 1.0
MG C:MG401 3.9 45.6 1.0
OE2 C:GLU210 4.0 57.1 1.0
C1 C:GRG500 4.1 56.3 1.0
CD C:GLN126 4.2 54.9 1.0
NE2 C:GLN126 4.2 52.6 1.0
NZ C:LYS151 4.3 59.8 1.0
O2B C:GRG500 4.4 52.2 1.0
CG C:ASP129 4.4 54.0 1.0
CB C:ASP64 4.5 47.2 1.0
O3A C:GRG500 4.5 51.4 1.0
CB C:ASP68 4.6 49.9 1.0
CD C:GLU210 4.9 54.8 1.0
OE1 C:GLU210 5.0 56.1 1.0
CB C:ASP129 5.0 51.5 1.0
NZ C:LYS212 5.0 58.8 1.0

Magnesium binding site 6 out of 12 in 2q80

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Magnesium binding site 6 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:45.6
occ:1.00
 OD2 C:ASP64 2.1 46.5 1.0
O2B C:GRG500 2.1 52.2 1.0
OD1 C:ASP68 2.2 49.1 1.0
O1A C:GRG500 2.9 47.8 1.0
CG C:ASP68 2.9 48.8 1.0
CB C:ASP68 3.0 49.9 1.0
CG C:ASP64 3.1 48.1 1.0
OD1 C:ASP64 3.6 48.8 1.0
PB C:GRG500 3.7 53.3 1.0
OE1 C:GLU210 3.8 56.1 1.0
O C:ASP64 3.9 47.6 1.0
MG C:MG400 3.9 45.7 1.0
OD1 C:ASP65 4.0 56.3 1.0
OG C:SER70 4.1 53.7 1.0
OD2 C:ASP68 4.1 47.9 1.0
NH1 C:ARG73 4.1 54.3 1.0
C C:ASP64 4.2 47.9 1.0
CB C:ASP64 4.2 47.2 1.0
PA C:GRG500 4.2 49.0 1.0
O3A C:GRG500 4.4 51.4 1.0
O1B C:GRG500 4.5 49.5 1.0
CA C:ASP68 4.5 50.2 1.0
CD C:GLU210 4.6 54.8 1.0
O3B C:GRG500 4.6 52.7 1.0
N C:ASP65 4.6 48.6 1.0
OE2 C:GLU210 4.6 57.1 1.0
CA C:ASP65 4.7 49.9 1.0
CA C:ASP64 4.8 47.4 1.0
CB C:SER70 5.0 52.5 1.0

Magnesium binding site 7 out of 12 in 2q80

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Magnesium binding site 7 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg400

b:44.6
occ:1.00
 OD1 D:ASP68 2.2 48.6 1.0
OD1 D:ASP64 2.2 47.6 1.0
O1A D:GRG500 2.2 46.9 1.0
CG D:ASP68 3.0 49.8 1.0
OD2 D:ASP129 3.1 56.8 1.0
OD2 D:ASP68 3.2 49.5 1.0
CG D:ASP64 3.2 48.0 1.0
PA D:GRG500 3.4 47.7 1.0
OD2 D:ASP64 3.6 47.9 1.0
OE1 D:GLN126 3.6 56.4 1.0
O2A D:GRG500 3.7 48.1 1.0
MG D:MG401 3.8 45.2 1.0
O1 D:GRG500 3.8 50.3 1.0
NZ D:LYS212 4.2 57.1 1.0
NE2 D:GLN126 4.2 55.5 1.0
NZ D:LYS151 4.2 57.8 1.0
OE2 D:GLU210 4.2 57.6 1.0
C1 D:GRG500 4.3 54.6 1.0
CD D:GLN126 4.3 54.1 1.0
CG D:ASP129 4.3 52.7 1.0
CB D:ASP68 4.5 49.8 1.0
CB D:ASP64 4.5 47.6 1.0
O3A D:GRG500 4.8 49.3 1.0
O2B D:GRG500 4.9 51.1 1.0
OE1 D:GLU67 5.0 57.0 1.0
CB D:ASP129 5.0 51.1 1.0

Magnesium binding site 8 out of 12 in 2q80

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Magnesium binding site 8 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


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 Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:45.2
occ:1.00
 O2B D:GRG500 2.1 51.1 1.0
OD1 D:ASP68 2.2 48.6 1.0
OD2 D:ASP64 2.2 47.9 1.0
O1A D:GRG500 2.3 46.9 1.0
CG D:ASP68 3.0 49.8 1.0
CB D:ASP68 3.2 49.8 1.0
CG D:ASP64 3.2 48.0 1.0
PB D:GRG500 3.5 52.5 1.0
OD1 D:ASP64 3.6 47.6 1.0
PA D:GRG500 3.7 47.7 1.0
MG D:MG400 3.8 44.6 1.0
OG D:SER70 3.8 54.7 1.0
OE1 D:GLU210 3.8 58.3 1.0
O3A D:GRG500 3.8 49.3 1.0
OD2 D:ASP68 4.2 49.5 1.0
O D:ASP64 4.3 47.7 1.0
O3B D:GRG500 4.3 52.6 1.0
NH1 D:ARG73 4.3 56.2 1.0
CE D:LYS202 4.4 69.5 1.0
NZ D:LYS202 4.5 70.7 1.0
OE2 D:GLU210 4.5 57.6 1.0
CD D:GLU210 4.6 54.7 1.0
O2A D:GRG500 4.6 48.1 1.0
CB D:ASP64 4.6 47.6 1.0
O1B D:GRG500 4.6 52.8 1.0
C D:ASP64 4.7 48.0 1.0
OD1 D:ASP65 4.7 55.8 1.0
CA D:ASP68 4.7 50.1 1.0
O1 D:GRG500 4.8 50.3 1.0
C1 D:GRG500 5.0 54.6 1.0

Magnesium binding site 9 out of 12 in 2q80

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Magnesium binding site 9 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg400

b:47.8
occ:1.00
 O1A E:GRG500 2.1 46.7 1.0
OD1 E:ASP64 2.2 48.8 1.0
OD1 E:ASP68 2.2 49.3 1.0
CG E:ASP68 3.1 49.9 1.0
PA E:GRG500 3.2 51.3 1.0
OD2 E:ASP68 3.3 50.3 1.0
CG E:ASP64 3.3 48.2 1.0
MG E:MG401 3.5 47.8 1.0
O2A E:GRG500 3.6 50.6 1.0
O1 E:GRG500 3.7 53.0 1.0
OD2 E:ASP64 3.7 49.2 1.0
OD2 E:ASP129 3.8 55.0 1.0
OE2 E:GLU210 4.0 59.4 1.0
OE1 E:GLN126 4.0 57.1 1.0
C1 E:GRG500 4.2 55.5 1.0
NE2 E:GLN126 4.4 52.6 1.0
NZ E:LYS151 4.4 56.6 1.0
CB E:ASP68 4.5 50.5 1.0
CB E:ASP64 4.6 47.4 1.0
CE E:LYS212 4.6 57.4 1.0
CD E:GLN126 4.6 55.0 1.0
O3A E:GRG500 4.6 51.6 1.0
O2B E:GRG500 4.6 50.1 1.0
CG E:ASP129 4.8 53.7 1.0
CD E:GLU210 4.9 55.9 1.0
OE1 E:GLU210 4.9 59.5 1.0

Magnesium binding site 10 out of 12 in 2q80

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Magnesium binding site 10 out of 12 in the Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:47.8
occ:1.00
 OD1 E:ASP68 2.1 49.3 1.0
OD2 E:ASP64 2.1 49.2 1.0
O2B E:GRG500 2.2 50.1 1.0
O1A E:GRG500 2.4 46.7 1.0
CG E:ASP68 2.9 49.9 1.0
CG E:ASP64 3.1 48.2 1.0
CB E:ASP68 3.1 50.5 1.0
OD1 E:ASP64 3.3 48.8 1.0
MG E:MG400 3.5 47.8 1.0
PB E:GRG500 3.7 52.6 1.0
PA E:GRG500 3.7 51.3 1.0
OE1 E:GLU210 3.8 59.5 1.0
O3A E:GRG500 4.0 51.6 1.0
OD2 E:ASP68 4.1 50.3 1.0
OG E:SER70 4.1 53.5 1.0
O E:ASP64 4.3 47.9 1.0
OE2 E:GLU210 4.4 59.4 1.0
CD E:GLU210 4.4 55.9 1.0
CB E:ASP64 4.5 47.4 1.0
NZ E:LYS202 4.5 66.0 1.0
O2A E:GRG500 4.5 50.6 1.0
NH1 E:ARG73 4.6 56.3 1.0
C E:ASP64 4.6 48.0 1.0
OD1 E:ASP65 4.6 55.2 1.0
O1B E:GRG500 4.6 52.4 1.0
O3B E:GRG500 4.6 53.0 1.0
CA E:ASP68 4.7 50.4 1.0
O1 E:GRG500 4.9 53.0 1.0

Reference:

K.L.Kavanagh, J.E.Dunford, G.Bunkoczi, R.G.Russell, U.Oppermann. The Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Reveals A Novel Hexameric Arrangement and Inhibitory Product Binding J.Biol.Chem. V. 281 22004 2006.
ISSN: ISSN 0021-9258
PubMed: 16698791
DOI: 10.1074/JBC.M602603200
Page generated: Mon Dec 14 07:36:07 2020

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