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Magnesium in PDB 3zmc: Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.

Enzymatic activity of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.

All present enzymatic activity of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.:
2.5.1.10;

Protein crystallography data

The structure of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate., PDB code: 3zmc was solved by J.W.Schmidberger, R.Schnell, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.86 / 1.87
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.963, 98.778, 130.554, 90.00, 90.00, 90.00
R / Rfree (%) 20.489 / 25.05

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate. (pdb code 3zmc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate., PDB code: 3zmc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3zmc

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Magnesium binding site 1 out of 5 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1296

b:19.0
occ:1.00
 O2B A:GPP1295 1.8 19.7 1.0
O1A A:GPP1295 2.0 18.3 1.0
OD2 A:ASP89 2.0 15.2 1.0
OD2 A:ASP83 2.1 11.0 1.0
O A:HOH2092 2.1 14.4 1.0
O A:HOH2084 2.2 13.5 1.0
CG A:ASP83 3.0 11.8 1.0
MG A:MG1297 3.1 16.2 1.0
PB A:GPP1295 3.1 19.8 1.0
CG A:ASP89 3.2 14.9 1.0
PA A:GPP1295 3.3 17.1 1.0
OD1 A:ASP83 3.3 11.7 1.0
O3A A:GPP1295 3.5 18.9 1.0
CB A:ASP89 3.7 15.1 1.0
O3B A:GPP1295 3.9 25.0 1.0
NH2 A:ARG94 4.0 17.6 1.0
OD2 A:ASP91 4.2 17.9 1.0
OD1 A:ASP89 4.2 16.9 1.0
O A:HOH2091 4.2 19.2 1.0
O1 A:GPP1295 4.3 21.2 1.0
O A:HOH2217 4.3 25.9 1.0
O1B A:GPP1295 4.3 24.0 1.0
CB A:ASP83 4.3 12.8 1.0
O A:ASP83 4.4 15.2 1.0
O2A A:GPP1295 4.4 19.0 1.0
OD1 A:ASP84 4.4 13.9 1.0
C1 A:GPP1295 4.5 18.3 1.0
C A:ASP83 4.7 13.8 1.0
O A:HOH2082 4.7 18.2 1.0
O A:HOH2083 4.8 13.0 1.0
O A:HOH2085 5.0 16.4 1.0

Magnesium binding site 2 out of 5 in 3zmc

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Magnesium binding site 2 out of 5 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1297

b:16.2
occ:1.00
 O1A A:GPP1295 2.0 18.3 1.0
O A:HOH2083 2.0 13.0 1.0
OD1 A:ASP83 2.0 11.7 1.0
O A:HOH2082 2.0 18.2 1.0
O A:HOH2091 2.2 19.2 1.0
OD2 A:ASP89 2.2 15.2 1.0
CG A:ASP83 3.0 11.8 1.0
CG A:ASP89 3.1 14.9 1.0
MG A:MG1296 3.1 19.0 1.0
PA A:GPP1295 3.1 17.1 1.0
OD1 A:ASP89 3.2 16.9 1.0
OD2 A:ASP83 3.3 11.0 1.0
O1 A:GPP1295 3.7 21.2 1.0
O2A A:GPP1295 3.7 19.0 1.0
NE2 A:GLN157 3.9 12.8 1.0
OE1 A:GLN157 4.1 13.7 1.0
O A:HOH2092 4.1 14.4 1.0
OD2 A:ASP160 4.2 17.0 1.0
CB A:ASP83 4.4 12.8 1.0
CB A:ASP89 4.4 15.1 1.0
CD A:GLN157 4.4 11.1 1.0
O2B A:GPP1295 4.4 19.7 1.0
O3A A:GPP1295 4.5 18.9 1.0
C1 A:GPP1295 4.5 18.3 1.0
C2 A:GPP1295 4.6 19.1 1.0
NZ A:LYS180 4.8 28.0 1.0
O A:ASP83 4.8 15.2 1.0
O A:HOH2084 4.9 13.5 1.0

Magnesium binding site 3 out of 5 in 3zmc

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Magnesium binding site 3 out of 5 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1293

b:17.2
occ:1.00
 O1B B:GPP1292 1.9 24.4 1.0
OD2 B:ASP89 2.0 17.8 1.0
O B:HOH2093 2.1 14.3 1.0
O1A B:GPP1292 2.1 19.9 1.0
O B:HOH2088 2.1 16.6 1.0
OD2 B:ASP83 2.2 16.8 1.0
CG B:ASP83 3.1 15.2 1.0
CG B:ASP89 3.1 18.2 1.0
MG B:MG1294 3.1 14.6 1.0
PB B:GPP1292 3.2 24.2 1.0
PA B:GPP1292 3.3 21.3 1.0
OD1 B:ASP83 3.4 15.8 1.0
CB B:ASP89 3.6 19.6 1.0
O3A B:GPP1292 3.6 21.8 1.0
O B:HOH2194 3.9 18.8 1.0
O2B B:GPP1292 3.9 26.0 1.0
OD2 B:ASP91 4.0 20.2 1.0
NH2 B:ARG94 4.1 19.3 1.0
O B:HOH2092 4.1 14.3 1.0
OD1 B:ASP89 4.1 20.5 1.0
O1 B:GPP1292 4.4 23.4 1.0
O2A B:GPP1292 4.4 19.7 1.0
O3B B:GPP1292 4.4 27.2 1.0
CB B:ASP83 4.4 13.8 1.0
O B:ASP83 4.4 13.3 1.0
OD1 B:ASP84 4.5 15.6 1.0
C1 B:GPP1292 4.5 22.9 1.0
O B:HOH2087 4.7 18.1 1.0
O B:HOH2086 4.8 16.9 1.0
C B:ASP83 4.8 13.1 1.0

Magnesium binding site 4 out of 5 in 3zmc

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Magnesium binding site 4 out of 5 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1294

b:14.6
occ:1.00
 O B:HOH2087 1.9 18.1 1.0
O1A B:GPP1292 2.0 19.9 1.0
OD1 B:ASP83 2.0 15.8 1.0
OD2 B:ASP89 2.1 17.8 1.0
O B:HOH2086 2.1 16.9 1.0
O B:HOH2092 2.2 14.3 1.0
CG B:ASP89 2.9 18.2 1.0
CG B:ASP83 3.0 15.2 1.0
MG B:MG1293 3.1 17.2 1.0
OD1 B:ASP89 3.2 20.5 1.0
PA B:GPP1292 3.2 21.3 1.0
OD2 B:ASP83 3.4 16.8 1.0
O1 B:GPP1292 3.7 23.4 1.0
O2A B:GPP1292 3.8 19.7 1.0
NE2 B:GLN157 3.9 15.8 1.0
O B:HOH2130 4.0 40.1 1.0
OE1 B:GLN157 4.2 17.8 1.0
O B:HOH2093 4.2 14.3 1.0
C1 B:GPP1292 4.3 22.9 1.0
OD2 B:ASP160 4.3 24.4 1.0
CB B:ASP89 4.3 19.6 1.0
CB B:ASP83 4.4 13.8 1.0
O1B B:GPP1292 4.5 24.4 1.0
CD B:GLN157 4.5 14.4 1.0
O3A B:GPP1292 4.6 21.8 1.0
C2 B:GPP1292 4.7 20.5 1.0
O B:ASP83 4.7 13.3 1.0
NZ B:LYS180 4.7 25.3 1.0
O B:HOH2088 4.9 16.6 1.0

Magnesium binding site 5 out of 5 in 3zmc

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Magnesium binding site 5 out of 5 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Substrate Molecule Geranyl Pyrophosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1295

b:42.5
occ:1.00
 O B:HOH2164 2.0 26.9 1.0
O B:HOH2197 2.1 34.7 1.0
OD1 B:ASP223 2.2 24.4 1.0
O B:HOH2168 2.2 33.1 1.0
O B:HOH2167 2.3 44.7 1.0
O B:HOH2137 2.7 27.6 1.0
CG B:ASP223 3.2 23.5 1.0
OD2 B:ASP223 3.5 22.5 1.0
OE1 B:GLN219 4.0 25.4 1.0
O B:HOH2169 4.2 39.5 1.0
O B:HOH2170 4.2 36.1 1.0
O B:HOH2142 4.4 29.5 1.0
O B:GLN219 4.4 18.8 1.0
CB B:ASP223 4.5 25.6 1.0
CE1 B:HIS177 4.6 20.0 1.0
N B:ASP223 4.7 22.4 1.0
CA B:ASP223 4.7 24.6 1.0
NE2 B:HIS177 4.8 20.6 1.0
CB B:ASP222 4.9 25.2 1.0

Reference:

J.W.Schmidberger, R.Schnell, G.Schneider. Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01 To Be Published.
Page generated: Mon Dec 14 09:04:01 2020

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