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Magnesium in PDB 4umj: Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.

Enzymatic activity of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.

All present enzymatic activity of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.:
2.5.1.10;

Protein crystallography data

The structure of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules., PDB code: 4umj 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) 65.66 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.310, 98.550, 131.320, 90.00, 90.00, 90.00
R / Rfree (%) 19.964 / 24.269

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules. (pdb code 4umj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules., PDB code: 4umj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4umj

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Magnesium binding site 1 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


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 Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1294

b:17.4
occ:1.00
 O A:HOH2108 2.0 22.9 1.0
O2 A:BFQ1297 2.0 16.4 1.0
O A:HOH2109 2.1 13.4 1.0
OD1 A:ASP83 2.1 18.8 1.0
OD2 A:ASP89 2.1 15.5 1.0
O A:HOH2119 2.1 17.2 1.0
CG A:ASP83 3.0 15.5 1.0
CG A:ASP89 3.1 16.0 1.0
MG A:MG1295 3.1 15.6 1.0
OD2 A:ASP83 3.2 13.8 1.0
P1 A:BFQ1297 3.2 17.7 1.0
OD1 A:ASP89 3.3 16.2 1.0
O5 A:BFQ1297 3.4 16.5 1.0
O A:HOH2121 4.0 20.1 1.0
NE2 A:GLN157 4.0 18.1 1.0
OE1 A:GLN157 4.1 21.2 1.0
O14 A:BFQ1299 4.2 21.4 0.8
O3 A:BFQ1297 4.2 18.3 1.0
O A:HOH2199 4.3 43.3 1.0
CB A:ASP89 4.4 16.0 1.0
CB A:ASP83 4.4 14.8 1.0
C19 A:BFQ1297 4.5 16.4 1.0
CD A:GLN157 4.5 17.3 1.0
O9 A:BFQ1297 4.5 18.2 1.0
C7 A:BFQ1297 4.6 16.4 1.0
C16 A:BFQ1297 4.7 16.7 1.0
O A:HOH2204 4.7 34.1 1.0
NZ A:LYS180 4.8 19.7 1.0
O A:HOH2110 4.8 13.0 1.0
O A:ASP83 4.9 18.1 1.0

Magnesium binding site 2 out of 9 in 4umj

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Magnesium binding site 2 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


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 Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1295

b:15.6
occ:1.00
 O9 A:BFQ1297 1.9 18.2 1.0
OD2 A:ASP83 2.0 13.8 1.0
O A:HOH2110 2.1 13.0 1.0
OD2 A:ASP89 2.1 15.5 1.0
O A:HOH2121 2.2 20.1 1.0
O2 A:BFQ1297 2.2 16.4 1.0
CG A:ASP83 3.1 15.5 1.0
MG A:MG1294 3.1 17.4 1.0
P8 A:BFQ1297 3.2 17.9 1.0
CG A:ASP89 3.2 16.0 1.0
OD1 A:ASP83 3.4 18.8 1.0
P1 A:BFQ1297 3.5 17.7 1.0
CB A:ASP89 3.7 16.0 1.0
C7 A:BFQ1297 3.7 16.4 1.0
O A:HOH2130 3.9 18.5 1.0
C16 A:BFQ1297 4.0 16.7 1.0
O12 A:BFQ1297 4.0 17.7 1.0
NH2 A:ARG94 4.0 19.7 1.0
O3 A:BFQ1297 4.1 18.3 1.0
OD2 A:ASP91 4.1 20.1 1.0
O10 A:BFQ1297 4.2 17.4 1.0
OD1 A:ASP89 4.3 16.2 1.0
O A:HOH2119 4.3 17.2 1.0
CB A:ASP83 4.4 14.8 1.0
O12 A:BFQ1299 4.4 24.7 0.8
OD1 A:ASP84 4.4 15.7 1.0
O A:ASP83 4.5 18.1 1.0
O5 A:BFQ1297 4.6 16.5 1.0
O A:HOH2108 4.7 22.9 1.0
C19 A:BFQ1297 4.8 16.4 1.0
C A:ASP83 4.8 14.2 1.0
O A:HOH2109 4.8 13.4 1.0
O10 A:BFQ1299 4.9 23.2 0.8
MG A:MG1300 4.9 19.0 1.0
O14 A:BFQ1299 5.0 21.4 0.8

Magnesium binding site 3 out of 9 in 4umj

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Magnesium binding site 3 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


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 Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1296

b:29.4
occ:1.00
 OE1 A:GLN219 2.0 21.8 1.0
O A:HOH2248 2.0 29.8 1.0
O A:HOH2250 2.1 20.0 1.0
O A:HOH2247 2.2 21.1 1.0
O A:HOH2302 2.2 24.8 1.0
O A:HOH2249 2.3 26.2 1.0
CD A:GLN219 3.0 21.1 1.0
NE2 A:GLN219 3.4 21.6 1.0
O14 A:BFQ1298 3.9 20.6 0.8
O2 A:BFQ1299 3.9 18.8 0.8
O3 A:BFQ1298 4.0 17.9 0.8
O5 A:BFQ1298 4.1 18.2 0.8
O A:HOH2254 4.2 25.4 1.0
O3 A:BFQ1299 4.2 18.9 0.8
CG A:GLN219 4.3 18.5 1.0
CA A:GLN219 4.3 19.0 1.0
O A:HOH2225 4.3 25.2 1.0
OD2 A:ASP222 4.3 36.0 1.0
OD1 A:ASP223 4.4 24.1 1.0
CB A:GLN219 4.4 19.8 1.0
CB A:ASP222 4.5 27.6 1.0
CE1 A:HIS177 4.5 17.9 1.0
O A:HOH2221 4.5 20.1 1.0
P1 A:BFQ1298 4.5 20.8 0.8
P1 A:BFQ1299 4.6 21.4 0.8
O A:GLN219 4.6 18.2 1.0
O A:HOH2251 4.6 24.1 1.0
C7 A:BFQ1298 4.8 22.2 0.8
CG A:ASP222 4.9 34.9 1.0
C A:GLN219 5.0 19.2 1.0
O A:HOH2255 5.0 25.6 1.0

Magnesium binding site 4 out of 9 in 4umj

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Magnesium binding site 4 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


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 Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1300

b:19.0
occ:1.00
 O3 A:BFQ1297 1.9 18.3 1.0
O2 A:BFQ1299 2.0 18.8 0.8
O12 A:BFQ1297 2.0 17.7 1.0
O12 A:BFQ1299 2.1 24.7 0.8
O3 A:BFQ1298 2.2 17.9 0.8
O12 A:BFQ1298 2.2 22.0 0.8
P8 A:BFQ1299 3.2 29.0 0.8
P8 A:BFQ1297 3.2 17.9 1.0
P1 A:BFQ1299 3.2 21.4 0.8
P1 A:BFQ1297 3.2 17.7 1.0
P8 A:BFQ1298 3.3 23.9 0.8
P1 A:BFQ1298 3.4 20.8 0.8
C7 A:BFQ1299 3.5 24.7 0.8
C7 A:BFQ1297 3.6 16.4 1.0
O14 A:BFQ1299 3.6 21.4 0.8
O14 A:BFQ1297 3.6 18.9 1.0
O A:HOH2306 3.7 30.8 1.0
O A:HOH2261 3.8 30.6 1.0
O2 A:BFQ1298 3.9 18.7 0.8
O9 A:BFQ1299 3.9 23.6 0.8
O9 A:BFQ1298 3.9 21.4 0.8
O A:HOH2250 3.9 20.0 1.0
C7 A:BFQ1298 4.0 22.2 0.8
O A:HOH2225 4.0 25.2 1.0
MG A:MG1301 4.0 27.9 1.0
O2 A:BFQ1297 4.0 16.4 1.0
O A:HOH2121 4.1 20.1 1.0
O9 A:BFQ1297 4.1 18.2 1.0
O A:HOH2302 4.1 24.8 1.0
O5 A:BFQ1299 4.2 21.4 0.8
O3 A:BFQ1299 4.3 18.9 0.8
O10 A:BFQ1297 4.3 17.4 1.0
O14 A:BFQ1298 4.4 20.6 0.8
O10 A:BFQ1299 4.4 23.2 0.8
O5 A:BFQ1297 4.4 16.5 1.0
O10 A:BFQ1298 4.5 22.7 0.8
O5 A:BFQ1298 4.6 18.2 0.8
MG A:MG1302 4.9 32.1 1.0
MG A:MG1295 4.9 15.6 1.0
C16 A:BFQ1299 5.0 27.6 0.8

Magnesium binding site 5 out of 9 in 4umj

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Magnesium binding site 5 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


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 Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:27.9
occ:1.00
 O A:HOH2304 1.9 23.6 1.0
O2 A:BFQ1298 2.0 18.7 0.8
O A:HOH2142 2.1 24.1 1.0
O9 A:BFQ1298 2.1 21.4 0.8
O10 A:BFQ1297 2.3 17.4 1.0
O12 A:BFQ1297 2.5 17.7 1.0
P8 A:BFQ1297 2.9 17.9 1.0
P8 A:BFQ1298 3.2 23.9 0.8
P1 A:BFQ1298 3.2 20.8 0.8
C7 A:BFQ1298 3.7 22.2 0.8
O A:HOH2305 3.7 28.9 1.0
O3 A:BFQ1298 3.7 17.9 0.8
C16 A:BFQ1298 3.8 22.4 0.8
O12 A:BFQ1298 3.8 22.0 0.8
O A:HOH2306 3.8 30.8 1.0
O14 A:BFQ1297 3.9 18.9 1.0
MG A:MG1300 4.0 19.0 1.0
NH1 A:ARG94 4.0 18.8 1.0
O9 A:BFQ1297 4.1 18.2 1.0
C7 A:BFQ1297 4.1 16.4 1.0
O A:HOH2130 4.1 18.5 1.0
O10 A:BFQ1298 4.3 22.7 0.8
O5 A:BFQ1298 4.4 18.2 0.8
C39 A:BFQ1298 4.5 27.1 0.8
C19 A:BFQ1298 4.8 25.2 0.8
O A:HOH2099 4.9 30.4 1.0
O A:HOH2144 4.9 27.9 1.0
N22 A:BFQ1298 4.9 26.7 0.8
C16 A:BFQ1297 5.0 16.7 1.0
O14 A:BFQ1298 5.0 20.6 0.8

Magnesium binding site 6 out of 9 in 4umj

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Magnesium binding site 6 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:32.1
occ:1.00
 O5 A:BFQ1299 1.9 21.4 0.8
O A:HOH2308 2.1 35.8 1.0
O A:HOH2260 2.1 29.4 1.0
O9 A:BFQ1299 2.1 23.6 0.8
O A:HOH2309 2.3 31.3 1.0
O A:HOH2261 2.4 30.6 1.0
P1 A:BFQ1299 3.2 21.4 0.8
P8 A:BFQ1299 3.4 29.0 0.8
C7 A:BFQ1299 3.7 24.7 0.8
O2 A:BFQ1299 3.7 18.8 0.8
C16 A:BFQ1299 3.8 27.6 0.8
O A:HOH2255 4.0 25.6 1.0
O12 A:BFQ1299 4.2 24.7 0.8
O12 A:BFQ1298 4.2 22.0 0.8
O A:HOH2254 4.4 25.4 1.0
O3 A:BFQ1299 4.4 18.9 0.8
O10 A:BFQ1299 4.4 23.2 0.8
OD2 A:ASP226 4.4 67.6 1.0
O A:HOH2302 4.7 24.8 1.0
MG A:MG1300 4.9 19.0 1.0

Magnesium binding site 7 out of 9 in 4umj

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Magnesium binding site 7 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1292

b:23.7
occ:1.00
 O B:HOH2111 1.9 30.5 1.0
O5 B:BFQ1294 1.9 23.8 0.8
OD2 B:ASP89 2.0 17.4 1.0
O B:HOH2112 2.1 23.6 1.0
OD1 B:ASP83 2.2 20.2 1.0
O B:HOH2119 2.2 31.8 1.0
CG B:ASP89 2.9 17.3 1.0
CG B:ASP83 3.0 21.8 1.0
MG B:MG1293 3.0 23.3 1.0
OD1 B:ASP89 3.1 22.2 1.0
OD2 B:ASP83 3.2 21.0 1.0
P1 B:BFQ1294 3.2 26.7 0.8
O3 B:BFQ1294 3.4 28.8 0.8
O B:HOH2120 3.9 22.5 1.0
O2 B:BFQ1294 4.0 32.0 0.8
NE2 B:GLN157 4.1 26.9 1.0
OE1 B:GLN157 4.2 28.9 1.0
CB B:ASP89 4.2 17.6 1.0
O9 B:BFQ1294 4.4 22.8 0.8
CB B:ASP83 4.4 20.7 1.0
C19 B:BFQ1294 4.5 29.8 0.8
C7 B:BFQ1294 4.6 27.2 0.8
CD B:GLN157 4.6 26.1 1.0
O B:HOH2113 4.6 17.7 1.0
O B:ASP83 4.7 17.5 1.0
C16 B:BFQ1294 4.8 29.2 0.8
OD2 B:ASP160 5.0 34.8 1.0
OD1 B:ASP160 5.0 41.6 1.0
O B:HOH2173 5.0 28.1 1.0
NZ B:LYS180 5.0 34.6 1.0

Magnesium binding site 8 out of 9 in 4umj

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Magnesium binding site 8 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1293

b:23.3
occ:1.00
 O9 B:BFQ1294 1.9 22.8 0.8
O B:HOH2113 2.0 17.7 1.0
OD2 B:ASP89 2.0 17.4 1.0
O B:HOH2120 2.1 22.5 1.0
OD2 B:ASP83 2.1 21.0 1.0
O5 B:BFQ1294 2.2 23.8 0.8
MG B:MG1292 3.0 23.7 1.0
CG B:ASP83 3.1 21.8 1.0
CG B:ASP89 3.1 17.3 1.0
P8 B:BFQ1294 3.3 24.0 0.8
P1 B:BFQ1294 3.4 26.7 0.8
OD1 B:ASP83 3.5 20.2 1.0
CB B:ASP89 3.7 17.6 1.0
C7 B:BFQ1294 3.9 27.2 0.8
O2 B:BFQ1294 3.9 32.0 0.8
O B:HOH2128 3.9 26.9 1.0
OD2 B:ASP91 4.0 32.4 1.0
O12 B:BFQ1294 4.1 24.9 0.8
NH2 B:ARG94 4.1 20.7 1.0
C16 B:BFQ1294 4.1 29.2 0.8
OD1 B:ASP89 4.2 22.2 1.0
O B:HOH2119 4.3 31.8 1.0
O10 B:BFQ1294 4.4 21.6 0.8
O B:HOH2251 4.4 28.8 1.0
OD1 B:ASP84 4.4 22.6 1.0
CB B:ASP83 4.4 20.7 1.0
O B:ASP83 4.5 17.5 1.0
O3 B:BFQ1294 4.5 28.8 0.8
O B:HOH2111 4.6 30.5 1.0
O B:HOH2112 4.7 23.6 1.0
C19 B:BFQ1294 4.8 29.8 0.8
C B:ASP83 4.8 16.8 1.0
MG B:MG1296 4.9 28.2 1.0

Magnesium binding site 9 out of 9 in 4umj

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Magnesium binding site 9 out of 9 in the Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Native Structure of Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa PA01, with Bound Ibandronic Acid Molecules. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1296

b:28.2
occ:1.00
 O B:HOH2251 2.0 28.8 1.0
O2 B:BFQ1295 2.0 21.2 0.5
O12 B:BFQ1294 2.1 24.9 0.8
O2 B:BFQ1294 2.1 32.0 0.8
O B:HOH2252 2.4 26.8 1.0
O12 B:BFQ1295 2.6 24.8 0.5
P8 B:BFQ1294 3.2 24.0 0.8
P1 B:BFQ1294 3.3 26.7 0.8
P1 B:BFQ1295 3.4 22.8 0.5
C7 B:BFQ1294 3.6 27.2 0.8
O14 B:BFQ1294 3.6 27.1 0.8
P8 B:BFQ1295 3.8 27.5 0.5
O14 B:BFQ1295 3.9 23.1 0.5
O B:HOH2253 3.9 32.2 1.0
O9 B:BFQ1294 4.0 22.8 0.8
O B:HOH2120 4.0 22.5 1.0
C7 B:BFQ1295 4.0 25.5 0.5
O5 B:BFQ1294 4.1 23.8 0.8
O5 B:BFQ1295 4.2 26.3 0.5
O3 B:BFQ1294 4.3 28.8 0.8
O3 B:BFQ1295 4.3 24.7 0.5
O10 B:BFQ1294 4.3 21.6 0.8
O9 B:BFQ1295 4.4 26.1 0.5
O B:HOH2222 4.5 37.2 1.0
MG B:MG1293 4.9 23.3 1.0

Reference:

J.W.Schmidberger, R.Schnell, G.Schneider. Structural Characterization of Substrate and Inhibitor Binding to Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa Acta Crystallogr.,Sect.D V. 71 721 2015.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004715001121
Page generated: Tue Aug 20 04:51:27 2024

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