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Magnesium in PDB 2z4x: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21):
2.5.1.1; 2.5.1.10; 2.5.1.29; 2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21), PDB code: 2z4x was solved by R.T.Guo, C.K.-M.Chen, M.Hudock, R.Cao, E.Oldfield, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.405, 47.874, 91.799, 90.00, 110.86, 90.00
R / Rfree (%) 19.6 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21) (pdb code 2z4x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21), PDB code: 2z4x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2z4x

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Magnesium binding site 1 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1201

b:21.4
occ:1.00
 O A:HOH1214 2.0 20.4 1.0
OD2 A:ASP80 2.0 18.7 1.0
OAC A:2521101 2.1 19.5 1.0
O A:HOH1224 2.1 18.1 1.0
OAF A:2521101 2.1 20.5 1.0
OD2 A:ASP84 2.2 19.4 1.0
CG A:ASP80 3.0 19.1 1.0
MG A:MG1202 3.1 14.6 1.0
CG A:ASP84 3.2 20.9 1.0
P1R A:2521101 3.3 20.0 1.0
OD1 A:ASP80 3.4 17.7 1.0
P1P A:2521101 3.4 23.2 1.0
CAP A:2521101 3.8 22.6 1.0
CB A:ASP84 3.8 18.2 1.0
OAH A:2521101 3.8 18.6 1.0
CAO A:2521101 3.9 24.0 1.0
O A:HOH1262 4.1 34.1 1.0
NH2 A:ARG89 4.2 22.2 1.0
O A:HOH1516 4.2 21.9 1.0
OAB A:2521101 4.2 22.8 1.0
OD1 A:ASP84 4.3 22.5 1.0
OE2 A:GLU236 4.3 32.1 1.0
O A:ASP80 4.3 13.8 1.0
CB A:ASP80 4.3 17.0 1.0
NZ A:LYS238 4.4 37.5 1.0
OD1 A:ASP81 4.5 20.1 1.0
OAE A:2521101 4.6 23.7 1.0
O A:HOH1512 4.6 25.8 1.0
C A:ASP80 4.7 17.3 1.0
OAG A:2521101 4.7 22.9 1.0
O A:HOH1481 4.7 22.9 1.0
CAN A:2521101 4.9 24.6 1.0
MG A:MG1203 5.0 25.9 1.0
O A:HOH1217 5.0 26.4 1.0

Magnesium binding site 2 out of 6 in 2z4x

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Magnesium binding site 2 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1202

b:14.6
occ:1.00
 O A:HOH1512 1.9 25.8 1.0
OD1 A:ASP80 2.0 17.7 1.0
OAC A:2521101 2.1 19.5 1.0
OD2 A:ASP84 2.1 19.4 1.0
O A:HOH1217 2.2 26.4 1.0
O A:HOH1516 2.2 21.9 1.0
CG A:ASP80 2.9 19.1 1.0
CG A:ASP84 2.9 20.9 1.0
OD1 A:ASP84 3.0 22.5 1.0
MG A:MG1201 3.1 21.4 1.0
OD2 A:ASP80 3.2 18.7 1.0
P1R A:2521101 3.3 20.0 1.0
OAG A:2521101 3.6 22.9 1.0
OE1 A:GLU236 4.0 30.0 1.0
NE2 A:GLN147 4.0 18.3 1.0
O A:HOH1224 4.0 18.1 1.0
OE1 A:GLN147 4.2 22.7 1.0
OD2 A:ASP150 4.3 33.2 1.0
OAH A:2521101 4.3 18.6 1.0
CB A:ASP80 4.4 17.0 1.0
CB A:ASP84 4.4 18.2 1.0
NZ A:LYS238 4.5 37.5 1.0
CAN A:2521101 4.5 24.6 1.0
CD A:GLN147 4.5 21.6 1.0
CAO A:2521101 4.5 24.0 1.0
CAP A:2521101 4.6 22.6 1.0
OE2 A:GLU236 4.7 32.1 1.0
O A:ASP80 4.7 13.8 1.0
CD A:GLU236 4.7 30.2 1.0
OAF A:2521101 4.7 20.5 1.0
O A:HOH1214 4.7 20.4 1.0
O A:HOH1365 4.8 44.2 1.0
CE A:LYS238 4.9 37.3 1.0
CA A:ASP80 5.0 17.3 1.0

Magnesium binding site 3 out of 6 in 2z4x

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Magnesium binding site 3 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1203

b:25.9
occ:1.00
 OAH A:2521101 1.9 18.6 1.0
O A:HOH1481 2.0 22.9 1.0
O A:HOH1477 2.0 29.4 1.0
OAB A:2521101 2.1 22.8 1.0
O A:HOH1555 2.1 31.1 1.0
O A:HOH1308 2.1 23.9 1.0
P1P A:2521101 3.2 23.2 1.0
P1R A:2521101 3.3 20.0 1.0
CAP A:2521101 3.6 22.6 1.0
OAD A:2521101 3.6 21.3 1.0
NZ A:LYS238 3.8 37.5 1.0
OD1 A:ASP233 4.0 22.6 1.0
O A:HOH1317 4.0 44.0 1.0
OAF A:2521101 4.1 20.5 1.0
CE A:LYS238 4.2 37.3 1.0
OAG A:2521101 4.2 22.9 1.0
O A:HOH1224 4.2 18.1 1.0
OAC A:2521101 4.2 19.5 1.0
OD2 A:ASP233 4.3 21.2 1.0
NE2 A:GLN211 4.4 28.3 1.0
OD1 A:ASP214 4.4 42.5 1.0
OAE A:2521101 4.5 23.7 1.0
CG A:ASP233 4.6 21.5 1.0
O A:HOH1541 4.7 34.5 1.0
CG A:ASP214 4.8 38.7 1.0
CB A:ASP214 4.8 33.9 1.0
OD2 A:ASP215 4.9 30.9 1.0
MG A:MG1201 5.0 21.4 1.0

Magnesium binding site 4 out of 6 in 2z4x

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Magnesium binding site 4 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1204

b:19.1
occ:1.00
 O B:HOH1222 1.9 19.9 1.0
OD1 B:ASP80 2.0 17.8 1.0
OAC B:2521102 2.0 18.8 1.0
OAF B:2521102 2.1 19.8 1.0
OD2 B:ASP84 2.1 19.8 1.0
O B:HOH1208 2.1 18.3 1.0
CG B:ASP80 2.9 20.0 1.0
MG B:MG1205 2.9 13.0 1.0
OD2 B:ASP80 3.1 17.4 1.0
P1R B:2521102 3.2 20.8 1.0
CG B:ASP84 3.2 23.9 1.0
P1P B:2521102 3.4 20.3 1.0
CAP B:2521102 3.8 21.5 1.0
OAH B:2521102 3.8 21.8 1.0
CB B:ASP84 3.8 18.2 1.0
CAO B:2521102 4.0 23.1 1.0
O B:HOH1336 4.1 19.5 1.0
O B:HOH1494 4.1 36.6 1.0
O B:HOH1238 4.1 40.0 1.0
OAB B:2521102 4.2 19.8 1.0
CB B:ASP80 4.3 16.1 1.0
NH2 B:ARG89 4.3 27.8 1.0
OD1 B:ASP84 4.3 21.8 1.0
O B:ASP80 4.3 14.8 1.0
OE1 B:GLU236 4.4 32.7 1.0
OAE B:2521102 4.5 21.9 1.0
OAG B:2521102 4.6 22.8 1.0
O B:HOH1239 4.6 23.2 1.0
C B:ASP80 4.6 17.5 1.0
O B:HOH1253 4.7 20.8 1.0
OD1 B:ASP81 4.7 23.5 1.0
O B:HOH1447 4.7 41.0 1.0
MG B:MG1206 4.9 26.6 1.0
CAN B:2521102 4.9 23.6 1.0
O B:HOH1338 4.9 21.1 1.0

Magnesium binding site 5 out of 6 in 2z4x

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Magnesium binding site 5 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1205

b:13.0
occ:1.00
 OD2 B:ASP80 1.9 17.4 1.0
OAC B:2521102 2.0 18.8 1.0
O B:HOH1336 2.1 19.5 1.0
OD2 B:ASP84 2.1 19.8 1.0
O B:HOH1239 2.1 23.2 1.0
O B:HOH1338 2.2 21.1 1.0
CG B:ASP84 2.9 23.9 1.0
MG B:MG1204 2.9 19.1 1.0
CG B:ASP80 2.9 20.0 1.0
OD1 B:ASP84 3.1 21.8 1.0
P1R B:2521102 3.2 20.8 1.0
OD1 B:ASP80 3.3 17.8 1.0
OAG B:2521102 3.5 22.8 1.0
O B:HOH1222 3.8 19.9 1.0
OE1 B:GLN147 4.0 25.4 1.0
OE2 B:GLU236 4.1 30.6 1.0
OAH B:2521102 4.3 21.8 1.0
NE2 B:GLN147 4.3 19.5 1.0
CB B:ASP80 4.3 16.1 1.0
OD2 B:ASP150 4.4 34.1 1.0
CB B:ASP84 4.4 18.2 1.0
CAN B:2521102 4.4 23.6 1.0
CAP B:2521102 4.6 21.5 1.0
CAO B:2521102 4.6 23.1 1.0
OAF B:2521102 4.6 19.8 1.0
CD B:GLN147 4.6 21.5 1.0
O B:ASP80 4.6 14.8 1.0
OE1 B:GLU236 4.7 32.7 1.0
CE B:LYS238 4.8 36.4 1.0
CD B:GLU236 4.8 32.2 1.0
O B:HOH1208 4.8 18.3 1.0
CA B:ASP80 5.0 15.7 1.0

Magnesium binding site 6 out of 6 in 2z4x

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Magnesium binding site 6 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1206

b:26.6
occ:1.00
 OAB B:2521102 1.9 19.8 1.0
O B:HOH1253 2.0 20.8 1.0
OAH B:2521102 2.0 21.8 1.0
O B:HOH1213 2.1 21.2 1.0
OD2 B:ASP214 2.4 34.6 1.0
OD1 B:ASP214 2.5 38.8 1.0
CG B:ASP214 2.8 39.2 1.0
P1P B:2521102 3.1 20.3 1.0
P1R B:2521102 3.3 20.8 1.0
CAP B:2521102 3.6 21.5 1.0
OAD B:2521102 3.7 23.0 1.0
NZ B:LYS238 3.8 43.8 1.0
OAF B:2521102 3.9 19.8 1.0
O B:HOH1222 4.0 19.9 1.0
OD1 B:ASP233 4.1 30.3 1.0
OAC B:2521102 4.3 18.8 1.0
O B:HOH1404 4.3 48.8 1.0
OAG B:2521102 4.3 22.8 1.0
O B:HOH1238 4.4 40.0 1.0
CE B:LYS238 4.4 36.4 1.0
CB B:ASP214 4.5 33.9 1.0
OD2 B:ASP233 4.5 30.2 1.0
OAE B:2521102 4.5 21.9 1.0
NE2 B:GLN211 4.6 30.8 1.0
OD1 B:ASP215 4.7 23.2 1.0
CG B:ASP233 4.7 28.7 1.0
MG B:MG1204 4.9 19.1 1.0
O B:ASP214 4.9 30.6 1.0

Reference:

C.K.-M.Chen, M.P.Hudock, Y.Zhang, R.-T.Guo, R.Cao, J.H.No, P.-H.Liang, T.-P.Ko, T.-H.Chang, S.-C.Chang, Y.Song, J.Axelson, A.Kumar, A.H.-J.Wang, E.Oldfield. Inhibition of Geranylgeranyl Diphosphate Synthase By Bisphosphonates: A Crystallographic and Computational Investigation J.Med.Chem. V. 51 5594 2008.
ISSN: ISSN 0022-2623
PubMed: 18800762
DOI: 10.1021/JM800325Y
Page generated: Sun Aug 10 16:52:59 2025

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