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Magnesium in PDB 2z52: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23:
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-23, PDB code: 2z52 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 / 2.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.086, 116.287, 128.411, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23 (pdb code 2z52). 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-23, PDB code: 2z52:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2z52

Go back to Magnesium Binding Sites List in 2z52
Magnesium binding site 1 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23


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-23 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:26.3
occ:1.00
 OD1 A:ASP80 2.1 16.0 1.0
O A:HOH1507 2.1 30.1 1.0
O A:HOH1496 2.1 24.0 1.0
OD2 A:ASP84 2.2 21.3 1.0
OAH A:H231001 2.2 23.2 1.0
O A:HOH1448 2.2 20.6 1.0
CG A:ASP84 3.0 20.9 1.0
CG A:ASP80 3.0 16.1 1.0
OD1 A:ASP84 3.1 18.5 1.0
MG A:MG1302 3.1 22.7 1.0
OD2 A:ASP80 3.3 15.8 1.0
PAU A:H231001 3.4 23.4 1.0
OAC A:H231001 3.6 23.6 1.0
NE2 A:GLN147 3.8 20.6 1.0
O A:HOH1487 4.1 19.1 1.0
OE1 A:GLN147 4.1 21.9 1.0
OE1 A:GLU236 4.2 24.6 1.0
CAQ A:H231001 4.4 24.1 1.0
CD A:GLN147 4.4 20.3 1.0
CB A:ASP80 4.4 15.2 1.0
CB A:ASP84 4.5 19.2 1.0
CAR A:H231001 4.5 21.7 1.0
OAG A:H231001 4.5 27.6 1.0
CAS A:H231001 4.6 22.9 1.0
OD2 A:ASP150 4.6 31.2 1.0
O A:ASP80 4.6 14.0 1.0
OAE A:H231001 4.6 22.5 1.0
NZ A:LYS238 4.7 33.8 1.0
OE2 A:GLU236 4.8 27.1 1.0
CD A:GLU236 4.9 26.9 1.0
CA A:ASP80 5.0 16.1 1.0
O A:HOH1315 5.0 14.6 1.0

Magnesium binding site 2 out of 6 in 2z52

Go back to Magnesium Binding Sites List in 2z52
Magnesium binding site 2 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23


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-23 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:22.7
occ:1.00
 OAE A:H231001 2.0 22.5 1.0
O A:HOH1487 2.1 19.1 1.0
OD2 A:ASP80 2.1 15.8 1.0
OD2 A:ASP84 2.1 21.3 1.0
OAH A:H231001 2.1 23.2 1.0
O A:HOH1315 2.2 14.6 1.0
CG A:ASP80 3.0 16.1 1.0
MG A:MG1301 3.1 26.3 1.0
CG A:ASP84 3.2 20.9 1.0
OD1 A:ASP80 3.4 16.0 1.0
PAT A:H231001 3.4 21.1 1.0
PAU A:H231001 3.4 23.4 1.0
CB A:ASP84 3.8 19.2 1.0
CAS A:H231001 3.8 22.9 1.0
OAG A:H231001 4.0 27.6 1.0
O A:HOH1479 4.0 40.4 1.0
CAR A:H231001 4.1 21.7 1.0
NH2 A:ARG89 4.1 22.0 1.0
O A:HOH1448 4.2 20.6 1.0
O A:HOH1443 4.3 41.9 1.0
OD1 A:ASP84 4.3 18.5 1.0
OE2 A:GLU236 4.3 27.1 1.0
OAF A:H231001 4.3 21.5 1.0
O A:ASP80 4.3 14.0 1.0
CB A:ASP80 4.4 15.2 1.0
OAB A:H231001 4.4 24.9 1.0
OD1 A:ASP81 4.5 18.1 1.0
O A:HOH1571 4.5 22.8 1.0
C A:ASP80 4.6 17.3 1.0
NZ A:LYS238 4.7 33.8 1.0
OAC A:H231001 4.7 23.6 1.0
O A:HOH1496 4.8 24.0 1.0
O A:HOH1337 4.9 35.1 1.0
O A:HOH1507 4.9 30.1 1.0
CAQ A:H231001 5.0 24.1 1.0
CD A:GLU236 5.0 26.9 1.0

Magnesium binding site 3 out of 6 in 2z52

Go back to Magnesium Binding Sites List in 2z52
Magnesium binding site 3 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23


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-23 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:22.2
occ:1.00
 OAF A:H231001 1.9 21.5 1.0
O A:HOH1570 2.0 27.0 1.0
O A:HOH1571 2.0 22.8 1.0
O A:HOH1569 2.1 24.7 1.0
OAG A:H231001 2.1 27.6 1.0
O A:HOH1534 2.4 19.8 1.0
OD1 A:ASP214 3.2 41.0 1.0
PAT A:H231001 3.3 21.1 1.0
PAU A:H231001 3.4 23.4 1.0
OAD A:H231001 3.6 22.3 1.0
CAS A:H231001 3.6 22.9 1.0
NZ A:LYS238 3.8 33.8 1.0
OAE A:H231001 3.9 22.5 1.0
CG A:ASP214 4.1 34.5 1.0
O A:HOH1487 4.1 19.1 1.0
OAH A:H231001 4.3 23.2 1.0
OD1 A:ASP233 4.4 21.4 1.0
CE A:LYS238 4.4 30.3 1.0
OAC A:H231001 4.4 23.6 1.0
OD2 A:ASP233 4.4 21.0 1.0
OAB A:H231001 4.4 24.9 1.0
O A:HOH1584 4.4 39.4 1.0
NE2 A:GLN211 4.5 19.0 1.0
O A:HOH1479 4.7 40.4 1.0
CB A:ASP214 4.8 28.5 1.0
OD2 A:ASP215 4.8 20.0 1.0
O A:HOH1432 4.8 41.1 1.0
CG A:ASP233 4.8 20.9 1.0
OD2 A:ASP214 4.9 37.2 1.0

Magnesium binding site 4 out of 6 in 2z52

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Magnesium binding site 4 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23


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-23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:22.9
occ:1.00
 OAE B:H231002 2.0 18.8 1.0
OAH B:H231002 2.0 21.8 1.0
O B:HOH1342 2.1 24.4 1.0
OD1 B:ASP80 2.1 23.1 1.0
OD2 B:ASP84 2.2 22.3 1.0
O B:HOH1559 2.2 17.3 1.0
MG B:MG1305 3.0 22.9 1.0
CG B:ASP80 3.0 22.7 1.0
OD2 B:ASP80 3.2 24.1 1.0
CG B:ASP84 3.2 20.6 1.0
PAU B:H231002 3.4 22.1 1.0
PAT B:H231002 3.4 20.7 1.0
CB B:ASP84 3.8 20.4 1.0
OAG B:H231002 3.8 26.3 1.0
CAS B:H231002 3.8 22.3 1.0
CAR B:H231002 4.1 23.4 1.0
OAF B:H231002 4.2 19.0 1.0
O B:HOH1316 4.2 20.6 1.0
OE1 B:GLU236 4.2 26.6 1.0
OD1 B:ASP84 4.3 23.6 1.0
O B:HOH1443 4.4 42.0 1.0
O B:ASP80 4.4 18.7 1.0
NH2 B:ARG89 4.4 23.3 1.0
O B:HOH1560 4.4 25.8 1.0
OAB B:H231002 4.4 26.2 1.0
CB B:ASP80 4.4 19.2 1.0
O B:HOH1515 4.5 36.6 1.0
OAC B:H231002 4.5 22.7 1.0
OD1 B:ASP81 4.6 21.2 1.0
C B:ASP80 4.7 19.0 1.0
O B:HOH1472 4.8 27.8 1.0
O B:HOH1436 4.9 25.7 1.0
MG B:MG1306 5.0 25.0 1.0
CD B:GLU236 5.0 24.8 1.0
O B:HOH1489 5.0 43.1 1.0

Magnesium binding site 5 out of 6 in 2z52

Go back to Magnesium Binding Sites List in 2z52
Magnesium binding site 5 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23


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-23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1305

b:22.9
occ:1.00
 OAH B:H231002 2.1 21.8 1.0
OD2 B:ASP80 2.1 24.1 1.0
OD2 B:ASP84 2.1 22.3 1.0
O B:HOH1472 2.2 27.8 1.0
O B:HOH1436 2.2 25.7 1.0
O B:HOH1316 2.3 20.6 1.0
CG B:ASP84 3.0 20.6 1.0
MG B:MG1304 3.0 22.9 1.0
CG B:ASP80 3.1 22.7 1.0
OD1 B:ASP84 3.2 23.6 1.0
PAU B:H231002 3.3 22.1 1.0
OAC B:H231002 3.4 22.7 1.0
OD1 B:ASP80 3.4 23.1 1.0
OE1 B:GLN147 3.8 25.8 1.0
O B:HOH1342 4.1 24.4 1.0
OE2 B:GLU236 4.1 23.1 1.0
NE2 B:GLN147 4.2 20.0 1.0
CAQ B:H231002 4.3 26.0 1.0
OAG B:H231002 4.3 26.3 1.0
CAR B:H231002 4.3 23.4 1.0
CD B:GLN147 4.4 23.5 1.0
OAE B:H231002 4.4 18.8 1.0
CB B:ASP84 4.4 20.4 1.0
CB B:ASP80 4.5 19.2 1.0
CAS B:H231002 4.5 22.3 1.0
O B:ASP80 4.7 18.7 1.0
OE1 B:GLU236 4.8 26.6 1.0
OD2 B:ASP150 4.8 29.1 1.0
CD B:GLU236 4.8 24.8 1.0
CE B:LYS238 4.9 37.4 1.0
O B:HOH1559 4.9 17.3 1.0
CAP B:H231002 4.9 27.8 1.0

Magnesium binding site 6 out of 6 in 2z52

Go back to Magnesium Binding Sites List in 2z52
Magnesium binding site 6 out of 6 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-23


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-23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1306

b:25.0
occ:1.00
 O B:HOH1560 2.0 25.8 1.0
OAF B:H231002 2.0 19.0 1.0
O B:HOH1561 2.1 27.0 1.0
OAG B:H231002 2.1 26.3 1.0
O B:HOH1323 2.3 18.3 1.0
OD2 B:ASP214 2.9 38.5 1.0
PAT B:H231002 3.3 20.7 1.0
PAU B:H231002 3.4 22.1 1.0
OAD B:H231002 3.6 25.4 1.0
CAS B:H231002 3.7 22.3 1.0
OAE B:H231002 4.0 18.8 1.0
NZ B:LYS238 4.0 41.7 1.0
CG B:ASP214 4.0 37.1 1.0
O B:HOH1342 4.1 24.4 1.0
OD1 B:ASP233 4.1 25.0 1.0
O B:HOH1489 4.3 43.1 1.0
OAH B:H231002 4.4 21.8 1.0
NE2 B:GLN211 4.4 18.6 1.0
OD2 B:ASP233 4.4 21.4 1.0
OAC B:H231002 4.5 22.7 1.0
CB B:ASP214 4.5 30.5 1.0
OAB B:H231002 4.5 26.2 1.0
O B:HOH1571 4.6 41.2 1.0
CE B:LYS238 4.6 37.4 1.0
CG B:ASP233 4.7 20.9 1.0
OD1 B:ASP215 4.7 18.0 1.0
MG B:MG1304 5.0 22.9 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: Wed Aug 14 07:46:58 2024

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