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Magnesium in PDB 2z4w: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749:
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-749, PDB code: 2z4w was solved by C.K.-M.Chen, R.T.Guo, 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 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.521, 116.545, 129.070, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749 (pdb code 2z4w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749, PDB code: 2z4w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2z4w

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Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749


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-749 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:28.8
occ:1.00
 OAG A:7491101 2.3 32.6 1.0
OD2 A:ASP84 2.4 28.2 1.0
OD1 A:ASP80 2.7 27.3 1.0
OD1 A:ASP84 3.0 25.6 1.0
CG A:ASP84 3.0 27.4 1.0
MG A:MG1302 3.2 31.7 1.0
OE1 A:GLU236 3.4 40.8 1.0
PBB A:7491101 3.6 32.3 1.0
CG A:ASP80 3.7 26.6 1.0
OD2 A:ASP80 4.0 28.1 1.0
O A:HOH1447 4.0 38.1 1.0
OAI A:7491101 4.1 31.2 1.0
OD2 A:ASP150 4.1 36.8 1.0
OAJ A:7491101 4.4 34.0 1.0
CD A:GLU236 4.4 40.8 1.0
NE2 A:GLN147 4.5 17.8 1.0
OE1 A:GLN147 4.5 21.7 1.0
CB A:ASP84 4.5 24.8 1.0
OE2 A:GLU236 4.5 40.7 1.0
NH1 A:ARG154 4.6 25.4 1.0
NZ A:LYS238 4.7 43.4 1.0
CAO A:7491101 4.8 28.4 1.0
CE A:LYS238 4.8 38.3 1.0
CD A:GLN147 4.9 18.9 1.0

Magnesium binding site 2 out of 4 in 2z4w

Go back to Magnesium Binding Sites List in 2z4w
Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749


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-749 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:31.7
occ:1.00
 OAG A:7491101 2.0 32.6 1.0
OAK A:7491101 2.1 30.5 1.0
O A:HOH1447 2.1 38.1 1.0
OD2 A:ASP80 2.2 28.1 1.0
OD2 A:ASP84 2.2 28.2 1.0
O A:HOH1335 2.5 22.5 1.0
PBB A:7491101 2.9 32.3 1.0
CG A:ASP80 3.0 26.6 1.0
MG A:MG1301 3.2 28.8 1.0
OD1 A:ASP80 3.2 27.3 1.0
OAJ A:7491101 3.3 34.0 1.0
PBC A:7491101 3.3 30.7 1.0
CG A:ASP84 3.5 27.4 1.0
CBA A:7491101 3.5 34.1 1.0
CAS A:7491101 3.8 29.1 1.0
OAL A:7491101 4.0 31.8 1.0
CB A:ASP84 4.2 24.8 1.0
CAO A:7491101 4.4 28.4 1.0
OE2 A:GLU236 4.4 40.7 1.0
OD1 A:ASP84 4.4 25.6 1.0
O A:HOH1448 4.4 60.3 1.0
OAI A:7491101 4.4 31.2 1.0
CB A:ASP80 4.5 25.4 1.0
OAH A:7491101 4.5 36.6 1.0
O A:HOH1304 4.5 33.7 1.0
O A:HOH1446 4.5 38.7 1.0
NH2 A:ARG89 4.5 40.3 1.0
O A:ASP80 4.7 24.2 1.0
OE1 A:GLU236 4.9 40.8 1.0
NZ A:LYS238 4.9 43.4 1.0
CAT A:7491101 5.0 35.3 1.0

Magnesium binding site 3 out of 4 in 2z4w

Go back to Magnesium Binding Sites List in 2z4w
Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749


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-749 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:27.9
occ:1.00
 OD2 B:ASP84 1.8 34.5 1.0
OD1 B:ASP80 2.0 28.4 1.0
OAG B:7491102 2.1 28.6 1.0
OAK B:7491102 2.3 23.0 1.0
O B:HOH1432 2.5 17.1 1.0
O B:HOH1352 2.5 35.0 1.0
OD2 B:ASP80 2.6 28.3 1.0
CG B:ASP80 2.7 25.3 1.0
MG B:MG1304 3.0 36.9 1.0
CG B:ASP84 3.1 33.8 1.0
PBB B:7491102 3.2 25.1 1.0
PBC B:7491102 3.6 25.7 1.0
CBA B:7491102 3.7 29.4 1.0
CAS B:7491102 3.7 28.6 1.0
CB B:ASP84 3.9 31.3 1.0
OAJ B:7491102 3.9 30.6 1.0
OD1 B:ASP84 4.0 35.6 1.0
CB B:ASP80 4.2 23.3 1.0
O B:ASP80 4.2 24.9 1.0
CAO B:7491102 4.3 29.6 1.0
OAL B:7491102 4.4 26.5 1.0
NH2 B:ARG89 4.5 38.5 1.0
OE1 B:GLU236 4.5 34.6 1.0
OAI B:7491102 4.6 28.6 1.0
C B:ASP80 4.6 25.2 1.0
OAH B:7491102 4.7 31.3 1.0
O B:HOH1401 4.7 33.1 1.0
OD1 B:ASP81 4.8 30.6 1.0
CA B:ASP80 5.0 23.2 1.0

Magnesium binding site 4 out of 4 in 2z4w

Go back to Magnesium Binding Sites List in 2z4w
Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-749


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-749 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:36.9
occ:1.00
 OAG B:7491102 2.2 28.6 1.0
OD2 B:ASP80 2.4 28.3 1.0
OD2 B:ASP84 2.5 34.5 1.0
MG B:MG1303 3.0 27.9 1.0
OD1 B:ASP84 3.1 35.6 1.0
CG B:ASP84 3.2 33.8 1.0
PBB B:7491102 3.4 25.1 1.0
CG B:ASP80 3.6 25.3 1.0
OAI B:7491102 3.8 28.6 1.0
OD2 B:ASP150 3.9 38.1 1.0
OE1 B:GLN147 3.9 27.9 1.0
OD1 B:ASP80 4.0 28.4 1.0
O B:HOH1352 4.1 35.0 1.0
OE2 B:GLU236 4.1 35.8 1.0
NE2 B:GLN147 4.4 29.0 1.0
OAJ B:7491102 4.4 30.6 1.0
CAO B:7491102 4.4 29.6 1.0
CD B:GLN147 4.5 26.8 1.0
NZ B:LYS238 4.6 37.7 1.0
CB B:ASP84 4.6 31.3 1.0
CAS B:7491102 4.8 28.6 1.0
CBA B:7491102 4.8 29.4 1.0
OE1 B:GLU236 4.8 34.6 1.0
CD B:GLU236 4.8 35.4 1.0
NZ B:LYS174 4.8 50.2 1.0
CB B:ASP80 4.8 23.3 1.0
OAK B:7491102 4.9 23.0 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 07:45:40 2024

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