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Magnesium in PDB 2e95: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675:
2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675, PDB code: 2e95 was solved by R.T.Guo, R.Cao, T.P.Ko, W.Y.Jeng, T.H.Chang, C.K.-M.Chen, P.H.Liang, 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) 34.90 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.390, 116.262, 128.695, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675 (pdb code 2e95). 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-675, PDB code: 2e95:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2e95

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Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675


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-675 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:36.3
occ:1.00
 OD2 A:ASP84 2.1 29.0 1.0
OD1 A:ASP80 2.2 30.6 1.0
OAH A:B751001 2.2 38.6 1.0
O A:HOH665 2.4 31.1 1.0
CG A:ASP84 3.0 28.4 1.0
MG A:MG1302 3.1 29.1 1.0
CG A:ASP80 3.1 29.1 1.0
OD1 A:ASP84 3.2 28.7 1.0
OD2 A:ASP80 3.2 30.7 1.0
PBJ A:B751001 3.4 40.6 1.0
OAI A:B751001 3.7 44.3 1.0
OAB A:B751001 3.8 48.1 1.0
O A:HOH416 4.0 27.2 1.0
O A:HOH531 4.1 34.4 1.0
OE1 A:GLN147 4.2 33.2 1.0
NE2 A:GLN147 4.2 35.1 1.0
CB A:ASP84 4.5 26.7 1.0
CB A:ASP80 4.5 27.1 1.0
CD A:GLN147 4.5 34.7 1.0
OAF A:B751001 4.6 41.0 1.0
OD2 A:ASP150 4.6 38.5 1.0
O A:HOH736 4.7 33.8 1.0
O A:ASP80 4.8 21.8 1.0
NZ A:LYS238 4.8 43.9 1.0
O A:HOH469 4.9 27.6 1.0
CE A:LYS238 4.9 39.0 1.0

Magnesium binding site 2 out of 4 in 2e95

Go back to Magnesium Binding Sites List in 2e95
Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675


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-675 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:29.1
occ:1.00
 OD2 A:ASP80 2.0 30.7 1.0
O A:HOH416 2.1 27.2 1.0
O A:HOH469 2.1 27.6 1.0
OAF A:B751001 2.1 41.0 1.0
OAH A:B751001 2.1 38.6 1.0
OD2 A:ASP84 2.2 29.0 1.0
MG A:MG1301 3.1 36.3 1.0
CG A:ASP80 3.1 29.1 1.0
CG A:ASP84 3.3 28.4 1.0
OD1 A:ASP80 3.5 30.6 1.0
PBI A:B751001 3.6 40.7 1.0
PBJ A:B751001 3.6 40.6 1.0
CB A:ASP84 3.8 26.7 1.0
NH2 A:ARG89 4.0 32.6 1.0
CBH A:B751001 4.1 45.7 1.0
O A:HOH664 4.2 46.0 1.0
OD1 A:ASP84 4.4 28.7 1.0
CB A:ASP80 4.4 27.1 1.0
OAB A:B751001 4.4 48.1 1.0
OE2 A:GLU236 4.4 51.8 1.0
O A:ASP80 4.5 21.8 1.0
OAG A:B751001 4.5 45.3 1.0
OAA A:B751001 4.5 48.0 1.0
OD1 A:ASP81 4.6 25.8 1.0
OAI A:B751001 4.6 44.3 1.0
OAE A:B751001 4.7 42.1 1.0
C A:ASP80 4.7 26.2 1.0

Magnesium binding site 3 out of 4 in 2e95

Go back to Magnesium Binding Sites List in 2e95
Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675


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-675 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:34.5
occ:1.00
 OAF B:B751002 1.8 35.4 1.0
OAH B:B751002 2.0 39.4 1.0
OD1 B:ASP80 2.0 34.5 1.0
OD2 B:ASP84 2.1 32.6 1.0
O B:HOH440 2.4 29.8 1.0
MG B:MG1304 2.9 30.9 1.0
CG B:ASP80 3.1 34.4 1.0
PBJ B:B751002 3.2 37.2 1.0
PBI B:B751002 3.2 38.6 1.0
CG B:ASP84 3.3 29.7 1.0
OD2 B:ASP80 3.4 35.5 1.0
CBH B:B751002 3.6 40.9 1.0
CAY B:B751002 3.7 47.0 1.0
OAB B:B751002 3.8 45.0 1.0
OAG B:B751002 4.0 39.8 1.0
CB B:ASP84 4.1 27.5 1.0
O B:HOH477 4.1 32.8 1.0
O B:HOH667 4.1 43.1 1.0
OD1 B:ASP84 4.2 32.5 1.0
OAA B:B751002 4.3 41.5 1.0
NH2 B:ARG89 4.3 34.2 1.0
CB B:ASP80 4.4 29.9 1.0
OE1 B:GLU236 4.4 35.0 1.0
OAI B:B751002 4.5 44.8 1.0
O B:ASP80 4.6 28.6 1.0
OD1 B:ASP81 4.7 28.9 1.0
C B:ASP80 4.8 28.4 1.0
CBA B:B751002 5.0 53.5 1.0
OAE B:B751002 5.0 38.6 1.0
NZ B:LYS238 5.0 45.5 1.0

Magnesium binding site 4 out of 4 in 2e95

Go back to Magnesium Binding Sites List in 2e95
Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-675


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-675 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:30.9
occ:1.00
 OAH B:B751002 2.0 39.4 1.0
OD2 B:ASP80 2.2 35.5 1.0
O B:HOH477 2.3 32.8 1.0
OD2 B:ASP84 2.3 32.6 1.0
MG B:MG1303 2.9 34.5 1.0
CG B:ASP80 3.0 34.4 1.0
OD1 B:ASP84 3.0 32.5 1.0
CG B:ASP84 3.1 29.7 1.0
OD1 B:ASP80 3.1 34.5 1.0
PBJ B:B751002 3.4 37.2 1.0
OAI B:B751002 3.7 44.8 1.0
OE1 B:GLN147 3.9 38.2 1.0
OE2 B:GLU236 4.3 33.2 1.0
OAB B:B751002 4.3 45.0 1.0
NE2 B:GLN147 4.3 32.1 1.0
CB B:ASP80 4.4 29.9 1.0
CAN B:B751002 4.4 53.4 1.0
CD B:GLN147 4.4 35.6 1.0
OAF B:B751002 4.4 35.4 1.0
CB B:ASP84 4.5 27.5 1.0
CAY B:B751002 4.6 47.0 1.0
O B:ASP80 4.7 28.6 1.0
CBH B:B751002 4.7 40.9 1.0
OD2 B:ASP150 4.8 35.3 1.0
NZ B:LYS238 4.8 45.5 1.0
O B:HOH440 4.9 29.8 1.0
OE1 B:GLU236 4.9 35.0 1.0
CA B:ASP80 4.9 29.0 1.0
CD B:GLU236 5.0 35.2 1.0
CBA B:B751002 5.0 53.5 1.0

Reference:

R.T.Guo, R.Cao, P.H.Liang, T.P.Ko, T.H.Chang, M.P.Hudock, W.Y.Jeng, C.K.-M.Chen, Y.Zhang, Y.Song, C.J.Kuo, F.Yin, E.Oldfield, A.H.-J.Wang. Bisphosphonates Target Multiple Sites in Both Cis- and Trans-Prenyltransferases Proc.Natl.Acad.Sci.Usa V. 104 10022 2007.
ISSN: ISSN 0027-8424
PubMed: 17535895
DOI: 10.1073/PNAS.0702254104
Page generated: Tue Aug 13 22:43:21 2024

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