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Magnesium in PDB 2e91: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91:
2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91, PDB code: 2e91 was solved by R.T.Guo, T.P.Ko, R.Cao, C.K.-M.Chen, W.Y.Jeng, T.H.Chang, 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) 30.00 / 2.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.657, 116.293, 126.946, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91 (pdb code 2e91). 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-91, PDB code: 2e91:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2e91

Go back to Magnesium Binding Sites List in 2e91
Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91


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-91 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:33.2
occ:1.00
 O10 A:ZOL901 2.0 30.4 1.0
O A:HOH636 2.1 33.2 1.0
OD1 A:ASP80 2.1 31.4 1.0
OD2 A:ASP84 2.2 33.2 1.0
O A:HOH638 2.2 38.4 1.0
O A:HOH637 2.3 40.6 1.0
CG A:ASP80 3.0 30.5 1.0
CG A:ASP84 3.1 34.9 1.0
MG A:MG1302 3.1 35.1 1.0
OD2 A:ASP80 3.2 29.4 1.0
OD1 A:ASP84 3.2 34.6 1.0
P9 A:ZOL901 3.3 35.7 1.0
O11 A:ZOL901 3.4 33.6 1.0
O A:HOH635 4.1 28.9 1.0
NE2 A:GLN147 4.1 37.2 1.0
C19 A:ZOL901 4.2 40.0 1.0
O12 A:ZOL901 4.2 37.2 1.0
OE1 A:GLU236 4.3 34.9 1.0
OE1 A:GLN147 4.3 43.6 1.0
CB A:ASP80 4.4 29.9 1.0
OD2 A:ASP150 4.4 42.1 1.0
C7 A:ZOL901 4.4 36.7 1.0
N15 A:ZOL901 4.5 40.1 1.0
O17 A:ZOL901 4.5 34.0 1.0
CB A:ASP84 4.5 33.8 1.0
NZ A:LYS238 4.5 35.3 1.0
C8 A:ZOL901 4.5 36.1 1.0
CD A:GLN147 4.7 38.1 1.0
O A:ASP80 4.8 26.9 1.0
OE2 A:GLU236 4.8 39.2 1.0
O A:HOH634 4.9 33.6 1.0
CA A:ASP80 5.0 28.4 1.0
CD A:GLU236 5.0 36.2 1.0
NZ A:LYS174 5.0 42.3 1.0
C18 A:ZOL901 5.0 38.0 1.0

Magnesium binding site 2 out of 4 in 2e91

Go back to Magnesium Binding Sites List in 2e91
Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91


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-91 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:35.1
occ:1.00
 OD2 A:ASP80 1.9 29.4 1.0
O17 A:ZOL901 2.0 34.0 1.0
O A:HOH634 2.1 33.6 1.0
O10 A:ZOL901 2.1 30.4 1.0
OD2 A:ASP84 2.3 33.2 1.0
O A:HOH635 2.3 28.9 1.0
CG A:ASP80 3.0 30.5 1.0
MG A:MG1301 3.1 33.2 1.0
CG A:ASP84 3.3 34.9 1.0
P9 A:ZOL901 3.4 35.7 1.0
OD1 A:ASP80 3.4 31.4 1.0
P14 A:ZOL901 3.4 38.9 1.0
C8 A:ZOL901 3.9 36.1 1.0
CB A:ASP84 3.9 33.8 1.0
O12 A:ZOL901 3.9 37.2 1.0
NH2 A:ARG89 4.0 35.2 1.0
C7 A:ZOL901 4.0 36.7 1.0
O16 A:ZOL901 4.2 35.8 1.0
CB A:ASP80 4.3 29.9 1.0
OD1 A:ASP81 4.3 28.2 1.0
O A:HOH638 4.4 38.4 1.0
O A:ASP80 4.4 26.9 1.0
OD1 A:ASP84 4.4 34.6 1.0
O A:HOH639 4.5 33.3 1.0
OE2 A:GLU236 4.5 39.2 1.0
O15 A:ZOL901 4.5 41.7 1.0
NZ A:LYS238 4.6 35.3 1.0
C A:ASP80 4.6 28.9 1.0
O11 A:ZOL901 4.7 33.6 1.0
O A:HOH636 4.9 33.2 1.0

Magnesium binding site 3 out of 4 in 2e91

Go back to Magnesium Binding Sites List in 2e91
Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91


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-91 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:39.3
occ:1.00
 O17 B:ZOL902 1.9 37.8 1.0
O10 B:ZOL902 2.1 37.8 1.0
OD1 B:ASP80 2.1 38.8 1.0
O B:HOH646 2.2 23.8 1.0
OD2 B:ASP84 2.3 33.9 1.0
CG B:ASP80 3.2 39.1 1.0
MG B:MG1304 3.3 34.2 1.0
P9 B:ZOL902 3.3 38.3 1.0
CG B:ASP84 3.3 36.2 1.0
P14 B:ZOL902 3.3 41.8 1.0
OD2 B:ASP80 3.5 40.2 1.0
O12 B:ZOL902 3.7 39.6 1.0
CB B:ASP84 3.8 33.6 1.0
C8 B:ZOL902 3.9 40.4 1.0
O16 B:ZOL902 4.0 38.5 1.0
O B:HOH647 4.2 33.4 1.0
C7 B:ZOL902 4.2 42.7 1.0
NH2 B:ARG89 4.4 46.3 1.0
OE1 B:GLU236 4.4 37.4 1.0
O B:ASP80 4.4 30.1 1.0
OD1 B:ASP84 4.5 36.2 1.0
O15 B:ZOL902 4.5 43.5 1.0
CB B:ASP80 4.5 35.6 1.0
OD1 B:ASP81 4.6 30.1 1.0
NZ B:LYS238 4.6 34.9 1.0
O11 B:ZOL902 4.7 36.9 1.0
C B:ASP80 4.8 31.7 1.0
O B:HOH651 4.8 30.8 1.0
O B:HOH648 4.9 29.6 1.0

Magnesium binding site 4 out of 4 in 2e91

Go back to Magnesium Binding Sites List in 2e91
Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-91


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-91 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:34.2
occ:1.00
 OD2 B:ASP80 2.1 40.2 1.0
O B:HOH648 2.1 29.6 1.0
O B:HOH649 2.1 31.1 1.0
O10 B:ZOL902 2.1 37.8 1.0
O B:HOH647 2.2 33.4 1.0
OD2 B:ASP84 2.2 33.9 1.0
CG B:ASP80 3.0 39.1 1.0
CG B:ASP84 3.1 36.2 1.0
OD1 B:ASP84 3.2 36.2 1.0
MG B:MG1303 3.3 39.3 1.0
OD1 B:ASP80 3.3 38.8 1.0
P9 B:ZOL902 3.4 38.3 1.0
O11 B:ZOL902 3.5 36.9 1.0
OE1 B:GLN147 3.9 43.9 1.0
O12 B:ZOL902 4.3 39.6 1.0
OD2 B:ASP150 4.3 40.4 1.0
NE2 B:GLN147 4.3 39.2 1.0
CD B:GLN147 4.3 42.0 1.0
OE2 B:GLU236 4.3 38.0 1.0
CB B:ASP80 4.4 35.6 1.0
C19 B:ZOL902 4.5 43.3 1.0
C7 B:ZOL902 4.5 42.7 1.0
CB B:ASP84 4.5 33.6 1.0
O17 B:ZOL902 4.6 37.8 1.0
NZ B:LYS238 4.6 34.9 1.0
C8 B:ZOL902 4.6 40.4 1.0
O B:ASP80 4.7 30.1 1.0
N15 B:ZOL902 4.7 45.4 1.0
CA B:ASP80 4.9 31.2 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 22:41:51 2024

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