Atomistry » Magnesium » PDB 2e75-2ein » 2e92
Atomistry »
  Magnesium »
    PDB 2e75-2ein »
      2e92 »

Magnesium in PDB 2e92: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261:
2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261, PDB code: 2e92 was solved by R.T.Guo, T.P.Ko, R.Cao, W.Y.Jeng, C.K.-M.Chen, 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 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.871, 116.051, 127.733, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261 (pdb code 2e92). 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-261, PDB code: 2e92:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2e92

Go back to Magnesium Binding Sites List in 2e92
Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


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-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:42.8
occ:1.00
 OD2 A:ASP84 2.1 36.1 1.0
O5 A:M0N901 2.2 38.9 1.0
OD1 A:ASP80 2.3 39.9 1.0
CG A:ASP84 3.0 35.0 1.0
CG A:ASP80 3.1 36.4 1.0
OD1 A:ASP84 3.2 34.5 1.0
OD2 A:ASP80 3.2 40.6 1.0
P2 A:M0N901 3.3 40.9 1.0
O4 A:M0N901 3.3 39.7 1.0
MG A:MG1302 3.4 53.9 1.0
NE2 A:GLN147 3.8 38.8 1.0
O6 A:M0N901 4.3 42.6 1.0
O A:HOH406 4.3 36.9 1.0
CB A:ASP84 4.4 35.4 1.0
CB A:ASP80 4.4 35.4 1.0
C8 A:M0N901 4.6 48.7 1.0
CD A:GLN147 4.6 39.6 1.0
C9 A:M0N901 4.6 44.3 1.0
OD2 A:ASP150 4.6 46.9 1.0
O A:ASP80 4.6 28.3 1.0
NZ A:LYS238 4.7 40.2 1.0
OE1 A:GLN147 4.8 39.6 1.0
O1 A:M0N901 4.8 42.8 1.0
C2 A:M0N901 4.8 53.9 1.0
CA A:ASP80 5.0 33.0 1.0

Magnesium binding site 2 out of 4 in 2e92

Go back to Magnesium Binding Sites List in 2e92
Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


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-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:53.9
occ:1.00
 OD2 A:ASP80 2.1 40.6 1.0
O5 A:M0N901 2.2 38.9 1.0
OD2 A:ASP84 2.3 36.1 1.0
O1 A:M0N901 2.3 42.8 1.0
CG A:ASP80 3.2 36.4 1.0
CG A:ASP84 3.3 35.0 1.0
MG A:MG1301 3.4 42.8 1.0
CB A:ASP84 3.6 35.4 1.0
P2 A:M0N901 3.6 40.9 1.0
P1 A:M0N901 3.7 44.0 1.0
OD1 A:ASP80 3.7 39.9 1.0
NH2 A:ARG89 4.0 41.1 1.0
O6 A:M0N901 4.0 42.6 1.0
OE2 A:GLU236 4.1 58.5 1.0
C9 A:M0N901 4.1 44.3 1.0
O A:ASP80 4.3 28.3 1.0
O2 A:M0N901 4.3 42.0 1.0
OD1 A:ASP81 4.3 37.5 1.0
C8 A:M0N901 4.4 48.7 1.0
OD1 A:ASP84 4.4 34.5 1.0
CB A:ASP80 4.4 35.4 1.0
OE1 A:GLU236 4.6 60.6 1.0
C A:ASP80 4.6 32.7 1.0
O A:HOH722 4.6 37.3 1.0
CD A:GLU236 4.7 59.8 1.0
O4 A:M0N901 4.8 39.7 1.0
O A:HOH406 4.8 36.9 1.0
O3 A:M0N901 4.9 49.0 1.0
O A:HOH566 4.9 41.8 1.0

Magnesium binding site 3 out of 4 in 2e92

Go back to Magnesium Binding Sites List in 2e92
Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


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-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:44.9
occ:1.00
 O1 B:M0N902 1.9 48.5 1.0
OD1 B:ASP80 2.0 44.6 1.0
O5 B:M0N902 2.1 48.0 1.0
OD2 B:ASP84 2.3 36.8 1.0
O B:HOH708 2.5 29.7 1.0
CG B:ASP80 3.1 46.3 1.0
P2 B:M0N902 3.1 48.9 1.0
MG B:MG1304 3.2 45.1 1.0
P1 B:M0N902 3.2 49.6 1.0
O6 B:M0N902 3.3 50.7 1.0
OD2 B:ASP80 3.4 47.6 1.0
CG B:ASP84 3.5 37.9 1.0
C9 B:M0N902 3.6 50.8 1.0
O2 B:M0N902 3.9 49.8 1.0
C8 B:M0N902 3.9 54.9 1.0
CB B:ASP84 4.2 34.9 1.0
NH2 B:ARG89 4.3 54.6 1.0
O3 B:M0N902 4.4 51.8 1.0
CB B:ASP80 4.4 42.9 1.0
O4 B:M0N902 4.5 46.4 1.0
OD1 B:ASP84 4.5 37.2 1.0
OE1 B:GLU236 4.5 52.8 1.0
O B:HOH707 4.5 38.5 1.0
O B:ASP80 4.6 42.9 1.0
NZ B:LYS238 4.6 43.1 1.0
O B:HOH595 4.8 47.0 1.0
OD1 B:ASP81 4.9 40.3 1.0
C B:ASP80 4.9 41.2 1.0
O B:M0N902 4.9 47.1 1.0

Magnesium binding site 4 out of 4 in 2e92

Go back to Magnesium Binding Sites List in 2e92
Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


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-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:45.1
occ:1.00
 OD2 B:ASP80 2.1 47.6 1.0
O5 B:M0N902 2.1 48.0 1.0
O B:HOH707 2.2 38.5 1.0
OD2 B:ASP84 2.3 36.8 1.0
CG B:ASP80 3.0 46.3 1.0
CG B:ASP84 3.1 37.9 1.0
OD1 B:ASP84 3.1 37.2 1.0
MG B:MG1303 3.2 44.9 1.0
OD1 B:ASP80 3.2 44.6 1.0
P2 B:M0N902 3.5 48.9 1.0
OE1 B:GLN147 3.6 54.2 1.0
O4 B:M0N902 3.9 46.4 1.0
OD2 B:ASP150 4.0 48.8 1.0
CD B:GLN147 4.3 50.1 1.0
CB B:ASP80 4.3 42.9 1.0
OE2 B:GLU236 4.4 49.4 1.0
O6 B:M0N902 4.4 50.7 1.0
NE2 B:GLN147 4.5 50.6 1.0
CB B:ASP84 4.5 34.9 1.0
O B:ASP80 4.6 42.9 1.0
NZ B:LYS238 4.6 43.1 1.0
O1 B:M0N902 4.7 48.5 1.0
C8 B:M0N902 4.8 54.9 1.0
C9 B:M0N902 4.8 50.8 1.0
CA B:ASP80 4.8 40.6 1.0
O B:HOH708 4.9 29.7 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 22:43:10 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy