Atomistry » Magnesium » PDB 2ynj-2z4w » 2z4w
Atomistry »
  Magnesium »
    PDB 2ynj-2z4w »
      2z4w »

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

Go back to Magnesium Binding Sites List in 2z4w
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy