Atomistry » Magnesium » PDB 2z4x-2zin » 2z7i
Atomistry »
  Magnesium »
    PDB 2z4x-2zin »
      2z7i »

Magnesium in PDB 2z7i: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742:
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 Inhibitor Bph-742, PDB code: 2z7i was solved by R.T.Guo, C.K.-M.Chen, T.-P.Ko, R.Cao, M.Hudock, 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) 24.44 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.111, 116.337, 129.434, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742 (pdb code 2z7i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742, PDB code: 2z7i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2z7i

Go back to Magnesium Binding Sites List in 2z7i
Magnesium binding site 1 out of 2 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742


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 Inhibitor Bph-742 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:26.3
occ:1.00
OAE A:7421302 1.9 25.6 1.0
O A:HOH469 2.0 19.1 1.0
OAF A:7421302 2.0 22.7 1.0
OD2 A:ASP80 2.1 27.1 1.0
OD2 A:ASP84 2.1 26.7 1.0
O A:HOH379 2.2 23.2 1.0
CG A:ASP80 3.1 29.6 1.0
PAX A:7421302 3.2 31.4 1.0
PAW A:7421302 3.3 30.6 1.0
CG A:ASP84 3.3 29.8 1.0
O A:HOH507 3.4 37.3 1.0
OD1 A:ASP80 3.4 32.7 1.0
CAV A:7421302 3.6 29.8 1.0
O A:HOH581 3.8 38.1 1.0
NH2 A:ARG89 4.0 24.0 1.0
OAG A:7421302 4.0 30.9 1.0
O A:HOH383 4.1 29.6 1.0
O A:HOH538 4.1 44.1 1.0
CB A:ASP84 4.1 25.8 1.0
OAH A:7421302 4.1 33.4 1.0
OD1 A:ASP84 4.2 31.3 1.0
O A:HOH486 4.3 34.2 1.0
OE2 A:GLU236 4.4 39.3 1.0
OAI A:7421302 4.4 30.7 1.0
CB A:ASP80 4.4 24.0 1.0
OAD A:7421302 4.5 30.2 1.0
O A:ASP80 4.5 17.5 1.0
OD1 A:ASP81 4.6 28.5 1.0
C A:ASP80 4.8 22.1 1.0
NZ A:LYS238 4.9 38.7 1.0
O A:HOH484 5.0 33.0 1.0

Magnesium binding site 2 out of 2 in 2z7i

Go back to Magnesium Binding Sites List in 2z7i
Magnesium binding site 2 out of 2 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742


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 Inhibitor Bph-742 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:33.2
occ:1.00
O B:HOH616 2.0 36.2 1.0
OAE B:7421303 2.1 25.1 1.0
OD2 B:ASP84 2.1 32.5 1.0
OAF B:7421303 2.1 27.3 1.0
OD1 B:ASP80 2.1 25.3 1.0
CG B:ASP80 3.1 30.3 1.0
PAX B:7421303 3.3 32.8 1.0
CG B:ASP84 3.3 33.1 1.0
PAW B:7421303 3.4 33.0 1.0
OD2 B:ASP80 3.4 30.7 1.0
O B:HOH603 3.7 44.7 1.0
CAV B:7421303 3.7 32.3 1.0
O B:HOH428 3.9 35.6 1.0
OAG B:7421303 4.0 31.0 1.0
CB B:ASP84 4.0 27.4 1.0
OAH B:7421303 4.2 33.4 1.0
NH2 B:ARG89 4.2 31.8 1.0
OD1 B:ASP84 4.2 32.7 1.0
O B:HOH535 4.3 39.2 1.0
O B:ASP80 4.3 24.8 1.0
CB B:ASP80 4.4 25.9 1.0
OE1 B:GLU236 4.5 39.2 1.0
NZ B:LYS238 4.5 37.4 1.0
OAD B:7421303 4.5 31.1 1.0
OAI B:7421303 4.5 33.6 1.0
OD1 B:ASP81 4.7 25.1 1.0
C B:ASP80 4.7 25.8 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: Mon Dec 14 07:50:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy