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Magnesium in PDB 3n46: Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+

Enzymatic activity of Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+

All present enzymatic activity of Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+, PDB code: 3n46 was solved by J.-M.Rondeau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.19 / 2.35
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.853, 110.853, 70.861, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+ (pdb code 3n46). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+, PDB code: 3n46:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3n46

Go back to Magnesium Binding Sites List in 3n46
Magnesium binding site 1 out of 3 in the Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg355

b:47.9
occ:1.00
O15 F:ZOL354 1.9 48.0 1.0
O F:HOH368 2.1 42.2 1.0
O11 F:ZOL354 2.1 47.3 1.0
OD1 F:ASP103 2.1 47.8 1.0
O F:HOH376 2.3 41.6 1.0
OD2 F:ASP107 2.4 44.5 1.0
P14 F:ZOL354 3.1 46.1 1.0
CG F:ASP103 3.2 49.6 1.0
MG F:MG3 3.2 47.8 1.0
P9 F:ZOL354 3.2 45.5 1.0
CG F:ASP107 3.5 41.8 1.0
OD2 F:ASP103 3.6 50.7 1.0
C8 F:ZOL354 3.6 44.9 1.0
O F:HOH369 3.9 41.8 1.0
C7 F:ZOL354 3.9 38.5 1.0
O17 F:ZOL354 4.0 42.3 1.0
O12 F:ZOL354 4.0 44.9 1.0
CB F:ASP107 4.0 43.5 1.0
O F:HOH385 4.1 44.1 1.0
NH2 F:ARG112 4.2 48.2 1.0
O F:ASP103 4.4 41.6 1.0
OG F:SER109 4.4 45.0 1.0
O16 F:ZOL354 4.4 47.8 1.0
O F:HOH402 4.5 49.0 1.0
CB F:ASP103 4.5 40.5 1.0
OD1 F:ASP104 4.6 45.2 1.0
OD1 F:ASP107 4.6 43.2 1.0
O F:HOH363 4.6 39.3 1.0
O10 F:ZOL354 4.6 48.7 1.0
O F:HOH409 4.7 50.8 1.0
O F:HOH390 4.7 46.4 1.0
C F:ASP103 4.7 40.7 1.0
N15 F:ZOL354 4.9 38.4 1.0
O F:HOH361 4.9 33.8 1.0

Magnesium binding site 2 out of 3 in 3n46

Go back to Magnesium Binding Sites List in 3n46
Magnesium binding site 2 out of 3 in the Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2

b:49.2
occ:1.00
O F:HOH410 1.9 51.8 1.0
O12 F:ZOL354 2.0 44.9 1.0
OD2 F:ASP243 2.1 46.5 1.0
O F:HOH402 2.1 49.0 1.0
O F:HOH381 2.2 44.9 1.0
O17 F:ZOL354 2.3 42.3 1.0
CG F:ASP243 3.1 51.8 1.0
P9 F:ZOL354 3.4 45.5 1.0
P14 F:ZOL354 3.5 46.1 1.0
O F:HOH390 3.6 46.4 1.0
OD1 F:ASP243 3.6 48.7 1.0
O13 F:ZOL354 3.7 42.3 1.0
C8 F:ZOL354 3.8 44.9 1.0
O F:ASP243 4.0 51.4 1.0
NE2 F:GLN240 4.0 51.9 1.0
OD2 F:ASP261 4.1 48.5 1.0
O F:HOH414 4.1 54.3 1.0
OD1 F:ASP244 4.1 55.4 1.0
OD1 F:ASP261 4.2 52.8 1.0
OD2 F:ASP247 4.2 50.1 1.0
O11 F:ZOL354 4.3 47.3 1.0
O F:HOH368 4.3 42.2 1.0
C F:ASP243 4.3 51.8 1.0
CB F:ASP243 4.3 48.0 1.0
O15 F:ZOL354 4.3 48.0 1.0
O10 F:ZOL354 4.4 48.7 1.0
CB F:ASP247 4.5 51.8 1.0
CG F:ASP247 4.5 53.6 1.0
NZ F:LYS257 4.5 46.5 1.0
CG F:ASP261 4.6 49.8 1.0
O16 F:ZOL354 4.7 47.8 1.0
N F:ASP244 4.7 50.6 1.0
CA F:ASP244 4.8 50.6 1.0
CA F:ASP243 4.9 50.6 1.0

Magnesium binding site 3 out of 3 in 3n46

Go back to Magnesium Binding Sites List in 3n46
Magnesium binding site 3 out of 3 in the Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Fpps Complex with NOV_980 and Zoledronic Acid/MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg3

b:47.8
occ:1.00
OD2 F:ASP103 2.0 50.7 1.0
O F:HOH385 2.2 44.1 1.0
O F:HOH413 2.2 54.5 1.0
O11 F:ZOL354 2.3 47.3 1.0
O F:HOH361 2.3 33.8 1.0
OD2 F:ASP107 2.3 44.5 1.0
CG F:ASP103 2.8 49.6 1.0
OD1 F:ASP103 3.0 47.8 1.0
CG F:ASP107 3.2 41.8 1.0
MG F:MG355 3.2 47.9 1.0
OD1 F:ASP107 3.3 43.2 1.0
P9 F:ZOL354 3.4 45.5 1.0
O10 F:ZOL354 3.6 48.7 1.0
NE2 F:GLN171 4.0 40.7 1.0
OE1 F:GLN171 4.0 42.9 1.0
OD2 F:ASP174 4.0 50.0 1.0
NZ F:LYS266 4.0 48.1 1.0
CB F:ASP103 4.3 40.5 1.0
C19 F:ZOL354 4.3 36.5 1.0
O F:HOH368 4.3 42.2 1.0
CD F:GLN171 4.4 47.0 1.0
O F:HOH390 4.4 46.4 1.0
CG F:ASP174 4.5 46.3 1.0
OD1 F:ASP174 4.6 47.9 1.0
C7 F:ZOL354 4.6 38.5 1.0
O12 F:ZOL354 4.6 44.9 1.0
N15 F:ZOL354 4.6 38.4 1.0
CB F:ASP107 4.6 43.5 1.0
C8 F:ZOL354 4.6 44.9 1.0
O F:ASP103 4.7 41.6 1.0
O15 F:ZOL354 4.7 48.0 1.0
NZ F:LYS200 4.9 35.8 1.0
CA F:ASP103 4.9 39.7 1.0
O F:HOH376 5.0 41.6 1.0

Reference:

W.Jahnke, J.M.Rondeau, S.Cotesta, A.Marzinzik, X.Pelle, M.Geiser, A.Strauss, M.Gotte, F.Bitsch, R.Hemmig, C.Henry, S.Lehmann, J.F.Glickman, T.P.Roddy, S.J.Stout, J.R.Green. Allosteric Non-Bisphosphonate Fpps Inhibitors Identified By Fragment-Based Discovery. Nat.Chem.Biol. V. 6 660 2010.
ISSN: ISSN 1552-4450
PubMed: 20711197
DOI: 10.1038/NCHEMBIO.421
Page generated: Mon Dec 14 08:27:35 2020

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