Magnesium in PDB 5cg6: Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate

Enzymatic activity of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate

All present enzymatic activity of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate, PDB code: 5cg6 was solved by T.Yokoyama, M.Mizuguchi, A.Ostermann, K.Kusaka, N.Niimura, T.E.Schrader, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.627, 111.627, 72.553, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 28.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate (pdb code 5cg6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate, PDB code: 5cg6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5cg6

Go back to Magnesium Binding Sites List in 5cg6
Magnesium binding site 1 out of 3 in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:15.6
occ:1.00
D2 A:DOD505 2.0 16.3 1.0
O A:DOD505 2.0 18.6 1.0
OD1 A:ASP103 2.1 17.1 1.0
O A:DOD539 2.1 16.3 1.0
O A:DOD526 2.1 17.8 1.0
O17 A:RIS404 2.1 16.0 1.0
OD2 A:ASP107 2.1 16.9 1.0
D1 A:DOD526 2.3 19.1 1.0
D2 A:DOD539 2.3 17.6 1.0
D2 A:DOD526 2.8 20.3 1.0
D1 A:DOD539 3.0 17.5 1.0
D1 A:DOD505 3.0 19.8 1.0
CG A:ASP107 3.0 14.5 1.0
CG A:ASP103 3.0 16.7 1.0
MG A:MG402 3.2 17.6 1.0
OD1 A:ASP107 3.3 15.9 1.0
P14 A:RIS404 3.3 16.9 1.0
OD2 A:ASP103 3.3 14.9 1.0
DE21 A:GLN171 3.4 15.9 1.0
HE21 A:GLN171 3.4 15.9 0.0
O16 A:RIS404 3.5 16.9 1.0
HZ2 A:LYS266 3.7 22.7 0.2
DZ2 A:LYS266 3.7 22.7 0.8
OD1 A:ASP174 4.0 20.4 1.0
DZ2 A:LYS200 4.0 19.2 1.0
HZ2 A:LYS200 4.0 19.2 0.0
D2 A:DOD506 4.1 19.2 1.0
HC72 A:RIS404 4.1 15.4 1.0
NE2 A:GLN171 4.2 15.4 1.0
HE3 A:LYS266 4.2 21.9 1.0
O A:DOD541 4.2 17.2 1.0
OE1 A:GLN171 4.2 19.5 1.0
O A:DOD506 4.3 17.8 1.0
D1 A:DOD541 4.3 16.1 1.0
O15 A:RIS404 4.3 14.6 1.0
OD2 A:ASP174 4.4 20.1 1.0
CB A:ASP103 4.4 14.4 1.0
HZ1 A:LYS266 4.4 24.1 0.1
DZ1 A:LYS266 4.4 24.1 0.9
NZ A:LYS266 4.4 26.2 1.0
CG A:ASP174 4.4 20.6 1.0
CB A:ASP107 4.4 16.4 1.0
HC1 A:RIS404 4.5 18.2 1.0
HB2 A:ASP103 4.5 18.4 1.0
HB2 A:ASP107 4.6 14.9 1.0
C1 A:RIS404 4.6 16.8 1.0
CD A:GLN171 4.6 18.5 1.0
C7 A:RIS404 4.6 14.7 1.0
HZ3 A:LYS200 4.6 19.9 0.0
DZ3 A:LYS200 4.6 19.9 1.0
C8 A:RIS404 4.6 15.9 1.0
C2 A:RIS404 4.7 15.7 1.0
HA A:ASP103 4.7 15.2 1.0
NZ A:LYS200 4.7 18.4 1.0
HB3 A:ASP107 4.7 16.6 1.0
CE A:LYS266 4.8 18.1 1.0
O A:DOD507 4.8 16.4 1.0
O12 A:RIS404 4.8 16.1 1.0
HE22 A:GLN171 4.8 14.6 0.0
DE22 A:GLN171 4.8 14.6 1.0
HD2 A:LYS200 4.8 18.6 1.0
O A:ASP103 4.8 15.0 1.0
HD22 A:LEU175 4.9 21.3 1.0
CA A:ASP103 5.0 15.6 1.0

Magnesium binding site 2 out of 3 in 5cg6

Go back to Magnesium Binding Sites List in 5cg6
Magnesium binding site 2 out of 3 in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.6
occ:1.00
O12 A:RIS404 2.0 16.1 1.0
O A:DOD541 2.0 17.2 1.0
O A:DOD507 2.1 16.4 1.0
O17 A:RIS404 2.1 16.0 1.0
OD2 A:ASP103 2.1 14.9 1.0
OD2 A:ASP107 2.2 16.9 1.0
D2 A:DOD541 2.6 16.3 1.0
D2 A:DOD507 2.6 15.5 1.0
D1 A:DOD541 2.9 16.1 1.0
D1 A:DOD507 2.9 19.3 1.0
D2 A:DOD535 3.0 19.9 1.0
CG A:ASP103 3.1 16.7 1.0
MG A:MG401 3.2 15.6 1.0
HC72 A:RIS404 3.2 15.4 1.0
P14 A:RIS404 3.3 16.9 1.0
P9 A:RIS404 3.3 16.9 1.0
CG A:ASP107 3.3 14.5 1.0
OD1 A:ASP103 3.4 17.1 1.0
HB2 A:ASP107 3.4 14.9 1.0
HH22 A:ARG112 3.6 17.3 0.2
DH22 A:ARG112 3.6 17.3 0.8
HB3 A:ASP107 3.7 16.6 1.0
C8 A:RIS404 3.7 15.9 1.0
CB A:ASP107 3.7 16.4 1.0
C7 A:RIS404 3.9 14.7 1.0
O15 A:RIS404 3.9 14.6 1.0
O A:DOD535 3.9 20.9 1.0
O10 A:RIS404 4.1 16.2 1.0
DH21 A:ARG112 4.1 17.5 1.0
HH21 A:ARG112 4.1 17.5 0.0
D2 A:DOD505 4.2 16.3 1.0
O A:DOD539 4.2 16.3 1.0
NH2 A:ARG112 4.2 17.2 1.0
D1 A:DOD534 4.2 16.7 1.0
O A:DOD517 4.3 17.6 1.0
CB A:ASP103 4.4 14.4 1.0
OG A:SER109 4.4 19.3 1.0
O A:ASP103 4.4 15.0 1.0
OD1 A:ASP107 4.4 15.9 1.0
OD1 A:ASP104 4.5 17.2 1.0
O A:DOD534 4.5 20.3 1.0
D2 A:DOD506 4.5 19.2 1.0
O11 A:RIS404 4.5 17.4 1.0
HB3 A:ASP103 4.5 17.9 1.0
HA A:ASP104 4.5 16.0 1.0
D2 A:DOD517 4.5 20.5 1.0
D1 A:DOD535 4.5 18.0 1.0
D1 A:DOD539 4.6 17.5 1.0
O16 A:RIS404 4.6 16.9 1.0
C A:ASP103 4.7 14.4 1.0
HC71 A:RIS404 4.7 17.6 1.0
DG A:SER109 4.7 18.1 0.9
HG A:SER109 4.7 18.1 0.1
D2 A:DOD534 4.7 21.9 1.0
O A:DOD509 4.8 19.9 1.0
MG A:MG403 4.8 17.9 1.0
O A:DOD505 4.8 18.6 1.0
HC1 A:RIS404 4.8 18.2 1.0
C2 A:RIS404 4.9 15.7 1.0
O A:DOD506 4.9 17.8 1.0
HG1 A:THR260 5.0 19.2 0.1
DG1 A:THR260 5.0 19.2 0.9
D2 A:DOD539 5.0 17.6 1.0
D1 A:DOD517 5.0 18.1 1.0
O A:DOD526 5.0 17.8 1.0

Magnesium binding site 3 out of 3 in 5cg6

Go back to Magnesium Binding Sites List in 5cg6
Magnesium binding site 3 out of 3 in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:17.9
occ:1.00
O10 A:RIS404 1.9 16.2 1.0
O15 A:RIS404 2.0 14.6 1.0
O A:DOD514 2.1 19.2 1.0
OD2 A:ASP243 2.1 17.8 1.0
O A:DOD517 2.2 17.6 1.0
O A:DOD521 2.3 18.6 1.0
D2 A:DOD521 2.5 24.1 1.0
D1 A:DOD521 2.6 19.7 1.0
D1 A:DOD514 2.6 18.2 1.0
D2 A:DOD517 2.8 20.5 1.0
D1 A:DOD517 2.8 18.1 1.0
D2 A:DOD514 2.9 17.6 1.0
P9 A:RIS404 3.1 16.9 1.0
CG A:ASP243 3.2 17.6 1.0
D2 A:DOD506 3.2 19.2 1.0
P14 A:RIS404 3.3 16.9 1.0
C8 A:RIS404 3.5 15.9 1.0
O13 A:RIS404 3.5 16.8 1.0
OD1 A:ASP243 3.6 20.5 1.0
DZ2 A:LYS257 3.6 19.5 0.9
HZ2 A:LYS257 3.6 19.5 0.1
DE22 A:GLN240 3.6 19.4 1.0
HE22 A:GLN240 3.6 19.4 0.0
D13 A:RIS404 3.9 16.1 1.0
D2 A:DOD541 3.9 16.3 1.0
O A:DOD506 3.9 17.8 1.0
HB2 A:ASP247 3.9 23.6 1.0
O12 A:RIS404 4.0 16.1 1.0
D1 A:DOD541 4.1 16.1 1.0
O A:DOD541 4.1 17.2 1.0
O17 A:RIS404 4.2 16.0 1.0
OD1 A:ASP247 4.2 24.2 1.0
D1 A:DOD506 4.2 19.4 1.0
DE21 A:GLN240 4.2 18.1 0.7
HE21 A:GLN240 4.2 18.1 0.3
NE2 A:GLN240 4.2 19.0 1.0
HE3 A:LYS257 4.2 22.0 1.0
O A:ASP243 4.3 19.4 1.0
O A:DOD502 4.3 29.5 1.0
O16 A:RIS404 4.3 16.9 1.0
O11 A:RIS404 4.3 17.4 1.0
OD2 A:ASP261 4.4 21.3 1.0
D1 A:DOD502 4.4 20.8 1.0
OD1 A:ASP261 4.4 22.4 1.0
HA A:ASP244 4.4 19.8 1.0
NZ A:LYS257 4.4 20.7 1.0
CB A:ASP243 4.4 16.9 1.0
OD1 A:ASP244 4.4 20.1 1.0
HB3 A:ASP243 4.4 20.0 1.0
C A:ASP243 4.6 16.4 1.0
DZ3 A:LYS257 4.7 20.9 0.6
HZ3 A:LYS257 4.7 20.9 0.4
D2 A:DOD535 4.7 19.9 1.0
CG A:ASP247 4.8 21.7 1.0
CB A:ASP247 4.8 21.5 1.0
CG A:ASP261 4.8 20.2 1.0
MG A:MG402 4.8 17.6 1.0
O A:DOD535 4.8 20.9 1.0
H51 A:IPE406 4.9 20.5 1.0
CE A:LYS257 4.9 21.6 1.0
N A:ASP244 5.0 17.0 1.0
HZ1 A:LYS257 5.0 18.0 0.0
DZ1 A:LYS257 5.0 18.0 1.0

Reference:

T.Yokoyama, M.Mizuguchi, A.Ostermann, K.Kusaka, N.Niimura, T.E.Schrader, I.Tanaka. Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase J.Med.Chem. V. 58 7549 2015.
ISSN: ISSN 0022-2623
PubMed: 26314394
DOI: 10.1021/ACS.JMEDCHEM.5B01147
Page generated: Mon Dec 14 20:06:44 2020

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