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Magnesium in PDB 4n9u: The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates

Enzymatic activity of The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates

All present enzymatic activity of The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates, PDB code: 4n9u was solved by M.K.Tsoumpra, J.R.C.Muniz, B.L.Barnett, E.Pilka, A.A.Kwaasi, K.L.Kavanagh, A.Evdokimov, R.L.Walter, F.H.Ebetino, U.Oppermann, R.G.G.Russell, J.E.Dunford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.69 / 2.11
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.110, 111.110, 69.580, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates (pdb code 4n9u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates, PDB code: 4n9u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4n9u

Go back to Magnesium Binding Sites List in 4n9u
Magnesium binding site 1 out of 3 in the The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:32.0
occ:1.00
 O A:HOH554 1.9 31.8 1.0
OD1 A:ASP103 2.0 46.6 1.0
O12 A:RIS404 2.0 48.7 1.0
OD2 A:ASP107 2.2 58.4 1.0
O A:HOH553 2.3 25.6 1.0
O15 A:RIS404 2.3 43.3 1.0
O A:HOH581 2.7 42.1 1.0
CG A:ASP103 3.0 47.0 1.0
MG A:MG403 3.2 34.8 1.0
CG A:ASP107 3.3 54.0 1.0
OD2 A:ASP103 3.4 47.6 1.0
P9 A:RIS404 3.4 46.1 1.0
P14 A:RIS404 3.5 50.9 1.0
O A:HOH582 3.6 31.2 1.0
CB A:ASP107 3.8 51.2 1.0
C8 A:RIS404 3.9 47.3 1.0
O A:HOH549 3.9 21.0 1.0
O A:HOH555 4.0 36.9 1.0
C7 A:RIS404 4.1 44.7 1.0
NH2 A:ARG112 4.1 45.9 1.0
O16 A:RIS404 4.2 48.6 1.0
O A:ASP103 4.3 48.2 1.0
O11 A:RIS404 4.3 45.1 1.0
CB A:ASP103 4.3 44.1 1.0
OD1 A:ASP107 4.4 50.3 1.0
O10 A:RIS404 4.4 41.0 1.0
OG A:SER109 4.4 52.6 1.0
O A:HOH583 4.5 44.7 1.0
C A:ASP103 4.6 46.9 1.0
O A:HOH557 4.6 41.2 1.0
OD1 A:ASP104 4.6 45.1 1.0
MG A:MG402 4.7 27.2 1.0
O A:HOH558 4.7 33.5 1.0
O17 A:RIS404 4.8 48.4 1.0
O A:HOH552 4.8 24.4 1.0

Magnesium binding site 2 out of 3 in 4n9u

Go back to Magnesium Binding Sites List in 4n9u
Magnesium binding site 2 out of 3 in the The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:27.2
occ:1.00
 O11 A:RIS404 1.9 45.1 1.0
O16 A:RIS404 2.0 48.6 1.0
O A:HOH550 2.0 37.2 1.0
O A:HOH552 2.1 24.4 1.0
OD2 A:ASP243 2.2 51.0 1.0
O A:HOH551 2.3 21.4 1.0
O A:HOH582 2.8 31.2 1.0
P9 A:RIS404 2.9 46.1 1.0
P14 A:RIS404 3.2 50.9 1.0
CG A:ASP243 3.2 55.5 1.0
O A:HOH581 3.3 42.1 1.0
C8 A:RIS404 3.3 47.3 1.0
O13 A:RIS404 3.4 44.1 1.0
OD1 A:ASP243 3.5 55.5 1.0
O12 A:RIS404 3.6 48.7 1.0
O A:HOH562 3.9 32.1 1.0
OD1 A:ASP247 4.0 59.3 1.0
O15 A:RIS404 4.0 43.3 1.0
O10 A:RIS404 4.2 41.0 1.0
O17 A:RIS404 4.3 48.4 1.0
NZ A:LYS257 4.4 66.0 1.0
OD1 A:ASP261 4.4 54.1 1.0
O A:ASP243 4.4 56.5 1.0
NE2 A:GLN240 4.4 56.3 1.0
CE A:LYS257 4.5 55.0 1.0
CB A:ASP243 4.5 50.8 1.0
O A:HOH554 4.6 31.8 1.0
OD2 A:ASP261 4.6 63.4 1.0
MG A:MG401 4.7 32.0 1.0
C A:ASP243 4.7 54.7 1.0
CG A:ASP247 4.7 58.9 1.0
O A:HOH549 4.8 21.0 1.0
CB A:ASP247 4.9 52.2 1.0
C7 A:RIS404 4.9 44.7 1.0
OD1 A:ASP244 4.9 45.2 1.0
CG A:ASP261 4.9 56.3 1.0

Magnesium binding site 3 out of 3 in 4n9u

Go back to Magnesium Binding Sites List in 4n9u
Magnesium binding site 3 out of 3 in the The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen- Containing Bisphosphonates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:34.8
occ:1.00
 OD2 A:ASP103 1.9 47.6 1.0
O A:HOH558 2.0 33.5 1.0
O15 A:RIS404 2.1 43.3 1.0
OD2 A:ASP107 2.2 58.4 1.0
O A:HOH557 2.2 41.2 1.0
O A:HOH556 2.4 51.1 1.0
CG A:ASP103 2.9 47.0 1.0
CG A:ASP107 3.0 54.0 1.0
OD1 A:ASP103 3.2 46.6 1.0
MG A:MG401 3.2 32.0 1.0
OD1 A:ASP107 3.2 50.3 1.0
P14 A:RIS404 3.4 50.9 1.0
O17 A:RIS404 3.6 48.4 1.0
O A:HOH581 3.7 42.1 1.0
OD2 A:ASP174 3.8 65.5 1.0
OE1 A:GLN171 4.2 58.0 1.0
CB A:ASP103 4.3 44.1 1.0
NE2 A:GLN171 4.3 55.5 1.0
O A:HOH562 4.3 32.1 1.0
O16 A:RIS404 4.4 48.6 1.0
CB A:ASP107 4.5 51.2 1.0
O A:HOH554 4.5 31.8 1.0
NZ A:LYS266 4.5 63.4 1.0
CE A:LYS266 4.6 55.1 1.0
C7 A:RIS404 4.7 44.7 1.0
C8 A:RIS404 4.7 47.3 1.0
O12 A:RIS404 4.7 48.7 1.0
CD A:GLN171 4.7 62.5 1.0
O A:HOH555 4.7 36.9 1.0
C2 A:RIS404 4.7 46.7 1.0
CG A:ASP174 4.7 60.2 1.0
C1 A:RIS404 4.8 46.1 1.0
O A:ASP103 4.8 48.2 1.0
CA A:ASP103 5.0 42.6 1.0

Reference:

M.K.Tsoumpra, J.R.C.Muniz, B.L.Barnett, E.Pilka, A.A.Kwaasi, K.L.Kavanagh, A.Evdokimov, R.L.Walter, F.H.Ebetino, U.Oppermann, R.G.G.Russell, J.E.Dunford. The Role of Lysine 200 in the Human Farnesyl Pyrophosphate Synthase Catalytic Mechanism and the Mode of Inhibition By the Nitrogen-Containing Bisphosphonates To Be Published.
Page generated: Mon Aug 19 23:26:42 2024

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