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Magnesium in PDB 4kpd: Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate

Enzymatic activity of Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate

All present enzymatic activity of Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate, PDB code: 4kpd was solved by B.L.Barnett, M.K.Tsoumpra, J.R.C.Muniz, R.L.Walter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.87 / 1.96
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.730, 111.730, 66.990, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate (pdb code 4kpd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate, PDB code: 4kpd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4kpd

Go back to Magnesium Binding Sites List in 4kpd
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, 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 Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:30.7
occ:1.00
 O A:HOH582 1.9 33.0 1.0
OD2 A:ASP107 2.0 47.1 1.0
O15 A:RIS405 2.1 39.2 1.0
O12 A:RIS405 2.1 44.9 1.0
OD2 A:ASP103 2.1 44.0 1.0
O A:HOH583 2.1 18.8 1.0
O A:HOH611 2.6 39.1 1.0
CG A:ASP103 3.1 43.4 1.0
CG A:ASP107 3.1 44.9 1.0
MG A:MG403 3.1 36.5 1.0
OD1 A:ASP103 3.4 44.6 1.0
P14 A:RIS405 3.4 39.7 1.0
P9 A:RIS405 3.4 43.0 1.0
CB A:ASP107 3.5 42.7 1.0
O A:HOH632 3.7 31.6 1.0
C8 A:RIS405 3.9 43.0 1.0
O16 A:RIS405 4.1 42.2 1.0
C7 A:RIS405 4.1 39.4 1.0
O A:HOH581 4.1 21.2 1.0
OD1 A:ASP107 4.2 44.9 1.0
O A:HOH575 4.2 34.4 1.0
O11 A:RIS405 4.2 39.9 1.0
O A:ASP103 4.2 41.9 1.0
NH2 A:ARG112 4.3 45.8 1.0
O A:HOH606 4.3 37.5 1.0
CB A:ASP103 4.4 38.2 1.0
O10 A:RIS405 4.4 33.2 1.0
OG A:SER109 4.5 46.0 1.0
O17 A:RIS405 4.5 33.5 1.0
C A:ASP103 4.6 41.4 1.0
OD1 A:ASP104 4.6 41.4 1.0
O A:HOH610 4.6 36.1 1.0
O A:HOH576 4.6 34.0 1.0
O A:HOH578 4.6 26.1 1.0
O A:HOH573 4.8 38.4 1.0
O A:HOH574 5.0 33.9 1.0

Magnesium binding site 2 out of 3 in 4kpd

Go back to Magnesium Binding Sites List in 4kpd
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, 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 Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:34.0
occ:1.00
 O16 A:RIS405 1.9 42.2 1.0
O11 A:RIS405 1.9 39.9 1.0
O A:HOH577 2.1 24.9 1.0
O A:HOH578 2.1 26.1 1.0
OD2 A:ASP243 2.2 51.0 1.0
O A:HOH579 2.2 50.2 1.0
O A:HOH632 3.0 31.6 1.0
CG A:ASP243 3.1 50.6 1.0
P9 A:RIS405 3.3 43.0 1.0
P14 A:RIS405 3.3 39.7 1.0
OD1 A:ASP243 3.5 50.2 1.0
O13 A:RIS405 3.6 41.6 1.0
C8 A:RIS405 3.7 43.0 1.0
O A:HOH576 3.8 34.0 1.0
O A:HOH611 3.8 39.1 1.0
OD1 A:ASP247 3.9 57.6 1.0
O A:ASP243 4.0 52.2 1.0
O12 A:RIS405 4.0 44.9 1.0
O A:HOH580 4.1 53.2 1.0
OD2 A:ASP261 4.2 59.1 1.0
O15 A:RIS405 4.2 39.2 1.0
NE2 A:GLN240 4.2 40.6 1.0
O17 A:RIS405 4.3 33.5 1.0
C A:ASP243 4.4 50.8 1.0
OD1 A:ASP244 4.4 51.5 1.0
CB A:ASP243 4.4 47.2 1.0
OD1 A:ASP261 4.4 52.7 1.0
O10 A:RIS405 4.4 33.2 1.0
CB A:ASP247 4.5 49.6 1.0
NZ A:LYS257 4.5 48.2 1.0
CG A:ASP247 4.6 55.3 1.0
CG A:ASP261 4.7 55.4 1.0
O A:HOH582 4.8 33.0 1.0
N A:ASP244 4.8 46.8 1.0
CE A:LYS257 4.8 55.0 1.0
O A:HOH581 4.9 21.2 1.0
CA A:ASP243 5.0 46.9 1.0

Magnesium binding site 3 out of 3 in 4kpd

Go back to Magnesium Binding Sites List in 4kpd
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, 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 Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:36.5
occ:1.00
 OD1 A:ASP103 1.9 44.6 1.0
O A:HOH573 2.1 38.4 1.0
O A:HOH575 2.1 34.4 1.0
OD2 A:ASP107 2.1 47.1 1.0
O15 A:RIS405 2.2 39.2 1.0
O A:HOH574 2.3 33.9 1.0
CG A:ASP103 2.9 43.4 1.0
CG A:ASP107 3.0 44.9 1.0
MG A:MG401 3.1 30.7 1.0
OD1 A:ASP107 3.2 44.9 1.0
OD2 A:ASP103 3.2 44.0 1.0
O17 A:RIS405 3.4 33.5 1.0
P14 A:RIS405 3.4 39.7 1.0
O A:HOH611 3.9 39.1 1.0
OD1 A:ASP174 3.9 47.7 1.0
OE1 A:GLN171 4.1 43.5 1.0
NE2 A:GLN171 4.1 43.4 1.0
O A:HOH576 4.2 34.0 1.0
CB A:ASP103 4.3 38.2 1.0
NZ A:LYS266 4.3 59.5 1.0
OD2 A:ASP174 4.4 51.4 1.0
CG A:ASP174 4.4 47.7 1.0
CB A:ASP107 4.4 42.7 1.0
O16 A:RIS405 4.5 42.2 1.0
C7 A:RIS405 4.5 39.4 1.0
O A:HOH582 4.6 33.0 1.0
CD A:GLN171 4.6 57.1 1.0
O12 A:RIS405 4.6 44.9 1.0
C2 A:RIS405 4.7 39.9 1.0
C8 A:RIS405 4.7 43.0 1.0
C1 A:RIS405 4.7 37.5 1.0
O A:ASP103 4.7 41.9 1.0
NZ A:LYS200 4.7 37.8 1.0
O A:HOH583 4.9 18.8 1.0
CA A:ASP103 4.9 36.8 1.0

Reference:

M.K.Tsoumpra, J.R.C.Muniz, B.L.Barnett, E.Pilka, A.Kwaasi, K.L.Kavanagh, A.G.Evdokimov, R.L.Walter, F.H.Ebetino, U.Oppermann, R.G.G.Russell, J.E.Dunford. Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate To Be Published.
Page generated: Sat Aug 17 03:52:43 2024

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