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Magnesium in PDB 4k10: Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+

Enzymatic activity of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+

All present enzymatic activity of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+, PDB code: 4k10 was solved by S.Aripirala, S.Gabelli, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 115.47 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.168, 143.743, 194.333, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 27.6

Other elements in 4k10:

The structure of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Sodium (Na) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ (pdb code 4k10). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+, PDB code: 4k10:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4k10

Go back to Magnesium Binding Sites List in 4k10
Magnesium binding site 1 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


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 Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:32.1
occ:1.00
 O A:HOH503 1.9 41.0 1.0
O A:HOH510 2.1 28.0 1.0
O A:HOH511 2.1 39.1 1.0
O A:HOH560 2.1 57.5 1.0
OD2 A:ASP250 2.2 44.0 1.0
O A:HOH512 2.4 40.1 1.0
O1 A:NI9406 3.0 85.9 1.0
CG A:ASP250 3.3 44.7 1.0
OD1 A:ASP250 3.7 47.6 1.0
NZ A:LYS273 4.1 48.1 1.0
O A:HOH509 4.3 34.6 1.0
O A:ASP250 4.3 43.9 1.0
OD2 A:ASP254 4.5 45.7 1.0
P2 A:NI9406 4.5 86.5 1.0
CB A:ASP250 4.5 44.1 1.0
OD1 A:ASP268 4.6 48.7 1.0
OD2 A:ASP268 4.6 47.0 1.0
OD1 A:ASP251 4.7 43.0 1.0
C A:ASP250 4.8 43.8 1.0
O6 A:NI9406 4.8 88.5 1.0
NE2 A:GLN247 4.9 43.9 1.0
O7 A:NI9406 4.9 88.0 1.0

Magnesium binding site 2 out of 8 in 4k10

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Magnesium binding site 2 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


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 Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:37.8
occ:1.00
 O A:HOH517 1.7 36.7 1.0
O4 A:NI9406 2.1 87.5 1.0
OD2 A:ASP98 2.3 39.5 1.0
OD2 A:ASP102 2.5 44.6 1.0
OD1 A:ASP98 2.6 40.0 1.0
CG A:ASP98 2.8 39.2 1.0
CG A:ASP102 3.5 45.8 1.0
P1 A:NI9406 3.6 88.3 1.0
O A:HOH558 3.8 47.9 1.0
OD1 A:ASP102 3.8 45.4 1.0
O A:HOH532 4.0 43.7 1.0
OD2 A:ASP170 4.2 39.8 1.0
O6 A:NI9406 4.3 88.5 1.0
CB A:ASP98 4.3 38.1 1.0
C2 A:NI9406 4.3 87.6 1.0
O7 A:NI9406 4.4 88.0 1.0
OE1 A:GLN167 4.5 40.4 1.0
O A:HOH563 4.6 40.2 1.0
C3 A:NI9406 4.6 87.9 1.0
O A:ASP98 4.7 37.1 1.0
CB A:ASP102 4.7 46.1 1.0
C1 A:NI9406 4.7 87.1 1.0
NZ A:LYS207 4.8 40.7 1.0
NE2 A:GLN167 4.8 40.5 1.0

Magnesium binding site 3 out of 8 in 4k10

Go back to Magnesium Binding Sites List in 4k10
Magnesium binding site 3 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


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 Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:41.0
occ:1.00
 OD2 B:ASP250 2.1 54.9 1.0
O B:HOH507 2.3 50.3 1.0
O B:HOH503 2.4 43.1 1.0
CG B:ASP250 3.2 54.5 1.0
O B:HOH502 3.5 54.6 1.0
NZ B:LYS273 3.6 56.4 1.0
OD1 B:ASP250 3.7 54.8 1.0
OD2 B:ASP254 4.1 64.9 1.0
NZ B:LYS264 4.3 77.9 1.0
OD2 B:ASP268 4.3 62.1 1.0
O3 B:NI9405 4.5 0.6 1.0
CB B:ASP250 4.5 54.5 1.0
OD1 B:ASP268 4.7 64.0 1.0
NE2 B:GLN247 4.8 52.2 1.0
O B:ASP250 4.9 55.2 1.0
CG B:ASP268 4.9 63.0 1.0
CE B:LYS273 5.0 56.5 1.0

Magnesium binding site 4 out of 8 in 4k10

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Magnesium binding site 4 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:28.1
occ:1.00
 OD2 B:ASP102 2.1 42.4 1.0
O B:HOH560 2.1 51.6 1.0
O B:HOH558 2.3 55.6 1.0
OD2 B:ASP98 2.4 42.8 1.0
OD1 B:ASP98 2.4 38.6 1.0
O7 B:NI9405 2.7 0.4 1.0
CG B:ASP98 2.7 41.5 1.0
CG B:ASP102 3.2 45.0 1.0
O4 B:NI9405 3.4 0.5 1.0
P1 B:NI9405 3.6 0.6 1.0
OD1 B:ASP102 3.7 45.6 1.0
OD2 B:ASP170 4.2 42.3 1.0
O B:HOH559 4.2 38.9 1.0
CB B:ASP98 4.3 41.3 1.0
C3 B:NI9405 4.3 0.4 1.0
O B:HOH570 4.4 48.4 1.0
CB B:ASP102 4.4 45.2 1.0
O6 B:NI9405 4.6 0.4 1.0
O B:ASP98 4.7 41.2 1.0
OE1 B:GLN167 4.8 37.5 1.0
C2 B:NI9405 4.8 0.0 1.0
NE2 B:GLN167 4.9 36.4 1.0
C1 B:NI9405 4.9 0.5 1.0

Magnesium binding site 5 out of 8 in 4k10

Go back to Magnesium Binding Sites List in 4k10
Magnesium binding site 5 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:50.5
occ:1.00
 O D:HOH517 1.9 60.0 1.0
OD2 D:ASP250 2.0 62.3 1.0
O D:HOH502 2.5 55.6 1.0
O D:HOH501 2.8 41.8 1.0
O D:HOH503 2.9 49.9 1.0
CG D:ASP250 3.1 61.8 1.0
OD1 D:ASP250 3.5 62.2 1.0
OD1 D:ASP254 4.4 65.6 1.0
OD1 D:ASP268 4.4 67.1 1.0
CB D:ASP250 4.4 61.2 1.0
O1 D:NI9405 4.4 0.8 1.0
OD2 D:ASP268 4.5 67.2 1.0
O D:ASP250 4.6 61.3 1.0
NE2 D:GLN247 4.8 60.7 1.0
O D:HOH554 4.9 54.8 1.0
CG D:ASP268 4.9 68.2 1.0
C D:ASP250 5.0 61.3 1.0

Magnesium binding site 6 out of 8 in 4k10

Go back to Magnesium Binding Sites List in 4k10
Magnesium binding site 6 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:29.4
occ:1.00
 OD2 D:ASP102 2.0 45.0 1.0
O D:HOH504 2.1 42.6 1.0
O D:HOH551 2.4 38.1 1.0
O D:HOH553 2.4 50.3 1.0
OD1 D:ASP98 2.4 43.0 1.0
OD2 D:ASP98 2.5 40.9 1.0
CG D:ASP98 2.8 40.3 1.0
CG D:ASP102 2.9 46.4 1.0
O6 D:NI9405 3.0 100.0 1.0
OD1 D:ASP102 3.1 49.3 1.0
OD1 D:ASP170 3.8 48.6 1.0
O4 D:NI9405 3.8 0.4 1.0
O D:HOH558 3.9 46.5 1.0
P1 D:NI9405 4.0 0.2 1.0
CB D:ASP98 4.3 39.0 1.0
CB D:ASP102 4.3 45.8 1.0
OE1 D:GLN167 4.6 43.5 1.0
O D:HOH552 4.7 43.0 1.0
O D:ASP98 4.9 38.1 1.0
C3 D:NI9405 4.9 99.8 1.0
C2 D:NI9405 4.9 0.1 1.0
CG D:ASP170 5.0 45.5 1.0
CA D:ASP98 5.0 38.9 1.0

Magnesium binding site 7 out of 8 in 4k10

Go back to Magnesium Binding Sites List in 4k10
Magnesium binding site 7 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:35.7
occ:1.00
 O C:HOH504 2.0 36.4 1.0
O C:HOH570 2.0 71.4 1.0
O C:HOH505 2.2 41.5 1.0
OD2 C:ASP250 2.3 42.1 1.0
O C:HOH563 2.5 42.6 1.0
CG C:ASP250 3.4 44.1 1.0
O5 C:NI9405 3.4 83.5 1.0
OD1 C:ASP250 3.9 46.2 1.0
NE2 C:GLN247 4.0 46.3 1.0
OD2 C:ASP268 4.5 49.3 1.0
OD2 C:ASP254 4.6 53.0 1.0
CB C:ASP250 4.6 43.5 1.0
O7 C:NI9405 4.7 85.1 1.0
OD1 C:ASP251 4.8 40.5 1.0
P2 C:NI9405 4.9 84.1 1.0
OD1 C:ASP268 4.9 51.8 1.0
O C:ASP250 4.9 43.0 1.0
O6 C:NI9405 5.0 83.9 1.0

Magnesium binding site 8 out of 8 in 4k10

Go back to Magnesium Binding Sites List in 4k10
Magnesium binding site 8 out of 8 in the Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Leshmaniasis Major Farnesyl Diphosphate Synthase in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Diphosphonoethyl)Pyridinium and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:35.4
occ:1.00
 OD2 C:ASP102 2.1 42.8 1.0
OD1 C:ASP98 2.5 35.5 1.0
OD2 C:ASP98 2.5 35.8 1.0
O4 C:NI9405 2.5 83.3 1.0
O C:HOH561 2.6 39.1 1.0
CG C:ASP98 2.8 35.7 1.0
CG C:ASP102 3.1 43.1 1.0
OD1 C:ASP102 3.4 42.9 1.0
P1 C:NI9405 4.0 84.5 1.0
OD2 C:ASP170 4.3 42.8 1.0
CB C:ASP98 4.3 35.5 1.0
CB C:ASP102 4.4 42.5 1.0
C2 C:NI9405 4.5 83.8 1.0
NZ C:LYS273 4.6 46.2 1.0
OE1 C:GLN167 4.6 43.9 1.0
O C:ASP98 4.7 35.9 1.0
O7 C:NI9405 4.8 85.1 1.0
O6 C:NI9405 4.8 83.9 1.0
NE2 C:GLN167 4.8 41.9 1.0
NZ C:LYS207 4.9 38.2 1.0
C3 C:NI9405 4.9 83.6 1.0
CD C:GLN167 5.0 41.9 1.0
O C:HOH571 5.0 38.9 1.0

Reference:

S.Aripirala, D.Gonzalez-Pacanowska, E.Oldfield, M.Kaiser, L.M.Amzel, S.B.Gabelli. Structural and Thermodynamic Basis of the Inhibition of Leishmania Major Farnesyl Diphosphate Synthase By Nitrogen-Containing Bisphosphonates. Acta Crystallogr.,Sect.D V. 70 802 2014.
ISSN: ISSN 0907-4449
PubMed: 24598749
DOI: 10.1107/S1399004713033221
Page generated: Sat Aug 17 03:22:41 2024

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