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Magnesium in PDB 3w7f: Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate

Enzymatic activity of Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate

All present enzymatic activity of Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate:
2.5.1.96;

Protein crystallography data

The structure of Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate, PDB code: 3w7f was solved by C.I.Liu, W.Y.Jeng, A.H.Wang, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.060, 80.060, 183.120, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate (pdb code 3w7f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate, PDB code: 3w7f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3w7f

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Magnesium binding site 1 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate


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 the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:34.7
occ:1.00
 O2A A:FPS301 1.8 46.2 1.0
OD2 A:ASP172 1.9 43.3 1.0
O A:HOH402 2.1 39.0 1.0
O A:HOH403 2.2 34.1 1.0
O A:HOH408 2.3 29.3 1.0
OD1 A:ASN168 2.3 35.0 1.0
CG A:ASP172 2.9 41.1 1.0
PA A:FPS301 3.3 48.6 1.0
CB A:ASP172 3.3 38.2 1.0
CG A:ASN168 3.4 36.5 1.0
OD2 A:ASP176 3.9 43.3 1.0
ND2 A:ASN168 3.9 37.6 1.0
OD1 A:ASP172 4.0 42.7 1.0
OD1 A:ASP176 4.0 45.0 1.0
O3A A:FPS301 4.1 48.9 1.0
O A:ASN168 4.1 31.9 1.0
S1 A:FPS301 4.2 50.2 1.0
O1A A:FPS301 4.3 44.1 1.0
NH2 A:ARG171 4.4 29.8 1.0
CG A:ASP176 4.4 45.9 1.0
C A:ASN168 4.5 31.9 1.0
CB A:ASN168 4.7 36.5 1.0
CA A:ASP172 4.8 37.4 1.0
O A:HOH440 4.9 55.4 1.0
N A:ILE169 5.0 32.5 1.0

Magnesium binding site 2 out of 6 in 3w7f

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Magnesium binding site 2 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate


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 the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:37.7
occ:1.00
 O A:HOH407 1.9 28.4 1.0
O1A A:FPS302 1.9 35.5 1.0
O3B A:FPS302 2.0 43.9 1.0
O2B A:FPS301 2.0 44.5 1.0
O1A A:FPS301 2.1 44.1 1.0
O A:HOH406 2.3 39.2 1.0
PB A:FPS302 3.1 41.6 1.0
PA A:FPS302 3.3 38.3 1.0
PB A:FPS301 3.5 48.1 1.0
PA A:FPS301 3.5 48.6 1.0
O3A A:FPS302 3.6 46.2 1.0
O2B A:FPS302 3.7 41.8 1.0
NH2 A:ARG265 3.8 63.3 1.0
O3A A:FPS301 3.8 48.9 1.0
NH2 A:ARG45 4.0 38.9 1.0
O1B A:FPS301 4.1 52.5 1.0
O2A A:FPS302 4.1 40.1 1.0
O A:HIS18 4.1 42.5 1.0
NH2 A:ARG171 4.1 29.8 1.0
C1 A:FPS301 4.3 48.6 1.0
O1B A:FPS302 4.5 47.4 1.0
O2A A:FPS301 4.5 46.2 1.0
O3B A:FPS301 4.6 49.3 1.0
S1 A:FPS302 4.6 46.9 1.0
S1 A:FPS301 4.7 50.2 1.0
C1 A:FPS302 4.9 48.0 1.0

Magnesium binding site 3 out of 6 in 3w7f

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Magnesium binding site 3 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate


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 the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:45.6
occ:1.00
 O A:HOH404 1.9 50.7 1.0
O A:HOH405 2.1 34.8 1.0
O3B A:FPS301 2.1 49.3 1.0
OD2 A:ASP48 2.2 41.5 1.0
O A:HOH401 2.3 35.9 1.0
OD1 A:ASP52 2.9 70.0 1.0
PB A:FPS301 3.2 48.1 1.0
CG A:ASP48 3.2 37.5 1.0
O3A A:FPS301 3.5 48.9 1.0
OD1 A:ASP48 3.5 38.7 1.0
O1B A:FPS301 3.8 52.5 1.0
CG A:ASP52 3.9 71.0 1.0
NH1 A:ARG45 4.0 30.7 1.0
CB A:ASP52 4.3 65.5 1.0
OD1 A:ASP49 4.4 39.2 1.0
C2 A:FPS301 4.4 47.6 1.0
O A:ASP48 4.4 40.5 1.0
C1 A:FPS301 4.5 48.6 1.0
O A:HOH464 4.5 44.6 1.0
CB A:ASP48 4.5 38.5 1.0
O2B A:FPS301 4.6 44.5 1.0
S1 A:FPS301 4.8 50.2 1.0
PA A:FPS301 4.8 48.6 1.0
C A:ASP48 4.9 39.1 1.0
OD2 A:ASP52 4.9 74.7 1.0

Magnesium binding site 4 out of 6 in 3w7f

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Magnesium binding site 4 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate


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 the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:42.0
occ:1.00
 O2A B:FPS301 1.7 56.0 1.0
OD2 B:ASP172 1.9 40.6 1.0
O B:HOH409 1.9 54.9 1.0
OD1 B:ASN168 2.1 31.9 1.0
O B:HOH404 2.2 34.4 1.0
O B:HOH406 2.6 34.3 1.0
CG B:ASP172 3.0 38.8 1.0
CG B:ASN168 3.1 31.4 1.0
PA B:FPS301 3.1 59.1 1.0
ND2 B:ASN168 3.5 32.6 1.0
CB B:ASP172 3.6 34.1 1.0
O B:HOH405 3.7 50.4 1.0
O B:ASN168 3.8 37.1 1.0
O B:HOH574 4.0 63.1 1.0
OD1 B:ASP172 4.0 43.8 1.0
O3A B:FPS301 4.0 58.0 1.0
O1A B:FPS301 4.1 55.4 1.0
S1 B:FPS301 4.1 63.0 1.0
OD1 B:ASP176 4.3 29.8 1.0
OD2 B:ASP176 4.3 34.2 1.0
C B:ASN168 4.3 34.0 1.0
NH2 B:ARG171 4.4 36.1 1.0
CB B:ASN168 4.5 31.3 1.0
CG B:ASP176 4.7 35.9 1.0
O B:HOH416 4.8 46.6 1.0
CA B:ASN168 4.9 31.5 1.0

Magnesium binding site 5 out of 6 in 3w7f

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Magnesium binding site 5 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate


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 the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:45.9
occ:1.00
 O B:HOH403 1.9 35.2 1.0
O1A B:FPS302 1.9 48.0 1.0
O3B B:FPS302 1.9 37.2 1.0
O1A B:FPS301 2.0 55.4 1.0
O B:HOH408 2.1 60.7 1.0
O3B B:FPS301 2.1 56.3 1.0
PB B:FPS302 3.2 38.3 1.0
PA B:FPS301 3.2 59.1 1.0
PA B:FPS302 3.3 45.3 1.0
O3A B:FPS301 3.4 58.0 1.0
PB B:FPS301 3.4 55.4 1.0
O3A B:FPS302 3.7 45.2 1.0
O2B B:FPS302 4.0 38.0 1.0
O B:HOH405 4.1 50.4 1.0
NH2 B:ARG265 4.1 55.1 1.0
O2B B:FPS301 4.1 59.1 1.0
NH2 B:ARG171 4.2 36.1 1.0
O2A B:FPS301 4.2 56.0 1.0
O2A B:FPS302 4.3 47.9 1.0
O B:HIS18 4.3 43.6 1.0
C1 B:FPS301 4.4 61.6 1.0
O1B B:FPS302 4.5 37.7 1.0
S1 B:FPS302 4.5 52.8 1.0
NH1 B:ARG45 4.6 40.9 1.0
O1B B:FPS301 4.6 52.7 1.0
ND2 B:ASN168 4.7 32.6 1.0
S1 B:FPS301 4.7 63.0 1.0

Magnesium binding site 6 out of 6 in 3w7f

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Magnesium binding site 6 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate


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 the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Farnesyl Thiopyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:62.1
occ:1.00
 OD2 B:ASP48 2.2 51.9 1.0
OD2 B:ASP52 2.2 68.5 1.0
O1B B:FPS301 2.3 52.7 1.0
O B:HOH407 2.5 42.9 1.0
O B:HOH401 2.6 51.2 1.0
OD1 B:ASP48 2.9 51.1 1.0
CG B:ASP48 2.9 51.1 1.0
O B:HOH574 3.1 63.1 1.0
O B:HOH402 3.1 44.7 1.0
PB B:FPS301 3.5 55.4 1.0
CG B:ASP52 3.5 69.7 1.0
S1 B:FPS301 3.6 63.0 1.0
C2 B:FPS301 3.8 60.7 1.0
O3A B:FPS301 3.8 58.0 1.0
C1 B:FPS301 3.9 61.6 1.0
CB B:ASP52 4.3 67.6 1.0
OD1 B:ASP52 4.3 67.2 1.0
NH2 B:ARG45 4.3 40.4 1.0
O2B B:FPS301 4.4 59.1 1.0
CB B:ASP48 4.4 50.1 1.0
PA B:FPS301 4.5 59.1 1.0
O3B B:FPS301 4.7 56.3 1.0
C3 B:FPS301 4.9 60.4 1.0

Reference:

C.I.Liu, G.Y.Liu, Y.Song, F.Yin, M.E.Hensler, W.Y.Jeng, V.Nizet, A.H.Wang, E.Oldfield. A Cholesterol Biosynthesis Inhibitor Blocks Staphylococcus Aureus Virulence. Science V. 319 1391 2008.
ISSN: ISSN 0036-8075
PubMed: 18276850
DOI: 10.1126/SCIENCE.1153018
Page generated: Thu Aug 15 13:13:44 2024

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