Magnesium in PDB 3ae0: Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl Thiopyrophosphate

The structure of Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl Thiopyrophosphate, PDB code: 3ae0 was solved by C.I.Liu, W.Y.Jeng, A.H.J.Wang, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.37
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.118, 80.118, 183.617, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 28.1

The binding sites of Magnesium atom in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl Thiopyrophosphate (pdb code 3ae0). 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 Geranylgeranyl Thiopyrophosphate, PDB code: 3ae0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl 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 Geranylgeranyl Thiopyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:42.7 occ:1.00 O1A A:GGS1002 1.6 68.0 1.0 O A:HOH529 1.8 24.3 1.0 OD1 A:ASP172 2.2 26.1 1.0 O A:HOH565 2.3 25.1 1.0 O A:HOH501 2.3 21.9 1.0 OD1 A:ASN168 2.3 30.5 1.0 PA A:GGS1002 3.1 67.5 1.0 CG A:ASP172 3.2 26.1 1.0 CG A:ASN168 3.3 27.6 1.0 CB A:ASP172 3.6 22.5 1.0 ND2 A:ASN168 3.6 29.9 1.0 O3A A:GGS1002 3.8 68.0 1.0 OD2 A:ASP176 3.9 35.9 1.0 O2A A:GGS1002 4.0 66.9 1.0 OD1 A:ASP176 4.0 35.8 1.0 S1 A:GGS1002 4.3 70.1 1.0 OD2 A:ASP172 4.3 29.1 1.0 O A:ASN168 4.4 24.5 1.0 CG A:ASP176 4.4 33.8 1.0 C A:ASN168 4.6 24.3 1.0 NH2 A:ARG171 4.7 19.9 1.0 CB A:ASN168 4.7 26.6 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl 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 Geranylgeranyl Thiopyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:55.3 occ:1.00 O2B A:GGS1001 1.7 57.1 1.0 O2A A:GGS1001 2.0 57.6 1.0 O A:HOH560 2.3 28.0 1.0 O2A A:GGS1002 2.3 66.9 1.0 O1B A:GGS1002 2.3 66.8 1.0 PB A:GGS1001 2.9 57.9 1.0 PA A:GGS1001 3.1 57.8 1.0 O3A A:GGS1001 3.3 58.7 1.0 NH2 A:ARG265 3.5 51.0 1.0 PB A:GGS1002 3.5 67.9 1.0 PA A:GGS1002 3.6 67.5 1.0 O3B A:GGS1001 3.6 48.5 1.0 O3A A:GGS1002 3.8 68.0 1.0 NH2 A:ARG171 4.0 19.9 1.0 O1A A:GGS1001 4.0 58.0 1.0 O2B A:GGS1002 4.0 67.9 1.0 O A:HIS18 4.1 41.1 1.0 O1B A:GGS1001 4.2 57.6 1.0 NH2 A:ARG45 4.2 38.1 1.0 C1 A:GGS1001 4.7 62.4 1.0 CZ A:ARG265 4.7 51.0 1.0 S1 A:GGS1002 4.7 70.1 1.0 O1A A:GGS1002 4.7 68.0 1.0 S1 A:GGS1001 4.7 57.2 1.0 O3B A:GGS1002 4.8 65.4 1.0 CZ A:ARG171 4.9 23.1 1.0 ND2 A:ASN168 5.0 29.9 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl 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 Geranylgeranyl Thiopyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1007 b:65.3 occ:1.00 O A:HOH535 1.9 46.6 1.0 OD2 A:ASP48 2.2 42.8 1.0 OD2 A:ASP52 2.7 48.2 1.0 O3B A:GGS1002 2.7 65.4 1.0 CG A:ASP48 3.3 39.4 1.0 OD1 A:ASP49 3.4 34.0 1.0 O A:ASP48 3.6 31.9 1.0 CG A:ASP52 3.6 44.9 1.0 CB A:ASP52 3.8 40.0 1.0 OD1 A:ASP48 4.0 46.1 1.0 NH1 A:ARG45 4.0 34.2 1.0 C A:ASP48 4.0 31.9 1.0 PB A:GGS1002 4.0 67.9 1.0 CG2 A:VAL53 4.2 36.3 1.0 CB A:ASP48 4.3 33.3 1.0 O2B A:GGS1002 4.4 67.9 1.0 N A:ASP49 4.5 32.5 1.0 CA A:ASP49 4.6 33.0 1.0 CG A:ASP49 4.6 35.5 1.0 C1 A:GGS1002 4.7 69.2 1.0 CA A:ASP48 4.7 30.9 1.0 OD1 A:ASP52 4.8 48.6 1.0 O3A A:GGS1002 4.8 68.0 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl 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 Geranylgeranyl Thiopyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1008 b:44.8 occ:1.00 O1A B:GGS1004 1.6 74.4 1.0 O B:HOH566 2.0 30.8 1.0 OD2 B:ASP172 2.1 27.5 1.0 OD1 B:ASN168 2.2 24.5 1.0 O B:HOH504 2.3 16.6 1.0 O B:HOH567 2.4 29.1 1.0 PA B:GGS1004 3.1 76.0 1.0 CG B:ASP172 3.2 25.0 1.0 CG B:ASN168 3.3 23.9 1.0 CB B:ASP172 3.6 21.1 1.0 ND2 B:ASN168 3.7 20.5 1.0 O B:HOH508 3.8 40.2 1.0 O2A B:GGS1004 3.9 76.5 1.0 O3A B:GGS1004 4.0 78.3 1.0 OD1 B:ASP176 4.1 17.6 1.0 O B:ASN168 4.1 25.8 1.0 OD2 B:ASP176 4.2 21.8 1.0 OD1 B:ASP172 4.3 26.0 1.0 S1 B:GGS1004 4.4 78.8 1.0 CB B:ASN168 4.6 23.9 1.0 C B:ASN168 4.6 24.4 1.0 CG B:ASP176 4.6 20.5 1.0 C1 B:GGS1004 4.6 78.2 1.0 NH2 B:ARG171 4.7 25.7 1.0 NE2 B:GLN165 4.8 40.8 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl 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 Geranylgeranyl Thiopyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1009 b:59.6 occ:1.00 O2B B:GGS1003 1.9 52.9 1.0 O2A B:GGS1003 2.1 64.7 1.0 O1B B:GGS1004 2.3 80.7 1.0 O2A B:GGS1004 2.4 76.5 1.0 O3A B:GGS1004 3.0 78.3 1.0 NH2 B:ARG265 3.1 48.1 1.0 PA B:GGS1004 3.2 76.0 1.0 PB B:GGS1003 3.3 56.7 1.0 PB B:GGS1004 3.3 80.2 1.0 PA B:GGS1003 3.5 62.6 1.0 O3A B:GGS1003 3.8 59.6 1.0 O3B B:GGS1003 3.8 57.1 1.0 NH2 B:ARG45 3.9 38.0 1.0 S1 B:GGS1004 4.1 78.8 1.0 O2B B:GGS1004 4.1 82.1 1.0 NH2 B:ARG171 4.2 25.7 1.0 O B:HIS18 4.2 39.6 1.0 CZ B:ARG265 4.3 47.9 1.0 C1 B:GGS1003 4.4 63.3 1.0 O B:HOH508 4.4 40.2 1.0 O1A B:GGS1003 4.4 64.7 1.0 O3B B:GGS1004 4.5 79.9 1.0 O1B B:GGS1003 4.5 54.7 1.0 O1A B:GGS1004 4.6 74.4 1.0 ND2 B:ASN168 4.9 20.5 1.0 S1 B:GGS1003 4.9 60.3 1.0 NH1 B:ARG265 5.0 50.3 1.0 CZ B:ARG45 5.0 37.9 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed with Geranylgeranyl 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 Geranylgeranyl Thiopyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1010 b:67.9 occ:1.00 O3B B:GGS1004 2.0 79.9 1.0 OD1 B:ASP48 2.1 47.3 1.0 OD1 B:ASP52 2.5 62.6 1.0 PB B:GGS1004 3.1 80.2 1.0 CG B:ASP48 3.1 45.6 1.0 O2B B:GGS1004 3.1 82.1 1.0 OD2 B:ASP48 3.3 51.6 1.0 CG B:ASP52 3.5 60.5 1.0 OD1 B:ASP49 3.8 48.0 1.0 CB B:ASP52 3.9 58.6 1.0 NH1 B:ARG45 4.0 37.8 1.0 C1 B:GGS1004 4.0 78.2 1.0 O1B B:GGS1004 4.1 80.7 1.0 O3A B:GGS1004 4.2 78.3 1.0 CB B:ASP48 4.5 40.8 1.0 C2 B:GGS1004 4.5 79.5 1.0 O B:ASP48 4.6 41.8 1.0 OD2 B:ASP52 4.6 61.6 1.0 S1 B:GGS1004 4.9 78.8 1.0 C B:ASP48 4.9 41.5 1.0 CG B:ASP49 5.0 48.2 1.0

F.Y.Lin, C.I.Liu, Y.L.Liu, Y.Zhang, K.Wang, W.Y.Jeng, T.P.Ko, R.Cao, A.H.Wang, E.Oldfield. Mechanism of Action and Inhibition of Dehydrosqualene Synthase. Proc.Natl.Acad.Sci.Usa V. 107 21337 2010.
ISSN: ISSN 0027-8424
PubMed: 21098670
DOI: 10.1073/PNAS.1010907107