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Magnesium in PDB 4ea0: Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651

Enzymatic activity of Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651

All present enzymatic activity of Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651:
2.5.1.96;

Protein crystallography data

The structure of Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651, PDB code: 4ea0 was solved by F.-Y.Lin, Y.-L.Liu, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.46 / 2.12
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.324, 80.324, 180.822, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651 (pdb code 4ea0). 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 Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651, PDB code: 4ea0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4ea0

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Magnesium binding site 1 out of 6 in the Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651


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 Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:34.2
occ:1.00
 O A:HOH422 1.9 31.5 1.0
OD1 A:ASP48 2.0 30.6 1.0
O2 A:POP304 2.0 25.8 1.0
OD1 A:ASP52 2.2 32.5 1.0
O5 A:POP304 2.2 30.5 1.0
O A:HOH427 2.2 34.0 1.0
CG A:ASP48 3.0 34.0 1.0
CG A:ASP52 3.2 30.1 1.0
MG A:MG303 3.2 29.1 1.0
P1 A:POP304 3.3 28.9 1.0
P2 A:POP304 3.3 28.9 1.0
OD2 A:ASP48 3.4 29.4 1.0
CB A:ASP52 3.5 31.9 1.0
NH2 A:ARG45 3.5 34.1 1.0
O A:POP304 3.6 27.1 1.0
O A:HOH499 3.8 51.6 1.0
O6 A:POP304 3.9 27.9 1.0
O1 A:POP304 3.9 27.9 1.0
O A:HOH487 4.1 29.2 1.0
OD2 A:ASP52 4.3 31.7 1.0
CB A:ASP48 4.3 30.0 1.0
OD1 A:ASP49 4.3 33.2 1.0
O A:HOH489 4.4 40.9 1.0
O3 A:POP304 4.5 28.0 1.0
O4 A:POP304 4.5 26.9 1.0
O A:HOH401 4.5 30.8 1.0
CZ A:ARG45 4.7 39.7 1.0
O A:ASP48 4.8 34.5 1.0
O A:HOH403 4.8 33.7 1.0
CA A:ASP52 5.0 31.1 1.0

Magnesium binding site 2 out of 6 in 4ea0

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Magnesium binding site 2 out of 6 in the Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651


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 Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:23.6
occ:1.00
 OD2 A:ASP172 1.9 32.6 1.0
O A:HOH403 2.1 33.7 1.0
OD1 A:ASN168 2.1 26.5 1.0
O6 A:POP304 2.2 27.9 1.0
O1 A:POP304 2.2 27.9 1.0
O A:HOH404 2.3 30.7 1.0
CG A:ASP172 3.0 37.1 1.0
CG A:ASN168 3.3 31.5 1.0
P2 A:POP304 3.4 28.9 1.0
P1 A:POP304 3.4 28.9 1.0
O A:POP304 3.5 27.1 1.0
CB A:ASP172 3.6 36.6 1.0
ND2 A:ASN168 3.8 37.2 1.0
O A:HOH405 3.9 27.1 1.0
OD1 A:ASP172 4.1 29.8 1.0
O A:ASN168 4.2 29.5 1.0
OD2 A:ASP176 4.3 40.6 1.0
O2 A:POP304 4.3 25.8 1.0
O A:HOH499 4.3 51.6 1.0
O5 A:POP304 4.4 30.5 1.0
O4 A:POP304 4.4 26.9 1.0
OD1 A:ASP176 4.4 37.8 1.0
O3 A:POP304 4.4 28.0 1.0
C A:ASN168 4.5 32.3 1.0
NH2 A:ARG171 4.5 47.0 1.0
O A:HOH422 4.5 31.5 1.0
CB A:ASN168 4.5 29.4 1.0
O A:HOH489 4.6 40.9 1.0
CG A:ASP176 4.8 43.9 1.0
NE2 A:GLN165 4.9 29.9 1.0
N A:ILE169 5.0 33.3 1.0

Magnesium binding site 3 out of 6 in 4ea0

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Magnesium binding site 3 out of 6 in the Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651


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 Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:29.1
occ:1.00
 O5 A:POP304 1.9 30.5 1.0
O A:HOH401 1.9 30.8 1.0
OD2 A:ASP48 2.0 29.4 1.0
O A:HOH487 2.1 29.2 1.0
O A:HOH402 2.2 20.9 1.0
OD1 A:ASP52 2.3 32.5 1.0
CG A:ASP48 3.0 34.0 1.0
P2 A:POP304 3.1 28.9 1.0
MG A:MG301 3.2 34.2 1.0
OD1 A:ASP48 3.2 30.6 1.0
CG A:ASP52 3.3 30.1 1.0
O4 A:POP304 3.3 26.9 1.0
OD2 A:ASP52 3.6 31.7 1.0
O A:HOH489 3.8 40.9 1.0
O6 A:POP304 3.9 27.9 1.0
OH A:TYR129 3.9 28.7 1.0
OD1 A:ASP114 4.1 40.2 1.0
O A:HOH422 4.2 31.5 1.0
CB A:ASP48 4.3 30.0 1.0
O A:POP304 4.4 27.1 1.0
CB A:ASP52 4.6 31.9 1.0
O2 A:POP304 4.6 25.8 1.0
NH1 A:ARG181 4.7 36.5 1.0
CG2 A:VAL111 4.7 28.0 1.0
CAN A:651306 4.8 39.6 1.0
CA A:ASP48 4.8 31.4 1.0
O A:ASP48 4.9 34.5 1.0
NAT A:651306 5.0 52.2 1.0

Magnesium binding site 4 out of 6 in 4ea0

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Magnesium binding site 4 out of 6 in the Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651


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 Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:29.6
occ:1.00
 O B:HOH444 1.6 28.5 1.0
OD1 B:ASN168 1.9 33.2 1.0
O3 B:POP304 2.2 33.2 1.0
OD2 B:ASP172 2.3 38.4 1.0
O5 B:POP304 2.4 30.9 1.0
O B:HOH406 2.4 39.2 1.0
CG B:ASN168 2.9 35.9 1.0
CG B:ASP172 3.4 45.2 1.0
ND2 B:ASN168 3.4 36.1 1.0
P1 B:POP304 3.4 31.1 1.0
P2 B:POP304 3.5 35.7 1.0
O B:POP304 3.5 33.1 1.0
CB B:ASP172 3.7 40.4 1.0
O B:ASN168 3.9 37.6 1.0
O B:HOH427 3.9 27.4 1.0
NH2 B:ARG171 4.1 54.5 1.0
C B:ASN168 4.3 38.0 1.0
CB B:ASN168 4.3 38.1 1.0
O2 B:POP304 4.4 26.6 1.0
O1 B:POP304 4.4 27.9 1.0
O6 B:POP304 4.4 31.1 1.0
OD1 B:ASP172 4.5 43.2 1.0
O4 B:POP304 4.5 37.5 1.0
OD1 B:ASP176 4.5 44.6 1.0
OD2 B:ASP176 4.6 45.5 1.0
NH2 B:ARG265 4.6 69.7 1.0
O B:HOH429 4.7 32.7 1.0
CA B:ASN168 4.8 37.3 1.0
N B:ILE169 4.8 37.6 1.0
NE2 B:GLN165 4.9 32.2 1.0

Magnesium binding site 5 out of 6 in 4ea0

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Magnesium binding site 5 out of 6 in the Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651


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 Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:33.1
occ:1.00
 O B:HOH402 1.9 26.1 1.0
O2 B:POP304 2.0 26.6 1.0
OD2 B:ASP48 2.1 35.5 1.0
O B:HOH424 2.1 33.8 1.0
O B:HOH401 2.1 27.4 1.0
OD2 B:ASP52 2.1 27.2 1.0
CG B:ASP52 3.0 37.0 1.0
CG B:ASP48 3.0 37.3 1.0
MG B:MG303 3.1 37.8 1.0
OD1 B:ASP52 3.2 23.9 1.0
P1 B:POP304 3.2 31.1 1.0
OD1 B:ASP48 3.4 38.9 1.0
O1 B:POP304 3.5 27.9 1.0
OH B:TYR129 3.9 35.4 1.0
OD2 B:ASP114 3.9 35.3 1.0
NH2 B:ARG181 4.0 38.7 1.0
O3 B:POP304 4.1 33.2 1.0
O B:HOH429 4.1 32.7 1.0
CB B:ASP48 4.4 33.0 1.0
O B:POP304 4.4 33.1 1.0
CB B:ASP52 4.4 35.1 1.0
O6 B:POP304 4.6 31.1 1.0
O B:HOH482 4.7 40.3 1.0
CG2 B:VAL111 4.8 27.5 1.0
O B:ASP48 4.8 33.5 1.0
CA B:ASP48 4.8 31.7 1.0
CG B:ASP114 4.9 41.3 1.0
CAN B:651305 4.9 39.6 1.0
O B:HOH427 5.0 27.4 1.0

Magnesium binding site 6 out of 6 in 4ea0

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Magnesium binding site 6 out of 6 in the Crystal Structure of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651


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 Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed with Diphosphate and Quinuclidine Bph-651 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:37.8
occ:1.00
 O6 B:POP304 1.9 31.1 1.0
OD1 B:ASP48 2.0 38.9 1.0
O B:HOH429 2.0 32.7 1.0
OD2 B:ASP52 2.0 27.2 1.0
O B:HOH482 2.1 40.3 1.0
O2 B:POP304 2.2 26.6 1.0
CG B:ASP48 2.9 37.3 1.0
CG B:ASP52 3.1 37.0 1.0
MG B:MG302 3.1 33.1 1.0
P2 B:POP304 3.1 35.7 1.0
OD2 B:ASP48 3.2 35.5 1.0
P1 B:POP304 3.3 31.1 1.0
NH2 B:ARG45 3.4 34.7 1.0
O B:POP304 3.4 33.1 1.0
CB B:ASP52 3.5 35.1 1.0
O5 B:POP304 4.0 30.9 1.0
O3 B:POP304 4.1 33.2 1.0
OD1 B:ASP52 4.2 23.9 1.0
O4 B:POP304 4.2 37.5 1.0
OD1 B:ASP49 4.3 42.7 1.0
CB B:ASP48 4.3 33.0 1.0
O B:HOH424 4.3 33.8 1.0
O1 B:POP304 4.5 27.9 1.0
O B:HOH402 4.6 26.1 1.0
CZ B:ARG45 4.6 37.5 1.0
O B:HOH401 4.7 27.4 1.0
O B:ASP48 4.7 33.5 1.0
C B:ASP48 4.8 34.7 1.0

Reference:

F.Y.Lin, Y.L.Liu, K.Li, R.Cao, W.Zhu, J.Axelson, R.Pang, E.Oldfield. Head-to-Head Prenyl Tranferases: Anti-Infective Drug Targets. J.Med.Chem. V. 55 4367 2012.
ISSN: ISSN 0022-2623
PubMed: 22486710
DOI: 10.1021/JM300208P
Page generated: Fri Aug 16 14:24:51 2024

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