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Magnesium in PDB 4lfe: Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;

Enzymatic activity of Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;

All present enzymatic activity of Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;, PDB code: 4lfe was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, H.J.Imker, N.Al Obaidi, M.Stead, J.Love, C.D.Poulter, J.A.Gerlt, S.C.Almo, Enzyme Functioninitiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.82 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.798, 75.789, 124.620, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex; (pdb code 4lfe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;, PDB code: 4lfe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4lfe

Go back to Magnesium Binding Sites List in 4lfe
Magnesium binding site 1 out of 5 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;


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 Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:32.5
occ:1.00
 O1A A:IPE301 2.1 32.5 1.0
OD1 A:ASP78 2.1 36.8 1.0
OD2 A:ASP84 2.1 30.2 1.0
O A:HOH454 2.1 38.6 1.0
O A:HOH436 2.1 31.0 1.0
O A:HOH471 2.2 40.5 1.0
CG A:ASP84 3.0 29.4 1.0
MG A:MG303 3.0 36.2 1.0
CG A:ASP78 3.0 30.8 1.0
OD1 A:ASP84 3.2 36.0 1.0
OD2 A:ASP78 3.3 35.1 1.0
PA A:IPE301 3.3 34.4 1.0
O A:HOH452 3.6 44.9 1.0
O1 A:IPE301 3.7 42.9 1.0
OD2 A:ASP152 3.9 39.8 1.0
C1 A:IPE301 3.9 52.1 1.0
O2A A:IPE301 4.0 49.1 1.0
NE2 A:GLN149 4.3 37.6 1.0
OE1 A:GLN149 4.3 34.7 1.0
CB A:ASP84 4.4 30.7 1.0
CB A:ASP78 4.4 29.9 1.0
O A:HOH457 4.5 39.2 1.0
O2B A:IPE301 4.6 32.8 1.0
O A:ASP78 4.6 24.5 1.0
O3A A:IPE301 4.7 37.2 1.0
CD A:GLN149 4.8 36.0 1.0
O A:HOH419 4.8 29.1 1.0

Magnesium binding site 2 out of 5 in 4lfe

Go back to Magnesium Binding Sites List in 4lfe
Magnesium binding site 2 out of 5 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;


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 Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:36.2
occ:1.00
 O2B A:IPE301 2.1 32.8 1.0
OD2 A:ASP84 2.1 30.2 1.0
OD2 A:ASP78 2.1 35.1 1.0
O1A A:IPE301 2.1 32.5 1.0
O A:HOH419 2.2 29.1 1.0
O A:HOH452 2.2 44.9 1.0
MG A:MG302 3.0 32.5 1.0
CG A:ASP78 3.0 30.8 1.0
CG A:ASP84 3.1 29.4 1.0
PA A:IPE301 3.3 34.4 1.0
OD1 A:ASP78 3.3 36.8 1.0
PB A:IPE301 3.3 42.3 1.0
O3A A:IPE301 3.6 37.2 1.0
CB A:ASP84 3.6 30.7 1.0
O A:HOH417 3.8 36.0 1.0
NH2 A:ARG89 3.9 38.4 1.0
O1B A:IPE301 4.1 45.1 1.0
O A:HOH436 4.1 31.0 1.0
OD1 A:ASP84 4.2 36.0 1.0
OD2 A:ASP86 4.3 28.1 0.5
O A:ASP78 4.3 24.5 1.0
O1 A:IPE301 4.3 42.9 1.0
O2A A:IPE301 4.4 49.1 1.0
CB A:ASP78 4.4 29.9 1.0
C1 A:IPE301 4.4 52.1 1.0
O3B A:IPE301 4.4 37.7 1.0
OD1 A:ASP79 4.5 29.4 1.0
C A:ASP78 4.7 25.2 1.0
O A:HOH454 4.7 38.6 1.0
O A:HOH471 4.8 40.5 1.0

Magnesium binding site 3 out of 5 in 4lfe

Go back to Magnesium Binding Sites List in 4lfe
Magnesium binding site 3 out of 5 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;


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 Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:28.6
occ:1.00
 OD2 B:ASP213 2.1 26.1 1.0
O2B B:IPE301 2.1 30.6 1.0
O2A B:IPE301 2.1 23.2 1.0
O B:HOH436 2.1 26.6 1.0
O B:HOH416 2.2 27.2 1.0
O B:HOH420 2.3 26.2 1.0
CG B:ASP213 3.1 30.8 1.0
O B:HOH484 3.2 34.3 1.0
PB B:IPE301 3.3 26.3 1.0
PA B:IPE301 3.3 23.6 1.0
O3A B:IPE301 3.4 21.9 1.0
OD1 B:ASP213 3.6 23.4 1.0
OD1 B:ASP217 4.0 30.2 1.0
O B:HOH474 4.1 26.6 1.0
O B:ASP213 4.2 26.8 1.0
O1A B:IPE301 4.2 24.7 1.0
NE2 B:GLN210 4.2 28.8 1.0
O1B B:IPE301 4.2 21.1 1.0
OD2 B:ASP232 4.3 28.0 1.0
CB B:ASP213 4.3 30.6 1.0
O3B B:IPE301 4.3 23.7 1.0
OD1 B:ASP232 4.4 27.4 1.0
NZ B:LYS227 4.4 26.5 1.0
O1 B:IPE301 4.5 29.8 1.0
C B:ASP213 4.5 29.2 1.0
CE B:LYS227 4.6 25.7 1.0
CG B:ASP217 4.6 40.8 1.0
CG B:ASP232 4.7 31.2 1.0
CB B:ASP217 4.8 26.4 1.0
OD1 B:ASP214 4.9 23.9 1.0

Magnesium binding site 4 out of 5 in 4lfe

Go back to Magnesium Binding Sites List in 4lfe
Magnesium binding site 4 out of 5 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;


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 Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:28.5
occ:1.00
 OD2 B:ASP84 2.1 21.6 1.0
OD1 B:ASP78 2.1 26.5 1.0
O1A B:IPE301 2.1 24.7 1.0
O B:HOH419 2.1 30.8 1.0
O B:HOH458 2.1 34.4 1.0
O B:HOH496 2.1 25.4 1.0
CG B:ASP84 3.0 26.6 1.0
CG B:ASP78 3.0 24.5 1.0
MG B:MG305 3.1 24.2 1.0
OD1 B:ASP84 3.2 24.3 1.0
PA B:IPE301 3.3 23.6 1.0
OD2 B:ASP78 3.3 28.6 1.0
O1 B:IPE301 3.5 29.8 1.0
OE1 B:GLN149 4.1 30.3 1.0
O B:HOH484 4.2 34.3 1.0
O B:HOH474 4.2 26.6 1.0
NE2 B:GLN149 4.2 27.1 1.0
OD1 B:ASP152 4.3 35.8 1.0
O2A B:IPE301 4.3 23.2 1.0
OD2 B:ASP152 4.3 38.6 1.0
CB B:ASP84 4.3 27.2 1.0
CB B:ASP78 4.4 29.8 1.0
NZ B:LYS237 4.4 32.2 1.0
O3A B:IPE301 4.5 21.9 1.0
CG B:ASP152 4.5 47.5 1.0
NZ B:LYS172 4.5 36.5 1.0
C5 B:IPE301 4.6 31.3 1.0
CD B:GLN149 4.6 27.3 1.0
O3B B:IPE301 4.7 23.7 1.0
C1 B:IPE301 4.8 36.8 1.0
O B:HOH431 4.8 24.8 1.0
O B:HOH517 4.9 24.6 1.0
O B:ASP78 4.9 20.6 1.0
CE B:LYS237 4.9 31.7 1.0

Magnesium binding site 5 out of 5 in 4lfe

Go back to Magnesium Binding Sites List in 4lfe
Magnesium binding site 5 out of 5 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex;


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 Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Partially Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:24.2
occ:1.00
 O B:HOH431 2.0 24.8 1.0
OD2 B:ASP78 2.1 28.6 1.0
OD2 B:ASP84 2.1 21.6 1.0
O3B B:IPE301 2.1 23.7 1.0
O1A B:IPE301 2.1 24.7 1.0
O B:HOH474 2.1 26.6 1.0
CG B:ASP78 3.1 24.5 1.0
CG B:ASP84 3.1 26.6 1.0
MG B:MG304 3.1 28.5 1.0
PB B:IPE301 3.3 26.3 1.0
PA B:IPE301 3.3 23.6 1.0
OD1 B:ASP78 3.4 26.5 1.0
CB B:ASP84 3.4 27.2 1.0
O3A B:IPE301 3.5 21.9 1.0
O B:HOH409 3.6 29.8 1.0
O2B B:IPE301 3.8 30.6 1.0
NH2 B:ARG89 4.1 28.2 1.0
O2A B:IPE301 4.2 23.2 1.0
OD1 B:ASP84 4.2 24.3 1.0
O B:HOH458 4.3 34.4 1.0
O B:HOH517 4.3 24.6 1.0
CB B:ASP78 4.4 29.8 1.0
O B:ASP78 4.4 20.6 1.0
OD1 B:ASP79 4.5 25.6 1.0
O1B B:IPE301 4.5 21.1 1.0
O1 B:IPE301 4.5 29.8 1.0
O B:HOH420 4.7 26.2 1.0
CE B:LYS231 4.7 31.7 1.0
O B:HOH484 4.7 34.3 1.0
C B:ASP78 4.7 25.6 1.0
NZ B:LYS231 4.8 29.0 1.0
O B:HOH419 4.9 30.8 1.0
O B:HOH496 5.0 25.4 1.0
CA B:ASP84 5.0 30.7 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, H.J.Imker, N.Al Obaidi, M.Stead, J.Love, C.D.Poulter, J.A.Gerlt, S.C.Almo. Crystal Structure of Geranylgeranyl Diphosphate Synthase From Streptococcus Uberis 0140J To Be Published.
Page generated: Mon Aug 19 17:43:25 2024

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