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Magnesium in PDB 4lfg: Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully 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, Fully 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, Fully 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, Fully Liganded Complex;, PDB code: 4lfg 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) 46.67 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.385, 74.326, 124.473, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.4

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, Fully Liganded Complex; (pdb code 4lfg). 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 Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully Liganded Complex;, PDB code: 4lfg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4lfg

Go back to Magnesium Binding Sites List in 4lfg
Magnesium binding site 1 out of 6 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully 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, Fully Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:18.9
occ:1.00
 OD1 A:ASP78 2.1 18.2 1.0
OD2 A:ASP84 2.1 19.6 1.0
O1A A:IPE301 2.1 17.8 1.0
O A:HOH495 2.1 24.1 1.0
O A:HOH490 2.1 20.2 1.0
O A:HOH431 2.2 23.5 1.0
CG A:ASP84 3.0 19.5 1.0
CG A:ASP78 3.0 21.1 1.0
MG A:MG304 3.0 18.7 1.0
OD2 A:ASP78 3.3 17.9 1.0
OD1 A:ASP84 3.3 21.3 1.0
PA A:IPE301 3.3 25.2 1.0
O1 A:IPE301 3.4 37.4 1.0
OD1 A:ASP152 4.0 23.8 0.5
OD2 A:ASP152 4.1 13.3 0.5
O2A A:IPE301 4.1 57.7 1.0
OE1 A:GLN149 4.1 20.3 1.0
O A:HOH415 4.2 20.5 1.0
NE2 A:GLN149 4.3 23.4 1.0
CB A:ASP84 4.4 19.1 1.0
NZ A:LYS237 4.4 44.2 1.0
CB A:ASP78 4.4 15.4 1.0
O A:HOH588 4.5 34.9 1.0
O A:HOH639 4.6 43.9 1.0
CG A:ASP152 4.6 20.0 0.5
O3A A:IPE301 4.6 22.0 1.0
O2B A:IPE301 4.6 19.1 1.0
CD A:GLN149 4.6 20.2 1.0
OD2 A:ASP152 4.8 31.1 0.5
O A:ASP78 4.8 18.5 1.0
C1 A:IPE301 4.8 50.0 1.0
NZ A:LYS172 4.9 27.9 1.0
O A:HOH422 4.9 17.8 1.0
CE A:LYS237 4.9 47.7 1.0

Magnesium binding site 2 out of 6 in 4lfg

Go back to Magnesium Binding Sites List in 4lfg
Magnesium binding site 2 out of 6 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully 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, Fully Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:18.7
occ:1.00
 O2B A:IPE301 2.0 19.1 1.0
OD2 A:ASP78 2.1 17.9 1.0
OD2 A:ASP84 2.1 19.6 1.0
O1A A:IPE301 2.1 17.8 1.0
O A:HOH415 2.1 20.5 1.0
O A:HOH422 2.2 17.8 1.0
CG A:ASP78 3.0 21.1 1.0
MG A:MG303 3.0 18.9 1.0
CG A:ASP84 3.1 19.5 1.0
PA A:IPE301 3.3 25.2 1.0
PB A:IPE301 3.3 20.4 1.0
OD1 A:ASP78 3.3 18.2 1.0
CB A:ASP84 3.5 19.1 1.0
O3A A:IPE301 3.6 22.0 1.0
O A:HOH440 3.9 25.8 1.0
O1B A:IPE301 4.0 21.8 1.0
NH2 A:ARG89 4.1 17.5 1.0
O A:HOH431 4.1 23.5 1.0
O A:HOH588 4.2 34.9 1.0
OD1 A:ASP84 4.2 21.3 1.0
O1 A:IPE301 4.3 37.4 1.0
O A:HOH580 4.3 42.5 1.0
O A:ASP78 4.4 18.5 1.0
O2A A:IPE301 4.4 57.7 1.0
CB A:ASP78 4.4 15.4 1.0
O3B A:IPE301 4.5 21.8 1.0
OD1 A:ASP79 4.5 18.8 1.0
O A:HOH507 4.6 34.2 1.0
O A:HOH636 4.6 55.7 1.0
O A:HOH495 4.7 24.1 1.0
O A:HOH490 4.7 20.2 1.0
C A:ASP78 4.8 17.3 1.0

Magnesium binding site 3 out of 6 in 4lfg

Go back to Magnesium Binding Sites List in 4lfg
Magnesium binding site 3 out of 6 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully 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, Fully Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:15.6
occ:1.00
 O A:HOH577 1.8 18.7 0.5
O1B A:IPE301 2.1 21.8 1.0
OD2 A:ASP217 2.1 27.4 0.5
OD2 A:ASP213 2.1 24.1 1.0
O A:HOH578 2.2 48.1 1.0
O A:HOH507 2.4 34.2 1.0
CG A:ASP213 3.0 25.6 1.0
CG A:ASP217 3.1 31.7 0.5
O2A A:IPE301 3.2 57.7 1.0
PB A:IPE301 3.3 20.4 1.0
OD1 A:ASP217 3.4 27.8 0.5
OD1 A:ASP213 3.4 21.7 1.0
O3A A:IPE301 3.4 22.0 1.0
O A:HOH580 3.7 42.5 1.0
PA A:IPE301 3.8 25.2 1.0
NZ A:LYS227 3.9 20.6 1.0
O3B A:IPE301 4.1 21.8 1.0
OD1 A:ASP217 4.2 40.2 0.5
OD2 A:ASP232 4.2 35.4 1.0
O A:ASP213 4.3 23.1 1.0
O A:HOH639 4.3 43.9 1.0
CE A:LYS227 4.3 24.5 1.0
CB A:ASP213 4.4 25.9 1.0
O2B A:IPE301 4.4 19.1 1.0
OD1 A:ASP232 4.4 42.5 1.0
CB A:ASP217 4.4 29.2 0.5
NE2 A:GLN210 4.4 25.1 1.0
CG A:ASP217 4.5 38.4 0.5
CB A:ASP217 4.5 28.8 0.5
C A:ASP213 4.6 23.2 1.0
O A:HOH415 4.7 20.5 1.0
O1A A:IPE301 4.7 17.8 1.0
CG A:ASP232 4.7 66.1 1.0

Magnesium binding site 4 out of 6 in 4lfg

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Magnesium binding site 4 out of 6 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully 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, Fully Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:15.5
occ:1.00
 O2B B:IPE301 2.1 15.2 1.0
OD2 B:ASP213 2.1 17.0 1.0
O2A B:IPE301 2.1 15.8 1.0
O B:HOH605 2.1 14.6 1.0
O B:HOH604 2.2 16.0 1.0
O B:HOH406 2.2 15.0 1.0
CG B:ASP213 3.1 17.1 1.0
PB B:IPE301 3.3 15.0 1.0
PA B:IPE301 3.3 15.8 1.0
O3A B:IPE301 3.4 14.0 1.0
OD1 B:ASP213 3.5 17.9 1.0
O B:HOH446 3.8 18.1 1.0
OD1 B:ASP217 4.0 21.7 1.0
OD2 B:ASP232 4.1 16.4 1.0
NE2 B:GLN210 4.2 15.5 1.0
O B:ASP213 4.2 13.0 1.0
O B:HOH408 4.2 15.8 1.0
O1A B:IPE301 4.2 12.3 1.0
NZ B:LYS227 4.3 16.9 1.0
O1B B:IPE301 4.3 14.6 1.0
CB B:ASP213 4.3 17.6 1.0
O3B B:IPE301 4.3 15.4 1.0
OD1 B:ASP232 4.4 19.7 1.0
C B:ASP213 4.5 13.7 1.0
O1 B:IPE301 4.5 16.9 1.0
CE B:LYS227 4.6 17.8 1.0
CG B:ASP217 4.6 22.3 1.0
CG B:ASP232 4.7 18.6 1.0
CB B:ASP217 4.8 14.5 1.0
OD1 B:ASP214 4.8 17.3 1.0
CA B:ASP213 5.0 13.6 1.0
N B:ASP214 5.0 14.7 1.0

Magnesium binding site 5 out of 6 in 4lfg

Go back to Magnesium Binding Sites List in 4lfg
Magnesium binding site 5 out of 6 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully 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, Fully Liganded Complex; within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:14.7
occ:1.00
 O1A B:IPE301 2.1 12.3 1.0
OD2 B:ASP84 2.1 15.9 1.0
OD1 B:ASP78 2.1 14.7 1.0
O B:HOH444 2.1 16.4 1.0
O B:HOH493 2.1 16.6 1.0
O B:HOH557 2.2 17.6 1.0
CG B:ASP84 3.0 15.4 1.0
CG B:ASP78 3.0 16.1 1.0
MG B:MG305 3.1 15.6 1.0
OD1 B:ASP84 3.2 17.9 1.0
PA B:IPE301 3.3 15.8 1.0
OD2 B:ASP78 3.3 13.3 1.0
O1 B:IPE301 3.5 16.9 1.0
OD1 B:ASP152 4.0 23.4 1.0
OE1 B:GLN149 4.1 18.5 1.0
NE2 B:GLN149 4.2 17.7 1.0
O B:HOH408 4.3 15.8 1.0
O2A B:IPE301 4.3 15.8 1.0
OD2 B:ASP152 4.3 21.6 1.0
O B:HOH446 4.3 18.1 1.0
CB B:ASP84 4.4 13.6 1.0
CG B:ASP152 4.4 24.1 1.0
O3A B:IPE301 4.4 14.0 1.0
CB B:ASP78 4.4 13.8 1.0
NZ B:LYS237 4.5 20.3 1.0
CD B:GLN149 4.6 17.9 1.0
NZ B:LYS172 4.6 21.7 1.0
C5 B:IPE301 4.6 22.4 1.0
O3B B:IPE301 4.7 15.4 1.0
C1 B:IPE301 4.8 18.5 1.0
CE B:LYS237 4.9 17.2 1.0
O B:ASP78 4.9 14.4 1.0
O B:HOH435 5.0 15.9 1.0
O B:HOH411 5.0 13.0 1.0

Magnesium binding site 6 out of 6 in 4lfg

Go back to Magnesium Binding Sites List in 4lfg
Magnesium binding site 6 out of 6 in the Crystal Structure of Geranylgeranyl Diphosphate Synthase SUB1274 (Target Efi-509455) From Streptococcus Uberis 0140J with Bound Magnesium and Isopentyl Diphosphate, Fully Liganded Complex;


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

b:15.6
occ:1.00
 O3B B:IPE301 2.1 15.4 1.0
OD2 B:ASP78 2.1 13.3 1.0
OD2 B:ASP84 2.1 15.9 1.0
O1A B:IPE301 2.1 12.3 1.0
O B:HOH408 2.1 15.8 1.0
O B:HOH411 2.2 13.0 1.0
CG B:ASP78 3.0 16.1 1.0
MG B:MG304 3.1 14.7 1.0
CG B:ASP84 3.1 15.4 1.0
PB B:IPE301 3.2 15.0 1.0
PA B:IPE301 3.3 15.8 1.0
OD1 B:ASP78 3.4 14.7 1.0
O3A B:IPE301 3.4 14.0 1.0
CB B:ASP84 3.5 13.6 1.0
O B:HOH447 3.6 20.0 1.0
O2B B:IPE301 3.9 15.2 1.0
NH2 B:ARG89 4.1 14.9 1.0
O2A B:IPE301 4.2 15.8 1.0
OD1 B:ASP84 4.3 17.9 1.0
O B:HOH557 4.3 17.6 1.0
CB B:ASP78 4.4 13.8 1.0
O B:HOH435 4.4 15.9 1.0
O B:ASP78 4.4 14.4 1.0
O1B B:IPE301 4.5 14.6 1.0
O B:HOH406 4.5 15.0 1.0
O1 B:IPE301 4.5 16.9 1.0
OD1 B:ASP79 4.5 17.8 1.0
C B:ASP78 4.7 12.6 1.0
CE B:LYS231 4.8 27.4 1.0
O B:HOH444 4.8 16.4 1.0
NZ B:LYS231 4.8 25.1 1.0
O B:HOH493 4.9 16.6 1.0
C5 B:IPE301 5.0 22.4 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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