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Magnesium in PDB 3n0g: Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate

Enzymatic activity of Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate

All present enzymatic activity of Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate:
4.2.3.27;

Protein crystallography data

The structure of Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate, PDB code: 3n0g was solved by M.Koksal, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.40 / 2.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 155.014, 155.014, 143.744, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate (pdb code 3n0g). 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 Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate, PDB code: 3n0g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3n0g

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Magnesium binding site 1 out of 6 in the Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate


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 Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg621

b:40.4
occ:0.75
 O4 A:DST601 2.3 56.3 0.8
OD1 A:ASP345 2.4 35.7 1.0
O6 A:DST601 2.7 54.4 0.8
P1 A:DST601 3.0 56.8 0.8
OE2 A:GLU423 3.3 38.4 1.0
CD1 A:PHE420 3.3 23.2 1.0
CG A:ASP345 3.5 36.0 1.0
O A:ASP345 3.5 30.5 1.0
CE1 A:PHE420 3.5 24.4 1.0
OD2 A:ASP349 3.8 44.0 1.0
CB A:ASP349 3.9 39.8 1.0
O2 A:DST601 3.9 55.9 0.8
CG A:ASP349 4.0 42.8 1.0
OD2 A:ASP345 4.1 40.2 1.0
C A:ASP345 4.2 28.9 1.0
O5 A:DST601 4.2 56.5 0.8
CG A:PHE420 4.3 22.5 1.0
CA A:ASP345 4.3 28.7 1.0
CB A:ASP345 4.4 32.5 1.0
N A:ASP349 4.4 29.8 1.0
CB A:TYR348 4.4 23.0 1.0
CD A:GLU423 4.5 36.3 1.0
MG A:MG623 4.6 42.4 1.0
CZ A:PHE420 4.6 23.0 1.0
OD1 A:ASP349 4.7 44.3 1.0
CB A:PHE420 4.8 23.2 1.0
CA A:ASP349 4.8 34.9 1.0
CA A:PHE420 4.9 23.4 1.0

Magnesium binding site 2 out of 6 in 3n0g

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Magnesium binding site 2 out of 6 in the Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate


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 Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg622

b:46.1
occ:0.75
 O8 A:DST601 2.6 53.5 0.8
OE2 A:GLU497 3.3 63.9 1.0
O5 A:DST601 3.4 56.5 0.8
O A:HOH733 3.5 27.8 1.0
O A:ALA504 3.6 44.6 1.0
P3 A:DST601 3.9 54.6 0.8
O7 A:DST601 4.0 53.5 0.8
OD1 A:ASP490 4.1 23.9 1.0
CD A:GLU497 4.1 65.2 1.0
OE1 A:GLU497 4.1 68.1 1.0
NH1 A:ARG486 4.2 18.4 1.0
P1 A:DST601 4.5 56.8 0.8
O2 A:DST601 4.5 55.9 0.8
OH A:TYR438 4.6 44.2 1.0
OG A:SER493 4.7 43.4 1.0
C A:ALA504 4.8 42.0 1.0
CG A:ASP490 4.8 23.8 1.0

Magnesium binding site 3 out of 6 in 3n0g

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Magnesium binding site 3 out of 6 in the Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate


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 Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg623

b:42.4
occ:1.00
 O2 A:DST601 2.4 55.9 0.8
OD2 A:ASP345 2.7 40.2 1.0
P3 A:DST601 3.1 54.6 0.8
OD1 A:ASP349 3.3 44.3 1.0
O4 A:DST601 3.3 56.3 0.8
S9 A:DST601 3.3 51.0 0.8
O8 A:DST601 3.4 53.5 0.8
P1 A:DST601 3.4 56.8 0.8
CG A:ASP345 3.6 36.0 1.0
OD2 A:ASP349 3.7 44.0 1.0
CG A:ASP349 3.7 42.8 1.0
OD1 A:ASP345 3.7 35.7 1.0
C10 A:DST601 3.8 48.8 0.8
O5 A:DST601 4.4 56.5 0.8
O7 A:DST601 4.5 53.5 0.8
O6 A:DST601 4.5 54.4 0.8
MG A:MG621 4.6 40.4 0.8
NH2 A:ARG308 4.6 85.4 1.0
OD1 A:ASP346 4.7 37.8 1.0
CB A:ASP349 5.0 39.8 1.0
CB A:ASP345 5.0 32.5 1.0

Magnesium binding site 4 out of 6 in 3n0g

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Magnesium binding site 4 out of 6 in the Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate


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 Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg631

b:42.1
occ:0.75
 OD1 B:ASP345 2.3 29.3 1.0
O4 B:DST612 2.3 56.9 0.8
O6 B:DST612 2.7 57.0 0.8
OD1 B:ASP349 3.1 52.0 1.0
P1 B:DST612 3.1 57.3 0.8
CG B:ASP345 3.4 31.5 1.0
CD1 B:PHE420 3.5 25.7 1.0
CE1 B:PHE420 3.5 26.4 1.0
O B:ASP345 3.6 31.4 1.0
CG B:ASP349 3.8 50.1 1.0
MG B:MG633 3.8 38.2 1.0
OE2 B:GLU423 3.8 43.9 1.0
CB B:ASP349 3.9 45.0 1.0
O2 B:DST612 4.0 56.5 0.8
OD2 B:ASP345 4.2 35.9 1.0
O5 B:DST612 4.3 57.4 0.8
C B:ASP345 4.3 29.3 1.0
CA B:ASP345 4.4 28.0 1.0
CB B:ASP345 4.4 29.1 1.0
CG B:PHE420 4.5 25.4 1.0
CZ B:PHE420 4.6 26.4 1.0
N B:ASP349 4.6 35.7 1.0
CB B:TYR348 4.7 33.2 1.0
OD2 B:ASP349 4.8 52.7 1.0
CA B:ASP349 4.9 39.5 1.0

Magnesium binding site 5 out of 6 in 3n0g

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Magnesium binding site 5 out of 6 in the Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate


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 Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg632

b:38.8
occ:0.75
 O B:HOH727 2.4 38.6 1.0
O7 B:DST612 2.4 55.3 0.8
O5 B:DST612 2.6 57.4 0.8
O8 B:DST612 3.0 55.1 0.8
P3 B:DST612 3.1 54.8 0.8
P1 B:DST612 3.6 57.3 0.8
O2 B:DST612 3.7 56.5 0.8
NH1 B:ARG486 4.0 19.0 1.0
O B:HOH610 4.0 31.9 1.0
O4 B:DST612 4.2 56.9 0.8
OE2 B:GLU497 4.3 58.9 1.0
OD1 B:ASP490 4.4 36.6 1.0
OD1 B:ASN489 4.5 37.7 1.0
O B:ALA504 4.7 60.7 1.0
MG B:MG633 4.9 38.2 1.0
S9 B:DST612 4.9 49.5 0.8
OE1 B:GLU497 5.0 60.2 1.0

Magnesium binding site 6 out of 6 in 3n0g

Go back to Magnesium Binding Sites List in 3n0g
Magnesium binding site 6 out of 6 in the Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate


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 Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex with Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg633

b:38.2
occ:1.00
 O8 B:DST612 2.4 55.1 0.8
O4 B:DST612 2.5 56.9 0.8
OD2 B:ASP345 2.6 35.9 1.0
O2 B:DST612 2.8 56.5 0.8
OD1 B:ASP349 3.0 52.0 1.0
P3 B:DST612 3.0 54.8 0.8
OD1 B:ASP345 3.1 29.3 1.0
CG B:ASP345 3.2 31.5 1.0
P1 B:DST612 3.2 57.3 0.8
CG B:ASP349 3.4 50.1 1.0
OD2 B:ASP349 3.4 52.7 1.0
MG B:MG631 3.8 42.1 0.8
C10 B:DST612 3.8 47.0 0.8
S9 B:DST612 3.8 49.5 0.8
O5 B:DST612 4.3 57.4 0.8
O6 B:DST612 4.3 57.0 0.8
O7 B:DST612 4.4 55.3 0.8
CB B:ASP349 4.6 45.0 1.0
CB B:ASP345 4.7 29.1 1.0
NH2 B:ARG308 4.7 72.7 1.0
O B:ASP345 4.7 31.4 1.0
OD1 B:ASP346 4.8 34.4 1.0
MG B:MG632 4.9 38.8 0.8
C B:ASP345 4.9 29.3 1.0

Reference:

M.Koksal, I.Zimmer, J.P.Schnitzler, D.W.Christianson. Structure of Isoprene Synthase Illuminates the Chemical Mechanism of Teragram Atmospheric Carbon Emission. J.Mol.Biol. V. 402 363 2010.
ISSN: ISSN 0022-2836
PubMed: 20624401
DOI: 10.1016/J.JMB.2010.07.009
Page generated: Wed Aug 14 19:32:34 2024

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