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Magnesium in PDB 3ulk: E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+

Enzymatic activity of E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+

All present enzymatic activity of E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+:
1.1.1.86;

Protein crystallography data

The structure of E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+, PDB code: 3ulk was solved by S.H.Wong, T.G.A.Lonhienne, D.J.Winzor, G.Schenk, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.15 / 2.30
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 144.459, 144.459, 217.545, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+ (pdb code 3ulk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+, PDB code: 3ulk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3ulk

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Magnesium binding site 1 out of 4 in the E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg498

b:18.8
occ:1.00
OD2 A:ASP217 2.2 22.5 1.0
OE1 A:GLU389 2.3 20.1 1.0
OE2 A:GLU393 2.5 38.1 1.0
O A:HOH761 2.5 22.5 1.0
OE1 A:GLU393 2.6 43.3 1.0
O A:HOH762 2.6 37.4 1.0
O A:HOH763 2.6 34.6 1.0
CD A:GLU393 2.9 37.8 1.0
CG A:ASP217 3.4 22.6 1.0
CD A:GLU389 3.5 26.5 1.0
MG A:MG499 3.9 36.0 1.0
CB A:ASP217 4.0 17.9 1.0
CA A:ASP217 4.1 16.2 1.0
O A:HOH789 4.2 39.0 1.0
OE2 A:GLU389 4.2 28.1 1.0
O A:HOH788 4.3 23.5 1.0
O A:ASP217 4.3 21.4 1.0
CD1 A:LEU225 4.3 16.7 1.0
OD1 A:ASP217 4.3 24.7 1.0
CA A:GLU389 4.4 16.0 1.0
CB A:GLU389 4.4 19.9 1.0
CG A:GLU393 4.4 28.2 1.0
CG A:GLU389 4.6 24.1 1.0
O A:GLU389 4.7 23.6 1.0
C A:ASP217 4.7 22.1 1.0
C A:GLU389 5.0 23.6 1.0
O A:HOH778 5.0 42.9 1.0

Magnesium binding site 2 out of 4 in 3ulk

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Magnesium binding site 2 out of 4 in the E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg499

b:36.0
occ:1.00
O A:HOH775 2.6 38.3 1.0
O A:HOH773 2.7 38.3 1.0
O A:HOH771 2.7 46.2 1.0
O A:HOH763 3.0 34.6 1.0
OD2 A:ASP217 3.0 22.5 1.0
OD1 A:ASP217 3.0 24.7 1.0
O A:HOH764 3.1 28.9 1.0
O A:HOH762 3.3 37.4 1.0
CG A:ASP217 3.4 22.6 1.0
OE1 A:GLU221 3.4 30.9 1.0
O A:HOH778 3.6 42.9 1.0
O A:HOH770 3.6 32.1 1.0
O A:HOH769 3.8 34.5 1.0
MG A:MG498 3.9 18.8 1.0
O A:HOH779 4.2 56.5 1.0
CD A:GLU221 4.5 32.8 1.0
CB A:ASP217 4.8 17.9 1.0

Magnesium binding site 3 out of 4 in 3ulk

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Magnesium binding site 3 out of 4 in the E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg497

b:14.4
occ:1.00
OD2 B:ASP217 2.2 22.9 1.0
OE1 B:GLU389 2.4 18.7 1.0
O B:HOH766 2.4 28.4 1.0
O B:HOH767 2.5 33.6 1.0
O B:HOH765 2.5 19.1 1.0
OE2 B:GLU393 2.5 38.4 1.0
OE1 B:GLU393 2.8 39.5 1.0
CD B:GLU393 3.0 37.1 1.0
CG B:ASP217 3.3 25.1 1.0
CD B:GLU389 3.6 23.4 1.0
MG B:MG498 3.8 41.4 1.0
CB B:ASP217 4.0 13.1 1.0
NZ B:LYS155 4.0 38.6 1.0
CA B:ASP217 4.1 20.8 1.0
O B:HOH796 4.2 24.6 1.0
CD1 B:LEU225 4.3 17.2 1.0
O B:ASP217 4.3 21.9 1.0
OD1 B:ASP217 4.3 28.0 1.0
OE2 B:GLU389 4.3 25.9 1.0
CB B:GLU389 4.4 15.1 1.0
CA B:GLU389 4.4 16.8 1.0
CG B:GLU393 4.5 24.4 1.0
O B:GLU389 4.5 22.4 1.0
CG B:GLU389 4.6 19.2 1.0
C B:ASP217 4.6 22.6 1.0
O B:HOH792 4.8 43.3 1.0
O B:HOH776 4.9 34.4 1.0
C B:GLU389 4.9 18.8 1.0
OE1 B:GLU221 4.9 21.6 1.0

Magnesium binding site 4 out of 4 in 3ulk

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Magnesium binding site 4 out of 4 in the E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Ketol-Acid Reductoisomerase in Complex with Nadph and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg498

b:41.4
occ:1.00
O B:HOH792 2.4 43.3 1.0
O B:HOH774 2.7 36.6 1.0
O B:HOH768 2.8 35.1 1.0
O B:HOH767 2.8 33.6 1.0
O B:HOH766 3.0 28.4 1.0
O B:HOH777 3.0 38.8 1.0
OD2 B:ASP217 3.1 22.9 1.0
OD1 B:ASP217 3.5 28.0 1.0
CG B:ASP217 3.6 25.1 1.0
O B:HOH776 3.8 34.4 1.0
MG B:MG497 3.8 14.4 1.0
O B:HOH772 4.0 19.1 1.0
OE1 B:GLU221 4.0 21.6 1.0
O B:HOH793 4.6 33.6 1.0
O B:HOH796 4.9 24.6 1.0

Reference:

S.H.Wong, T.G.A.Lonhienne, D.J.Winzor, G.Schenk, L.W.Guddat. Bacterial and Plant Ketol-Acid Reductoisomerases Have Different Mechanisms of Induced Fit During the Catalytic Cycle J.Mol.Biol. V. 424 168 2012.
ISSN: ISSN 0022-2836
PubMed: 23036858
DOI: 10.1016/J.JMB.2012.09.018
Page generated: Mon Dec 14 08:56:57 2020

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