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Magnesium in PDB 3fr8: Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph

Enzymatic activity of Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph

All present enzymatic activity of Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph:
1.1.1.86;

Protein crystallography data

The structure of Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph, PDB code: 3fr8 was solved by E.W.W.Leung, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.22 / 2.80
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 162.060, 162.060, 196.470, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph (pdb code 3fr8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph, PDB code: 3fr8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3fr8

Go back to Magnesium Binding Sites List in 3fr8
Magnesium binding site 1 out of 3 in the Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:63.5
occ:1.00
O7 A:PE46061 2.3 59.4 1.0
O A:HOH663 2.4 36.4 1.0
OD2 A:ASP315 2.6 42.2 1.0
OE2 A:GLU496 3.2 42.8 1.0
OE2 A:GLU492 3.3 43.0 1.0
OE1 A:GLU496 3.3 42.8 1.0
C13 A:PE46061 3.5 59.5 1.0
CD A:GLU496 3.6 42.2 1.0
OE1 A:GLU492 3.8 42.6 1.0
CG A:ASP315 3.8 41.8 1.0
CD A:GLU492 3.9 42.8 1.0
CD1 A:LEU323 4.0 41.3 1.0
O A:HOH616 4.2 48.5 1.0
OD1 A:ASP315 4.5 42.1 1.0
OE1 A:GLU319 4.6 40.9 1.0
C14 A:PE46061 4.7 59.5 1.0
CB A:ASP315 4.7 41.5 1.0
O A:HOH661 4.8 39.2 1.0
CA A:ASP315 4.9 41.4 1.0
O A:ASP315 4.9 41.3 1.0

Magnesium binding site 2 out of 3 in 3fr8

Go back to Magnesium Binding Sites List in 3fr8
Magnesium binding site 2 out of 3 in the Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:77.2
occ:1.00
O B:HOH667 1.9 55.3 1.0
O4 B:PEG6073 2.3 54.9 1.0
OD1 B:ASP315 2.3 43.5 1.0
OE1 B:GLU319 2.7 43.1 1.0
CD B:GLU319 3.5 43.0 1.0
CG B:ASP315 3.5 43.5 1.0
OE2 B:GLU319 3.5 43.1 1.0
NE2 B:HIS226 3.6 47.6 1.0
C4 B:PEG6073 3.6 55.0 1.0
CE1 B:HIS226 3.6 47.6 1.0
O2D B:NDP600 3.8 49.2 1.0
OG B:SER518 3.9 43.4 1.0
CD2 B:HIS226 4.0 47.6 1.0
ND1 B:HIS226 4.0 47.6 1.0
OD2 B:ASP315 4.1 43.7 1.0
CG B:HIS226 4.2 47.6 1.0
MG B:MG597 4.3 43.6 1.0
CB B:ASP315 4.5 43.5 1.0
O B:HOH50 4.6 37.6 1.0
C3 B:PEG6073 4.6 55.1 1.0
O B:ASP315 4.7 43.4 1.0
O2 B:PEG6073 4.7 55.0 1.0
C B:ASP315 4.8 43.4 1.0
C2D B:NDP600 4.8 49.2 1.0
C6N B:NDP600 4.9 48.6 1.0
CB B:THR520 4.9 43.1 1.0
CG B:GLU319 4.9 42.9 1.0
N B:ILE316 5.0 43.3 1.0
CB B:SER518 5.0 43.5 1.0
CG2 B:THR520 5.0 43.0 1.0
N1N B:NDP600 5.0 48.7 1.0

Magnesium binding site 3 out of 3 in 3fr8

Go back to Magnesium Binding Sites List in 3fr8
Magnesium binding site 3 out of 3 in the Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rice Ketolacid Reductoisomerase in Complex with MG2+-Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg597

b:43.6
occ:1.00
O2 B:PEG6073 2.1 55.0 1.0
OD2 B:ASP315 2.5 43.7 1.0
O B:HOH670 2.8 36.0 1.0
O4 B:PEG6073 3.2 54.9 1.0
CG B:ASP315 3.3 43.5 1.0
OD1 B:ASP315 3.3 43.5 1.0
C3 B:PEG6073 3.3 55.1 1.0
OE2 B:GLU496 3.4 46.0 1.0
C4 B:PEG6073 3.7 55.0 1.0
OE1 B:GLU496 3.9 46.1 1.0
C5N B:NDP600 4.0 48.6 1.0
CD B:GLU496 4.1 45.8 1.0
MG B:MG1 4.3 77.2 1.0
OE1 B:GLU319 4.3 43.1 1.0
C4N B:NDP600 4.5 48.6 1.0
OE2 B:GLU492 4.6 46.2 1.0
O B:PRO251 4.6 50.0 1.0
NZ B:LYS252 4.7 51.1 1.0
CB B:ASP315 4.7 43.5 1.0
O B:HOH50 4.8 37.6 1.0
C6N B:NDP600 4.8 48.6 1.0

Reference:

E.W.Leung, L.W.Guddat. Conformational Changes in A Plant Ketol-Acid Reductoisomerase Upon Mg(2+) and Nadph Binding As Revealed By Two Crystal Structures J.Mol.Biol. V. 389 167 2009.
ISSN: ISSN 0022-2836
PubMed: 19362563
DOI: 10.1016/J.JMB.2009.04.012
Page generated: Mon Dec 14 08:09:12 2020

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