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Magnesium in PDB 1yve: Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)

Enzymatic activity of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)

All present enzymatic activity of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate):
1.1.1.86;

Protein crystallography data

The structure of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate), PDB code: 1yve was solved by V.Biou, R.Dumas, C.Cohen-Addad, R.Douce, D.Job, E.Pebay-Peyroula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.430, 61.940, 162.540, 90.00, 95.08, 90.00
R / Rfree (%) 19.7 / 23.9

Other elements in 1yve:

The structure of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) (pdb code 1yve). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate), PDB code: 1yve:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1yve

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Magnesium binding site 1 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:7.2
occ:1.00
 O I:HOH899 2.0 7.4 1.0
O I:HOH900 2.0 4.9 1.0
O2 I:HIO603 2.1 9.5 1.0
O12 I:HIO603 2.1 6.7 1.0
OD1 I:ASP315 2.1 7.9 1.0
OE1 I:GLU319 2.3 7.8 1.0
C2 I:HIO603 2.9 9.7 1.0
C1 I:HIO603 3.0 6.6 1.0
CG I:ASP315 3.2 6.5 1.0
CD I:GLU319 3.2 6.5 1.0
OE2 I:GLU319 3.5 6.1 1.0
OD2 I:ASP315 3.6 7.4 1.0
O I:HOH896 3.9 9.7 1.0
MG I:MG602 3.9 10.0 1.0
NE2 I:HIS226 4.0 7.6 1.0
N3 I:HIO603 4.1 10.7 1.0
CE1 I:HIS226 4.1 7.3 1.0
O I:HOH898 4.2 7.6 1.0
O11 I:HIO603 4.2 6.2 1.0
O2D I:NDP600 4.3 7.4 1.0
CD2 I:HIS226 4.3 6.8 1.0
OG I:SER518 4.3 4.7 1.0
O I:ASP315 4.4 5.7 1.0
ND1 I:HIS226 4.5 6.4 1.0
CB I:ASP315 4.5 6.1 1.0
O I:HOH897 4.5 8.7 1.0
CG I:HIS226 4.6 5.9 1.0
CG I:GLU319 4.6 7.4 1.0
C I:ASP315 4.7 5.8 1.0
O3 I:HIO603 4.7 18.7 1.0
CB I:ALA521 4.9 5.1 1.0
CB I:GLU319 5.0 6.7 1.0

Magnesium binding site 2 out of 8 in 1yve

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Magnesium binding site 2 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg602

b:10.0
occ:1.00
 O I:HOH895 1.9 6.9 1.0
O I:HOH897 2.0 8.7 1.0
O I:HOH896 2.1 9.7 1.0
OD2 I:ASP315 2.1 7.4 1.0
O3 I:HIO603 2.2 18.7 1.0
O2 I:HIO603 2.3 9.5 1.0
N3 I:HIO603 2.9 10.7 1.0
C2 I:HIO603 3.0 9.7 1.0
CG I:ASP315 3.1 6.5 1.0
OD1 I:ASP315 3.5 7.9 1.0
OE1 I:GLU496 3.9 9.9 1.0
MG I:MG601 3.9 7.2 1.0
NZ I:LYS252 3.9 7.7 1.0
OE1 I:GLU492 4.0 10.4 1.0
OE2 I:GLU496 4.1 8.6 1.0
OE2 I:GLU492 4.2 8.6 1.0
O I:HOH898 4.2 7.6 1.0
CB I:ASP315 4.3 6.1 1.0
C4 I:HIO603 4.3 10.2 1.0
OE1 I:GLU319 4.4 7.8 1.0
CD I:GLU496 4.4 8.7 1.0
C1 I:HIO603 4.5 6.6 1.0
O I:HOH899 4.5 7.4 1.0
O I:PRO251 4.5 7.0 1.0
CE I:LYS252 4.5 8.4 1.0
CD I:GLU492 4.6 6.8 1.0
CA I:ASP315 4.8 5.7 1.0
O I:ASP315 4.8 5.7 1.0
C5N I:NDP600 4.8 7.7 1.0
O12 I:HIO603 4.8 6.7 1.0
C4N I:NDP600 4.9 7.6 1.0
CD I:LYS252 4.9 6.8 1.0
C41 I:HIO603 4.9 9.7 1.0
CD1 I:LEU323 4.9 5.5 1.0
CA I:LYS252 5.0 7.2 1.0
C42 I:HIO603 5.0 9.7 1.0

Magnesium binding site 3 out of 8 in 1yve

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Magnesium binding site 3 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg601

b:12.3
occ:1.00
 O J:HOH930 2.0 8.4 1.0
O L:HOH796 2.0 9.9 1.0
O12 J:HIO603 2.1 9.9 1.0
OD1 J:ASP315 2.2 9.2 1.0
O2 J:HIO603 2.2 10.8 1.0
OE1 J:GLU319 2.3 8.6 1.0
C2 J:HIO603 2.9 11.2 1.0
C1 J:HIO603 3.0 10.3 1.0
CD J:GLU319 3.2 9.3 1.0
CG J:ASP315 3.3 8.9 1.0
OE2 J:GLU319 3.5 9.3 1.0
OD2 J:ASP315 3.7 9.2 1.0
O J:HOH927 3.9 12.8 1.0
NE2 J:HIS226 4.0 9.9 1.0
MG J:MG602 4.0 12.4 1.0
CE1 J:HIS226 4.1 8.6 1.0
O11 J:HIO603 4.2 9.4 1.0
O2D L:NDP600 4.2 9.0 1.0
N3 J:HIO603 4.2 12.6 1.0
O J:HOH929 4.2 9.4 1.0
CD2 J:HIS226 4.3 10.6 1.0
OG J:SER518 4.3 9.7 1.0
ND1 J:HIS226 4.5 9.0 1.0
O J:ASP315 4.5 7.9 1.0
CB J:ASP315 4.5 6.3 1.0
CG J:HIS226 4.6 9.2 1.0
O J:HOH928 4.6 14.2 1.0
CG J:GLU319 4.6 7.9 1.0
C J:ASP315 4.7 7.9 1.0
O3 J:HIO603 4.8 19.7 1.0
CB J:ALA521 4.9 8.1 1.0
CB J:GLU319 5.0 6.8 1.0

Magnesium binding site 4 out of 8 in 1yve

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Magnesium binding site 4 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg602

b:12.4
occ:1.00
 O J:HOH926 1.9 9.8 1.0
O J:HOH928 2.0 14.2 1.0
O J:HOH927 2.1 12.8 1.0
OD2 J:ASP315 2.2 9.2 1.0
O3 J:HIO603 2.2 19.7 1.0
O2 J:HIO603 2.3 10.8 1.0
N3 J:HIO603 3.0 12.6 1.0
C2 J:HIO603 3.0 11.2 1.0
CG J:ASP315 3.1 8.9 1.0
OD1 J:ASP315 3.5 9.2 1.0
NZ J:LYS252 3.8 9.3 1.0
OE1 J:GLU496 3.9 11.0 1.0
MG J:MG601 4.0 12.3 1.0
OE2 J:GLU496 4.1 11.3 1.0
OE1 J:GLU492 4.1 14.5 1.0
O J:HOH929 4.1 9.4 1.0
OE2 J:GLU492 4.2 10.6 1.0
CB J:ASP315 4.4 6.3 1.0
CE J:LYS252 4.4 13.7 1.0
C4 J:HIO603 4.4 12.7 1.0
OE1 J:GLU319 4.4 8.6 1.0
C1 J:HIO603 4.4 10.3 1.0
CD J:GLU496 4.4 9.3 1.0
O J:PRO251 4.4 10.0 1.0
O L:HOH796 4.5 9.9 1.0
CD J:GLU492 4.6 12.8 1.0
C5N L:NDP600 4.7 9.1 1.0
CA J:ASP315 4.8 7.8 1.0
O J:ASP315 4.8 7.9 1.0
CD J:LYS252 4.9 13.2 1.0
O12 J:HIO603 4.9 9.9 1.0
CA J:LYS252 4.9 10.3 1.0
C4N L:NDP600 4.9 10.3 1.0
CD1 J:LEU323 4.9 9.7 1.0

Magnesium binding site 5 out of 8 in 1yve

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Magnesium binding site 5 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg601

b:19.7
occ:1.00
 O K:HOH716 2.2 13.1 1.0
O2D K:NDP600 2.8 12.0 1.0
O2 K:HIO603 2.9 13.8 1.0
OD1 K:ASP315 3.0 14.9 1.0
O K:HOH715 3.1 12.6 1.0
O12 K:HIO603 3.1 11.7 1.0
CG K:HIS226 3.2 9.5 1.0
C6N K:NDP600 3.3 13.9 1.0
ND1 K:HIS226 3.4 10.1 1.0
N1N K:NDP600 3.4 12.0 1.0
CD2 K:HIS226 3.5 10.6 1.0
CB K:HIS226 3.5 9.8 1.0
CG K:ASP315 3.6 16.0 1.0
OD2 K:ASP315 3.7 12.5 1.0
C1D K:NDP600 3.7 12.2 1.0
C2D K:NDP600 3.8 10.9 1.0
CE1 K:HIS226 3.8 11.4 1.0
C5N K:NDP600 3.8 13.7 1.0
NE2 K:HIS226 3.8 12.1 1.0
C2 K:HIO603 3.8 13.9 1.0
C1 K:HIO603 3.9 11.9 1.0
O K:HOH717 3.9 15.2 1.0
C2N K:NDP600 4.2 12.6 1.0
C4N K:NDP600 4.3 11.5 1.0
O K:SER225 4.3 11.1 1.0
MG K:MG602 4.4 14.7 1.0
OE1 K:GLU319 4.5 14.1 1.0
CA K:HIS226 4.5 10.4 1.0
C3N K:NDP600 4.5 12.4 1.0
OE2 K:GLU311 4.7 10.4 1.0
O11 K:HIO603 4.8 12.1 1.0
CB K:ASP315 4.8 13.1 1.0

Magnesium binding site 6 out of 8 in 1yve

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Magnesium binding site 6 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg602

b:14.7
occ:1.00
 O K:HOH718 2.0 11.9 1.0
O K:HOH719 2.0 18.8 1.0
O K:HOH717 2.0 15.2 1.0
O3 K:HIO603 2.1 22.5 1.0
OD2 K:ASP315 2.2 12.5 1.0
O2 K:HIO603 2.3 13.8 1.0
N3 K:HIO603 2.8 16.1 1.0
C2 K:HIO603 2.9 13.9 1.0
CG K:ASP315 3.2 16.0 1.0
OD1 K:ASP315 3.6 14.9 1.0
OE1 K:GLU496 3.9 12.6 1.0
NZ K:LYS252 3.9 13.5 1.0
OE2 K:GLU496 4.0 15.2 1.0
OE1 K:GLU492 4.1 16.1 1.0
OE2 K:GLU492 4.1 14.9 1.0
O K:HOH716 4.2 13.1 1.0
C4 K:HIO603 4.3 14.3 1.0
CD K:GLU496 4.4 12.9 1.0
CB K:ASP315 4.4 13.1 1.0
C1 K:HIO603 4.4 11.9 1.0
MG K:MG601 4.4 19.7 1.0
OE1 K:GLU319 4.5 14.1 1.0
O K:PRO251 4.5 12.5 1.0
CD K:GLU492 4.6 14.7 1.0
C5N K:NDP600 4.7 13.7 1.0
CE K:LYS252 4.7 16.7 1.0
CD K:LYS252 4.7 16.1 1.0
CA K:ASP315 4.8 13.4 1.0
O12 K:HIO603 4.8 11.7 1.0
C4N K:NDP600 4.8 11.5 1.0
CA K:LYS252 4.9 13.5 1.0
O K:ASP315 4.9 10.3 1.0
CD1 K:LEU323 4.9 9.9 1.0
C41 K:HIO603 4.9 12.5 1.0

Magnesium binding site 7 out of 8 in 1yve

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Magnesium binding site 7 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:12.8
occ:1.00
 O L:HOH817 1.9 12.3 1.0
O L:HOH818 2.0 12.1 1.0
O2 L:HIO603 2.1 18.1 1.0
O12 L:HIO603 2.2 15.7 1.0
OD1 L:ASP315 2.2 13.7 1.0
OE1 L:GLU319 2.4 13.4 1.0
C2 L:HIO603 2.9 16.8 1.0
C1 L:HIO603 2.9 18.0 1.0
CG L:ASP315 3.2 14.0 1.0
CD L:GLU319 3.3 11.4 1.0
OE2 L:GLU319 3.5 12.5 1.0
OD2 L:ASP315 3.6 15.1 1.0
O L:HOH814 3.9 19.5 1.0
MG L:MG602 3.9 16.4 1.0
NE2 L:HIS226 4.1 13.0 1.0
CE1 L:HIS226 4.1 11.4 1.0
O11 L:HIO603 4.1 16.0 1.0
O L:HOH816 4.2 12.3 1.0
N3 L:HIO603 4.2 19.7 1.0
O2D K:NDP605 4.2 13.5 1.0
OG L:SER518 4.3 13.0 1.0
CD2 L:HIS226 4.4 11.9 1.0
ND1 L:HIS226 4.4 10.5 1.0
O L:HOH815 4.4 17.6 1.0
O L:ASP315 4.5 12.6 1.0
CB L:ASP315 4.5 12.0 1.0
CG L:HIS226 4.5 12.0 1.0
CG L:GLU319 4.7 10.3 1.0
C L:ASP315 4.8 13.4 1.0
O3 L:HIO603 4.8 23.2 1.0
CB L:ALA521 4.9 11.8 1.0
C6N K:NDP605 5.0 13.5 1.0

Magnesium binding site 8 out of 8 in 1yve

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Magnesium binding site 8 out of 8 in the Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Magnesium and Inhibitor Ipoha (N-Hydroxy-N- Isopropyloxamate) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg602

b:16.4
occ:1.00
 O L:HOH813 1.9 12.0 1.0
O L:HOH815 1.9 17.6 1.0
O L:HOH814 2.0 19.5 1.0
OD2 L:ASP315 2.2 15.1 1.0
O2 L:HIO603 2.2 18.1 1.0
O3 L:HIO603 2.3 23.2 1.0
N3 L:HIO603 2.9 19.7 1.0
C2 L:HIO603 2.9 16.8 1.0
CG L:ASP315 3.1 14.0 1.0
OD1 L:ASP315 3.5 13.7 1.0
NZ L:LYS252 3.9 16.5 1.0
MG L:MG601 3.9 12.8 1.0
OE1 L:GLU496 3.9 18.4 1.0
OE2 L:GLU496 4.1 17.6 1.0
OE1 L:GLU492 4.1 18.2 1.0
O L:HOH816 4.2 12.3 1.0
OE2 L:GLU492 4.2 19.5 1.0
OE1 L:GLU319 4.3 13.4 1.0
C4 L:HIO603 4.3 17.1 1.0
CB L:ASP315 4.3 12.0 1.0
C1 L:HIO603 4.4 18.0 1.0
O L:HOH817 4.4 12.3 1.0
CD L:GLU496 4.5 18.4 1.0
CE L:LYS252 4.5 16.1 1.0
O L:PRO251 4.5 13.2 1.0
CD L:GLU492 4.6 16.9 1.0
C5N K:NDP605 4.7 13.2 1.0
O L:ASP315 4.7 12.6 1.0
CA L:ASP315 4.7 12.7 1.0
C4N K:NDP605 4.9 13.8 1.0
O12 L:HIO603 4.9 15.7 1.0
C42 L:HIO603 4.9 16.2 1.0
C41 L:HIO603 4.9 17.5 1.0
CA L:LYS252 4.9 14.6 1.0
CD L:LYS252 5.0 17.6 1.0

Reference:

V.Biou, R.Dumas, C.Cohen-Addad, R.Douce, D.Job, E.Pebay-Peyroula. The Crystal Structure of Plant Acetohydroxy Acid Isomeroreductase Complexed with Nadph, Two Magnesium Ions and A Herbicidal Transition State Analog Determined at 1.65 A Resolution. Embo J. V. 16 3405 1997.
ISSN: ISSN 0261-4189
PubMed: 9218783
DOI: 10.1093/EMBOJ/16.12.3405
Page generated: Tue Aug 13 19:55:02 2024

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