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Magnesium in PDB 5wkc: Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam

Enzymatic activity of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam

All present enzymatic activity of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam:
2.2.1.6;

Protein crystallography data

The structure of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam, PDB code: 5wkc was solved by W.L.Guddat, G.T.Lonhienne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.79 / 2.33
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 218.213, 218.213, 361.940, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18

Other elements in 5wkc:

The structure of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam also contains other interesting chemical elements:

Fluorine (F) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam (pdb code 5wkc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam, PDB code: 5wkc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5wkc

Go back to Magnesium Binding Sites List in 5wkc
Magnesium binding site 1 out of 4 in the Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:23.7
occ:1.00
 OD1 A:ASP550 2.1 21.4 1.0
OD1 A:ASN577 2.1 28.8 1.0
OAK A:AUJ705 2.1 20.4 1.0
O A:HOH845 2.2 25.4 1.0
O A:GLU579 2.2 24.8 1.0
OAI A:AUJ705 2.3 19.7 1.0
CG A:ASN577 3.1 29.1 1.0
CG A:ASP550 3.2 26.8 1.0
PBE A:AUJ705 3.2 25.0 1.0
PBD A:AUJ705 3.3 28.6 1.0
C A:GLU579 3.4 28.0 1.0
ND2 A:ASN577 3.4 20.8 1.0
OAT A:AUJ705 3.4 25.9 1.0
OAF A:AUJ705 3.7 26.8 1.0
OD2 A:ASP550 3.7 25.2 1.0
N A:GLY581 3.9 26.6 1.0
N A:ASP550 3.9 23.1 1.0
OAS A:AUJ705 4.0 26.8 1.0
N A:GLU579 4.0 28.6 1.0
OAG A:AUJ705 4.1 21.4 1.0
CA A:GLU579 4.3 30.3 1.0
N A:ALA551 4.3 21.9 1.0
CG A:GLU579 4.3 26.7 1.0
N A:GLN580 4.3 26.4 1.0
N A:ASN577 4.4 29.9 1.0
O A:LEU575 4.4 25.5 1.0
CB A:ASP550 4.4 19.8 1.0
CB A:ASN577 4.4 27.1 1.0
CA A:GLN580 4.4 23.3 1.0
OAJ A:AUJ705 4.5 23.3 1.0
CA A:ASP550 4.6 22.0 1.0
CA A:GLY581 4.7 26.6 1.0
CA A:GLY549 4.7 24.6 1.0
C A:GLN580 4.7 26.2 1.0
C A:GLY549 4.7 27.7 1.0
N A:GLU578 4.8 25.8 1.0
CA A:ASN577 4.8 30.1 1.0
C A:ASN577 4.8 29.1 1.0
CB A:ALA551 4.9 19.3 1.0
CB A:GLU579 4.9 19.9 1.0

Magnesium binding site 2 out of 4 in 5wkc

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Magnesium binding site 2 out of 4 in the Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:23.3
occ:1.00
 O1A B:TP9704 2.1 25.6 1.0
O B:HOH897 2.1 21.3 1.0
OD1 B:ASP550 2.1 26.7 1.0
O2B B:TP9704 2.2 20.1 1.0
OD1 B:ASN577 2.2 30.1 1.0
O B:GLU579 2.2 24.1 1.0
CG B:ASN577 3.1 25.0 1.0
PA B:TP9704 3.2 26.6 1.0
PB B:TP9704 3.2 27.8 1.0
CG B:ASP550 3.3 27.1 1.0
O3A B:TP9704 3.4 25.0 1.0
C B:GLU579 3.4 26.6 1.0
ND2 B:ASN577 3.4 24.2 1.0
O3B B:TP9704 3.7 17.9 1.0
OD2 B:ASP550 3.8 24.8 1.0
O7 B:TP9704 3.9 27.2 1.0
N B:ASP550 3.9 23.5 1.0
N B:GLY581 3.9 27.3 1.0
O2A B:TP9704 4.1 25.6 1.0
N B:GLU579 4.1 27.6 1.0
N B:ALA551 4.3 22.3 1.0
O1B B:TP9704 4.3 21.1 1.0
CA B:GLU579 4.3 27.3 1.0
N B:GLN580 4.3 26.1 1.0
CG B:GLU579 4.4 27.4 1.0
CA B:GLN580 4.4 23.2 1.0
N B:ASN577 4.4 25.9 1.0
O B:LEU575 4.4 25.4 1.0
CB B:ASP550 4.5 20.5 1.0
CB B:ASN577 4.5 23.0 1.0
CA B:GLY549 4.6 20.0 1.0
CA B:ASP550 4.6 21.0 1.0
C B:GLY549 4.7 23.7 1.0
C B:GLN580 4.7 26.5 1.0
CA B:GLY581 4.7 25.9 1.0
CB B:ALA551 4.8 20.0 1.0
N B:GLU578 4.8 22.1 1.0
CA B:ASN577 4.9 23.6 1.0
C B:ASN577 4.9 25.9 1.0
CB B:GLU579 5.0 22.3 1.0

Magnesium binding site 3 out of 4 in 5wkc

Go back to Magnesium Binding Sites List in 5wkc
Magnesium binding site 3 out of 4 in the Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:26.7
occ:1.00
 OD1 E:ASP550 2.0 25.4 1.0
O2A E:TP9704 2.1 25.5 1.0
O E:HOH831 2.1 23.3 1.0
OD1 E:ASN577 2.2 37.1 1.0
O3B E:TP9704 2.2 22.3 1.0
O E:GLU579 2.2 30.7 1.0
CG E:ASN577 3.1 36.3 1.0
PA E:TP9704 3.1 30.4 1.0
CG E:ASP550 3.2 27.8 1.0
PB E:TP9704 3.2 32.4 1.0
O3A E:TP9704 3.4 33.0 1.0
ND2 E:ASN577 3.4 26.4 1.0
C E:GLU579 3.5 32.2 1.0
OD2 E:ASP550 3.7 27.3 1.0
O1B E:TP9704 3.8 32.1 1.0
N E:ASP550 3.9 24.5 1.0
O7 E:TP9704 3.9 32.8 1.0
N E:GLY581 3.9 31.3 1.0
N E:GLU579 4.1 34.6 1.0
O1A E:TP9704 4.2 24.5 1.0
N E:ALA551 4.3 26.5 1.0
O2B E:TP9704 4.3 28.2 1.0
CA E:GLU579 4.4 35.5 1.0
O E:LEU575 4.4 31.3 1.0
CB E:ASP550 4.4 23.8 1.0
N E:GLN580 4.4 30.5 1.0
CG E:GLU579 4.4 33.6 1.0
N E:ASN577 4.4 33.8 1.0
CA E:GLN580 4.5 29.5 1.0
CB E:ASN577 4.5 33.4 1.0
CA E:ASP550 4.6 23.7 1.0
CA E:GLY549 4.6 29.6 1.0
C E:GLY549 4.6 29.8 1.0
CA E:GLY581 4.7 29.5 1.0
C E:GLN580 4.8 31.8 1.0
N E:GLU578 4.8 35.3 1.0
CB E:ALA551 4.9 22.1 1.0
CA E:ASN577 4.9 35.0 1.0
C E:ASP550 5.0 27.0 1.0
C E:ASN577 5.0 35.7 1.0

Magnesium binding site 4 out of 4 in 5wkc

Go back to Magnesium Binding Sites List in 5wkc
Magnesium binding site 4 out of 4 in the Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Saccharomyces Cerevisiae Acetohydroxyacid Synthase in Complex with the Herbicide Penoxsulam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:20.1
occ:1.00
 O3B D:TP9704 2.0 22.3 1.0
O2A D:TP9704 2.1 18.8 1.0
OD1 D:ASP550 2.1 22.1 1.0
O D:HOH922 2.1 18.1 1.0
OD1 D:ASN577 2.2 32.9 1.0
O D:GLU579 2.2 19.4 1.0
CG D:ASN577 3.1 25.1 1.0
PB D:TP9704 3.2 26.4 1.0
PA D:TP9704 3.2 24.0 1.0
CG D:ASP550 3.3 26.4 1.0
ND2 D:ASN577 3.3 23.8 1.0
O3A D:TP9704 3.4 24.6 1.0
C D:GLU579 3.4 25.6 1.0
O1B D:TP9704 3.6 19.6 1.0
OD2 D:ASP550 3.8 26.3 1.0
N D:ASP550 3.8 24.3 1.0
O7 D:TP9704 3.8 25.2 1.0
O1A D:TP9704 4.0 18.8 1.0
N D:GLY581 4.0 25.1 1.0
N D:GLU579 4.1 28.6 1.0
N D:ALA551 4.3 21.1 1.0
CA D:GLU579 4.3 27.7 1.0
N D:GLN580 4.4 25.4 1.0
O2B D:TP9704 4.4 20.7 1.0
CG D:GLU579 4.4 24.2 1.0
O D:LEU575 4.4 26.4 1.0
N D:ASN577 4.4 31.0 1.0
CB D:ASP550 4.5 21.3 1.0
CA D:GLN580 4.5 23.1 1.0
CB D:ASN577 4.5 24.3 1.0
CA D:GLY549 4.6 17.7 1.0
CA D:ASP550 4.6 21.9 1.0
C D:GLY549 4.6 23.4 1.0
C D:GLN580 4.8 24.9 1.0
CA D:GLY581 4.8 19.0 1.0
N D:GLU578 4.8 27.9 1.0
CA D:ASN577 4.9 28.6 1.0
CB D:ALA551 4.9 21.1 1.0
C D:ASN577 5.0 27.6 1.0
C D:ASP550 5.0 23.6 1.0

Reference:

T.Lonhienne, M.D.Garcia, G.Pierens, M.Mobli, A.Nouwens, L.W.Guddat. Structural Insights Into the Mechanism of Inhibition of Ahas By Herbicides. Proc. Natl. Acad. Sci. V. 115 E1945 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29440497
DOI: 10.1073/PNAS.1714392115
Page generated: Mon Sep 30 06:36:04 2024

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