Magnesium in PDB 7ke2: Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565, PDB code: 7ke2 was solved by J.L.Kurz, K.P.Patel, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.18 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.446, 94.063, 97.203, 90, 90, 90
R / Rfree (%) 23.6 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565 (pdb code 7ke2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565, PDB code: 7ke2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7ke2

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Magnesium binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565


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 Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:40.4
occ:1.00
 OE2 B:GLU194 2.0 40.6 1.0
O13 A:WBY402 2.1 45.2 1.0
O B:HOH510 2.1 46.2 1.0
OD2 B:ASP190 2.1 43.3 1.0
O12 A:WBY402 2.2 44.8 1.0
O B:HOH511 2.3 39.5 1.0
N03 A:WBY402 2.8 43.9 1.0
C04 A:WBY402 2.9 42.6 1.0
CD B:GLU194 3.0 41.7 1.0
CG B:ASP190 3.1 42.9 1.0
OE1 B:GLU194 3.4 41.7 1.0
OD1 B:ASP190 3.4 40.8 1.0
O B:HOH504 3.9 45.3 1.0
O B:HOH502 4.0 41.2 1.0
O A:HOH513 4.1 42.2 1.0
MG B:MG402 4.2 41.3 1.0
C02 A:WBY402 4.2 42.7 1.0
N05 A:WBY402 4.3 40.4 1.0
CG B:GLU194 4.4 39.1 1.0
NE2 B:HIS107 4.4 48.9 1.0
OG A:SER251 4.4 39.8 1.0
CB B:ASP190 4.4 42.5 1.0
CD1 B:LEU191 4.6 43.9 1.0
CE1 B:HIS107 4.6 49.3 1.0
O B:ASP190 4.6 45.3 1.0
CB A:ALA254 4.7 38.2 1.0
O01 A:WBY402 4.8 41.9 1.0
C B:ASP190 4.9 43.5 1.0
CD2 B:HIS107 4.9 49.1 1.0

Magnesium binding site 2 out of 4 in 7ke2

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Magnesium binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565


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 Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:41.3
occ:1.00
 O A:HOH513 2.0 42.2 1.0
OD1 B:ASP190 2.1 40.8 1.0
O A:HOH512 2.1 39.6 1.0
O B:HOH502 2.3 41.2 1.0
O01 A:WBY402 2.3 41.9 1.0
O13 A:WBY402 2.3 45.2 1.0
C02 A:WBY402 3.0 42.7 1.0
N03 A:WBY402 3.1 43.9 1.0
CG B:ASP190 3.2 42.9 1.0
OD2 B:ASP190 3.7 43.3 1.0
OE1 A:GLU226 4.0 49.3 1.0
OE2 B:GLU194 4.1 40.6 1.0
MG B:MG401 4.2 40.4 1.0
O A:HOH508 4.2 39.5 1.0
NZ B:LYS130 4.3 55.0 1.0
CB B:ASP190 4.3 42.5 1.0
C04 A:WBY402 4.5 42.6 1.0
C07 A:WBY402 4.5 43.1 1.0
O B:HOH510 4.6 46.2 1.0
O A:HOH506 4.7 49.0 1.0
OE1 A:GLU230 4.8 72.0 1.0
CD A:GLU226 4.9 45.7 1.0
OE2 A:GLU226 4.9 44.6 1.0
CG A:GLU230 5.0 53.7 1.0
CA B:ASP190 5.0 42.8 1.0

Magnesium binding site 3 out of 4 in 7ke2

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Magnesium binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565


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 Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:45.0
occ:1.00
 OE2 A:GLU194 2.0 41.5 1.0
O12 A:WBY401 2.1 39.3 1.0
O13 A:WBY401 2.1 42.1 1.0
O A:HOH514 2.1 44.5 1.0
O A:HOH519 2.2 45.0 1.0
OD2 A:ASP190 2.2 48.3 1.0
C04 A:WBY401 2.8 40.8 1.0
N03 A:WBY401 2.8 42.9 1.0
CD A:GLU194 3.1 43.3 1.0
CG A:ASP190 3.3 45.5 1.0
OE1 A:GLU194 3.5 41.8 1.0
OD1 A:ASP190 3.7 43.3 1.0
O A:HOH505 3.8 47.1 1.0
NE2 A:HIS107 4.1 51.4 1.0
O A:HOH507 4.1 45.4 1.0
OG B:SER251 4.1 40.5 1.0
N05 A:WBY401 4.2 37.3 1.0
MG A:MG404 4.2 47.8 1.0
C02 A:WBY401 4.2 43.0 1.0
CD2 A:HIS107 4.3 49.7 1.0
CG A:GLU194 4.4 41.3 1.0
CE1 A:HIS107 4.5 51.5 1.0
CB A:ASP190 4.6 49.6 1.0
O A:HOH518 4.7 51.2 1.0
CB B:ALA254 4.7 37.6 1.0
CD1 A:LEU191 4.8 43.9 1.0
O01 A:WBY401 4.8 43.2 1.0
CG A:HIS107 4.8 48.2 1.0
ND1 A:HIS107 4.9 50.2 1.0
O A:ASP190 4.9 45.2 1.0

Magnesium binding site 4 out of 4 in 7ke2

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Magnesium binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565


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 Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+ and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:47.8
occ:1.00
 OD1 A:ASP190 2.0 43.3 1.0
O B:HOH501 2.1 48.0 1.0
O A:HOH518 2.1 51.2 1.0
O13 A:WBY401 2.2 42.1 1.0
O01 A:WBY401 2.3 43.2 1.0
O A:HOH507 2.3 45.4 1.0
C02 A:WBY401 3.0 43.0 1.0
N03 A:WBY401 3.0 42.9 1.0
CG A:ASP190 3.1 45.5 1.0
OD2 A:ASP190 3.6 48.3 1.0
O A:HOH502 3.7 51.2 1.0
OE2 B:GLU226 3.9 50.9 1.0
OE2 B:GLU230 4.2 60.8 1.0
MG A:MG403 4.2 45.0 1.0
NZ A:LYS130 4.2 54.1 1.0
CB A:ASP190 4.3 49.6 1.0
OE2 A:GLU194 4.3 41.5 1.0
C04 A:WBY401 4.4 40.8 1.0
O A:HOH510 4.5 44.0 1.0
C07 A:WBY401 4.5 44.2 1.0
OE1 B:GLU226 4.6 60.6 1.0
CD B:GLU226 4.7 53.8 1.0
O A:HOH514 4.7 44.5 1.0
CE A:LYS130 4.8 54.0 1.0
O B:HOH516 4.9 50.9 1.0
O12 A:WBY401 5.0 39.3 1.0
CA A:ASP190 5.0 47.9 1.0

Reference:

X.Lin, J.L.Kurz, K.M.Patel, S.J.Wun, W.M.Hussein, T.Lonhienne, N.P.West, R.P.Mcgeary, G.Schenk, L.W.Guddat. Discovery of A Pyrimidinedione Derivative with Potent Inhibitory Activity Against Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase. Chemistry V. 27 3130 2021.
ISSN: ISSN 0947-6539
PubMed: 33215746
DOI: 10.1002/CHEM.202004665
Page generated: Wed Oct 2 22:14:02 2024

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