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Magnesium in PDB 7kh7: Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, and NSC116565

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

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

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, and NSC116565, PDB code: 7kh7 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) 48.84 / 2.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.922, 92.085, 101.645, 90, 90, 90
R / Rfree (%) 24.6 / 30.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, and NSC116565 (pdb code 7kh7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, and NSC116565, PDB code: 7kh7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7kh7

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Magnesium binding site 1 out of 5 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, 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+, Nadph, and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:45.8
occ:1.00
 O A:HOH613 2.0 46.8 1.0
OD1 A:ASP190 2.1 50.6 1.0
O B:HOH503 2.2 50.8 1.0
O13 B:WBY401 2.2 54.5 1.0
O01 B:WBY401 2.3 56.3 1.0
O A:HOH602 2.4 45.5 1.0
C02 B:WBY401 3.0 61.0 1.0
N03 B:WBY401 3.0 54.4 1.0
CG A:ASP190 3.2 50.8 1.0
NZ A:LYS130 3.8 46.5 1.0
OD2 A:ASP190 3.8 49.6 1.0
MG A:MG504 4.0 46.4 1.0
OE2 A:GLU194 4.0 51.0 1.0
OE1 B:GLU230 4.1 56.5 1.0
O A:PRO129 4.1 64.4 1.0
CE A:LYS130 4.1 54.0 1.0
OE2 B:GLU230 4.1 58.5 1.0
C5N A:NAP501 4.2 58.0 0.7
CB A:ASP190 4.3 47.8 1.0
OE1 B:GLU226 4.4 49.4 1.0
OE2 B:GLU226 4.4 55.3 1.0
C04 B:WBY401 4.4 51.5 1.0
C5N A:NDP502 4.4 58.1 0.3
C07 B:WBY401 4.5 63.0 1.0
CD A:LYS130 4.5 58.2 1.0
CD B:GLU230 4.5 58.0 1.0
CA A:LYS130 4.6 59.2 1.0
C4N A:NDP502 4.7 57.6 0.3
C4N A:NAP501 4.8 57.7 0.7
CD B:GLU226 4.8 53.9 1.0
O A:HOH607 4.9 53.1 1.0
C6N A:NDP502 4.9 57.3 0.3
CA A:ASP190 4.9 43.5 1.0
C6N A:NAP501 4.9 57.3 0.7
N A:GLY131 4.9 60.4 1.0
O12 B:WBY401 4.9 63.5 1.0

Magnesium binding site 2 out of 5 in 7kh7

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Magnesium binding site 2 out of 5 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, 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+, Nadph, and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:46.4
occ:1.00
 OE2 A:GLU194 1.9 51.0 1.0
O A:HOH607 2.0 53.1 1.0
O13 B:WBY401 2.1 54.5 1.0
OD2 A:ASP190 2.1 49.6 1.0
O12 B:WBY401 2.2 63.5 1.0
O A:HOH612 2.2 44.5 1.0
N03 B:WBY401 2.8 54.4 1.0
C04 B:WBY401 2.8 51.5 1.0
CD A:GLU194 3.0 49.5 1.0
CG A:ASP190 3.0 50.8 1.0
OD1 A:ASP190 3.3 50.6 1.0
OE1 A:GLU194 3.5 37.6 1.0
MG A:MG503 4.0 45.8 1.0
CD2 A:HIS107 4.1 49.9 1.0
NE2 A:HIS107 4.1 58.5 1.0
C02 B:WBY401 4.1 61.0 1.0
O2D A:NAP501 4.2 58.3 0.7
N05 B:WBY401 4.2 46.5 1.0
CG A:HIS107 4.3 51.1 1.0
CG A:GLU194 4.3 32.9 1.0
CE1 A:HIS107 4.3 52.2 1.0
ND1 A:HIS107 4.4 55.1 1.0
O A:HOH602 4.4 45.5 1.0
OG B:SER251 4.4 43.1 1.0
O2D A:NDP502 4.4 58.0 0.3
CB A:ASP190 4.4 47.8 1.0
C6N A:NAP501 4.6 57.3 0.7
C6N A:NDP502 4.6 57.3 0.3
O A:HOH613 4.6 46.8 1.0
O01 B:WBY401 4.7 56.3 1.0
N1N A:NDP502 4.8 59.0 0.3
N1N A:NAP501 4.8 59.0 0.7
C5N A:NAP501 4.8 58.0 0.7
CB A:HIS107 4.9 46.8 1.0

Magnesium binding site 3 out of 5 in 7kh7

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Magnesium binding site 3 out of 5 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, 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+, Nadph, and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:85.2
occ:1.00
 OE1 A:GLU98 2.1 96.8 1.0
O A:ALA73 2.4 90.2 1.0
ND2 A:ASN101 2.6 92.7 1.0
OD1 A:ASN101 3.1 84.6 1.0
CG A:ASN101 3.1 88.6 1.0
CD A:GLU98 3.2 91.2 1.0
C A:ALA73 3.4 88.2 1.0
CA A:ASP74 3.6 82.9 1.0
OE2 A:GLU98 3.8 90.1 1.0
N A:ASP74 3.9 85.2 1.0
O A:LYS71 3.9 89.6 1.0
O A:VAL70 4.0 92.7 1.0
OD2 A:ASP74 4.0 85.2 1.0
O A:GLN72 4.1 98.5 1.0
CG A:GLU98 4.3 88.9 1.0
CB A:GLU98 4.4 89.4 1.0
C A:ASP74 4.5 77.2 1.0
CB A:ASN101 4.5 87.7 1.0
CB A:ASP74 4.5 83.2 1.0
O A:ASP74 4.5 77.1 1.0
C A:GLN72 4.5 94.1 1.0
CG A:ASP74 4.6 87.8 1.0
CA A:ALA73 4.6 91.7 1.0
C A:LYS71 4.7 92.5 1.0
N A:ALA73 4.7 92.0 1.0
N A:GLU98 4.8 87.7 1.0

Magnesium binding site 4 out of 5 in 7kh7

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Magnesium binding site 4 out of 5 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, 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+, Nadph, and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:52.8
occ:1.00
 O B:HOH517 1.9 44.6 1.0
O B:HOH516 2.1 37.2 1.0
O01 B:WBY402 2.1 40.3 1.0
O B:HOH511 2.2 37.5 1.0
O13 B:WBY402 2.2 44.7 1.0
OD1 B:ASP190 2.2 43.9 1.0
C02 B:WBY402 2.8 43.7 1.0
N03 B:WBY402 2.9 44.5 1.0
CG B:ASP190 3.3 42.6 1.0
O B:HOH510 3.5 46.4 1.0
NZ B:LYS130 3.8 31.1 1.0
OD2 B:ASP190 3.9 51.0 1.0
OE1 A:GLU226 4.1 46.3 1.0
OE2 B:GLU194 4.2 43.2 1.0
MG B:MG404 4.2 45.2 1.0
C07 B:WBY402 4.3 38.5 1.0
C04 B:WBY402 4.3 39.6 1.0
OE2 A:GLU226 4.5 41.1 1.0
CB B:ASP190 4.5 42.9 1.0
O B:HOH505 4.5 43.4 1.0
OE1 A:GLU230 4.6 67.0 1.0
O B:HOH508 4.7 33.5 1.0
CD A:GLU226 4.7 42.9 1.0
CD B:LYS130 4.8 46.4 1.0
O12 B:WBY402 4.8 43.7 1.0
CE B:LYS130 4.9 37.1 1.0

Magnesium binding site 5 out of 5 in 7kh7

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Magnesium binding site 5 out of 5 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, and NSC116565


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with MG2+, Nadph, and NSC116565 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:45.2
occ:1.00
 OE2 B:GLU194 1.8 43.2 1.0
OD2 B:ASP190 1.9 51.0 1.0
O B:HOH508 2.0 33.5 1.0
O12 B:WBY402 2.0 43.7 1.0
O13 B:WBY402 2.2 44.7 1.0
O B:HOH524 2.2 46.4 1.0
C04 B:WBY402 2.8 39.6 1.0
CD B:GLU194 2.8 41.2 1.0
N03 B:WBY402 2.8 44.5 1.0
CG B:ASP190 3.0 42.6 1.0
OE1 B:GLU194 3.2 44.1 1.0
OD1 B:ASP190 3.4 43.9 1.0
N05 B:WBY402 4.1 42.3 1.0
CG B:GLU194 4.2 37.2 1.0
O B:HOH501 4.2 49.4 1.0
NE2 B:HIS107 4.2 57.0 1.0
MG B:MG403 4.2 52.8 1.0
CB B:ASP190 4.2 42.9 1.0
C02 B:WBY402 4.3 43.7 1.0
O B:HOH511 4.3 37.5 1.0
CE1 B:HIS107 4.3 52.8 1.0
OG A:SER251 4.4 45.8 1.0
O B:HOH516 4.7 37.2 1.0
CD2 B:HIS107 4.7 50.3 1.0
O B:ASP190 4.8 38.8 1.0
O01 B:WBY402 4.8 40.3 1.0
ND1 B:HIS107 4.8 49.2 1.0
C B:ASP190 4.9 43.4 1.0
CB A:ALA254 4.9 41.7 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 22:16:21 2024

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