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Magnesium in PDB 6vo2: Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor.

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor.

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor.:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor., PDB code: 6vo2 was solved by T.Bayaraa, K.M.Patel, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.16 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.039, 80.825, 66.803, 90.00, 92.61, 90.00
R / Rfree (%) 16.3 / 20

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor. (pdb code 6vo2). 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 Mg, Nadph and Inhibitor., PDB code: 6vo2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6vo2

Go back to Magnesium Binding Sites List in 6vo2
Magnesium binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor.


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 Mg, Nadph and Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:14.9
occ:1.00
 O07 B:R67403 2.1 14.0 1.0
OD2 A:ASP190 2.1 14.0 1.0
O A:HOH568 2.1 14.0 1.0
O A:HOH673 2.1 13.4 1.0
OE2 A:GLU194 2.2 13.1 1.0
O09 B:R67403 2.2 15.2 1.0
C05 B:R67403 2.8 16.9 1.0
C06 B:R67403 2.8 13.3 1.0
CG A:ASP190 3.1 13.2 1.0
CD A:GLU194 3.1 13.3 1.0
OE1 A:GLU194 3.4 13.8 1.0
OD1 A:ASP190 3.5 14.5 1.0
MG A:MG402 3.7 15.4 1.0
O A:HOH657 3.8 14.7 1.0
O08 B:R67403 4.1 13.5 1.0
C04 B:R67403 4.3 14.9 1.0
O A:HOH618 4.3 12.3 1.0
NE2 A:HIS107 4.4 15.5 1.0
OG B:SER251 4.4 13.6 1.0
CB A:ASP190 4.4 13.0 1.0
CE1 A:HIS107 4.4 15.2 1.0
O2D A:NDP404 4.4 13.4 1.0
O A:HOH589 4.5 15.2 1.0
O A:ASP190 4.5 12.0 1.0
CG A:GLU194 4.5 12.9 1.0
CB B:ALA254 4.5 11.9 1.0
CD2 A:HIS107 4.6 14.1 1.0
ND1 A:HIS107 4.7 14.0 1.0
C A:ASP190 4.7 13.4 1.0
CG A:HIS107 4.8 13.7 1.0
CB A:GLU194 4.9 11.2 1.0
C4N A:NDP404 5.0 16.7 1.0

Magnesium binding site 2 out of 4 in 6vo2

Go back to Magnesium Binding Sites List in 6vo2
Magnesium binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor.


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 Mg, Nadph and Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:15.4
occ:1.00
 OD1 A:ASP190 2.0 14.5 1.0
O B:HOH542 2.0 13.7 1.0
O09 B:R67403 2.0 15.2 1.0
O A:HOH657 2.1 14.7 1.0
O10 B:R67403 2.1 17.9 1.0
O A:HOH589 2.1 15.2 1.0
CG A:ASP190 3.0 13.2 1.0
C05 B:R67403 3.0 16.9 1.0
S02 B:R67403 3.2 17.3 1.0
OD2 A:ASP190 3.4 14.0 1.0
C04 B:R67403 3.6 14.9 1.0
MG A:MG401 3.7 14.9 1.0
C01 B:R67403 4.0 16.4 1.0
OE1 B:GLU226 4.1 14.8 1.0
OE2 B:GLU226 4.1 16.8 1.0
OE2 A:GLU194 4.1 13.1 1.0
NZ A:LYS130 4.1 13.2 1.0
O A:HOH618 4.1 12.3 1.0
OE2 B:GLU230 4.1 18.1 1.0
CB A:ASP190 4.2 13.0 1.0
OE1 B:GLU230 4.2 19.4 1.0
O A:HOH673 4.3 13.4 1.0
C06 B:R67403 4.4 13.3 1.0
O03 B:R67403 4.4 18.2 1.0
CD B:GLU230 4.4 20.3 1.0
O A:PRO129 4.5 16.1 1.0
CE A:LYS130 4.5 12.1 1.0
CD B:GLU226 4.6 17.4 1.0
O A:ASP190 4.6 12.0 1.0
C4N A:NDP404 4.6 16.7 1.0
CA A:ASP190 4.6 16.3 1.0
C5N A:NDP404 4.6 18.1 1.0
O07 B:R67403 4.7 14.0 1.0
N A:GLY131 4.9 12.8 1.0
CA A:LYS130 5.0 15.0 1.0
C A:ASP190 5.0 13.4 1.0

Magnesium binding site 3 out of 4 in 6vo2

Go back to Magnesium Binding Sites List in 6vo2
Magnesium binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor.


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 Mg, Nadph and Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:14.2
occ:1.00
 OD1 B:ASP190 2.0 13.2 1.0
O09 A:R67403 2.0 16.6 1.0
O10 A:R67403 2.1 16.3 1.0
O A:HOH539 2.1 12.1 1.0
O A:HOH664 2.1 13.2 1.0
O B:HOH587 2.1 14.9 1.0
CG B:ASP190 3.0 11.6 1.0
C05 A:R67403 3.0 17.6 1.0
S02 A:R67403 3.2 16.8 1.0
OD2 B:ASP190 3.4 13.5 1.0
MG B:MG402 3.6 13.8 1.0
C04 A:R67403 3.6 16.0 1.0
C01 A:R67403 4.0 15.3 1.0
OE2 B:GLU194 4.1 12.7 1.0
OE1 A:GLU230 4.1 14.9 1.0
NZ B:LYS130 4.1 12.2 1.0
OE2 A:GLU226 4.2 14.2 1.0
OE1 A:GLU226 4.2 13.3 1.0
O B:HOH563 4.2 14.3 1.0
CB B:ASP190 4.2 12.2 1.0
OE2 A:GLU230 4.2 14.9 0.8
O B:HOH628 4.2 13.0 1.0
C06 A:R67403 4.4 13.2 1.0
CD A:GLU230 4.4 18.7 1.0
O03 A:R67403 4.4 18.0 1.0
CE B:LYS130 4.5 12.0 1.0
O B:PRO129 4.6 14.7 1.0
CA B:ASP190 4.6 11.1 1.0
O B:ASP190 4.6 12.4 1.0
C4N B:NDP404 4.6 13.9 1.0
CD A:GLU226 4.6 12.8 1.0
C5N B:NDP404 4.6 16.8 1.0
O08 A:R67403 4.8 12.6 1.0
N B:GLY131 4.9 13.8 1.0
C B:ASP190 4.9 12.1 1.0
CA B:LYS130 5.0 12.3 1.0

Magnesium binding site 4 out of 4 in 6vo2

Go back to Magnesium Binding Sites List in 6vo2
Magnesium binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Mg, Nadph and Inhibitor.


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 Mg, Nadph and Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:13.8
occ:1.00
 OD2 B:ASP190 2.0 13.5 1.0
O B:HOH628 2.1 13.0 1.0
O B:HOH551 2.1 12.4 1.0
O08 A:R67403 2.1 12.6 1.0
O09 A:R67403 2.2 16.6 1.0
OE2 B:GLU194 2.2 12.7 1.0
C05 A:R67403 2.8 17.6 1.0
C06 A:R67403 2.8 13.2 1.0
CG B:ASP190 3.0 11.6 1.0
CD B:GLU194 3.1 13.0 1.0
OE1 B:GLU194 3.4 13.0 1.0
OD1 B:ASP190 3.4 13.2 1.0
MG B:MG401 3.6 14.2 1.0
O A:HOH664 3.9 13.2 1.0
O07 A:R67403 4.0 13.8 1.0
C04 A:R67403 4.2 16.0 1.0
O B:HOH563 4.3 14.3 1.0
CB B:ASP190 4.4 12.2 1.0
OG A:SER251 4.4 12.2 1.0
NE2 B:HIS107 4.4 14.6 1.0
O2D B:NDP404 4.4 13.2 1.0
CE1 B:HIS107 4.4 13.5 1.0
O B:HOH587 4.5 14.9 1.0
O B:ASP190 4.5 12.4 1.0
CG B:GLU194 4.5 12.3 1.0
CB A:ALA254 4.5 10.9 1.0
CD2 B:HIS107 4.6 13.0 1.0
ND1 B:HIS107 4.6 13.7 1.0
C B:ASP190 4.7 12.1 1.0
CG B:HIS107 4.8 15.5 1.0
C4N B:NDP404 4.9 13.9 1.0
O10 A:R67403 4.9 16.3 1.0
CB B:GLU194 5.0 10.1 1.0

Reference:

T.Bayaraa, J.L.Kurz, K.M.Patel, W.M.Hussein, J.K.Bilyj, N.P.West, G.Schenk, R.P.Mcgeary, L.W.Guddat. Discovery, Synthesis and Evaluation of A Novel Ketol-Acid Reductoisomerase Inhibitor. Chemistry 2020.
ISSN: ISSN 0947-6539
PubMed: 32198779
DOI: 10.1002/CHEM.202000899
Page generated: Tue Oct 1 22:11:26 2024

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