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Magnesium in PDB 6c55: Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3, PDB code: 6c55 was solved by A.Kandale, K.M.Patel, S.Zheng, L.You, L.W.Guddat, G.Schenk, M.Schmbri, R.P.Mcgeary, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.52 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.724, 79.032, 69.640, 90.00, 101.39, 90.00
R / Rfree (%) 16.3 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3 (pdb code 6c55). 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 Reductosimerrase with Hydroxyoxamate Inhibitor 3, PDB code: 6c55:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6c55

Go back to Magnesium Binding Sites List in 6c55
Magnesium binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3


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 Reductosimerrase with Hydroxyoxamate Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:22.2
occ:1.00
 O13 A:EKA407 2.0 25.1 0.5
O12 A:EKD404 2.0 25.3 0.4
O A:HOH544 2.1 20.6 1.0
O A:HOH602 2.1 20.2 1.0
OD2 A:ASP190 2.1 22.3 1.0
OE2 A:GLU194 2.2 24.5 1.0
O11 A:EKD404 2.3 28.2 0.4
O12 A:EKA407 2.4 28.2 0.5
C02 A:EKA407 2.7 27.9 0.5
C02 A:EKD404 2.7 27.9 0.4
C03 A:EKD404 2.8 28.9 0.4
C03 A:EKA407 2.8 28.9 0.5
CG A:ASP190 3.1 26.4 1.0
CD A:GLU194 3.1 25.7 1.0
OE1 A:GLU194 3.3 23.5 1.0
OD1 A:ASP190 3.4 25.9 1.0
MG A:MG402 3.7 33.1 1.0
O01 A:EKA407 3.8 28.3 0.5
O01 A:EKD404 3.8 28.4 0.4
O A:HOH617 3.9 32.9 1.0
N04 A:EKD404 4.2 32.7 0.4
N04 A:EKA407 4.2 32.7 0.5
O A:HOH549 4.2 24.8 1.0
OG B:SER251 4.2 26.3 1.0
NE2 A:HIS107 4.3 23.1 1.0
O2D A:NAP403 4.4 22.9 0.7
O2D A:NAP403 4.4 23.0 0.3
CB A:ASP190 4.5 24.3 1.0
CE1 A:HIS107 4.5 24.5 1.0
O A:HOH518 4.5 25.3 1.0
CD2 A:HIS107 4.5 24.8 1.0
CG A:GLU194 4.5 24.4 1.0
O A:ASP190 4.6 21.3 1.0
CB B:ALA254 4.6 21.0 1.0
ND1 A:HIS107 4.8 24.2 1.0
CG A:HIS107 4.8 25.2 1.0
C A:ASP190 4.9 23.1 1.0
C6N A:NAP403 4.9 25.1 0.3
O05 A:EKA407 4.9 35.9 0.5
C6N A:NAP403 5.0 25.1 0.7
C5N A:NAP403 5.0 26.6 0.3

Magnesium binding site 2 out of 4 in 6c55

Go back to Magnesium Binding Sites List in 6c55
Magnesium binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3


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 Reductosimerrase with Hydroxyoxamate Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:33.1
occ:1.00
 O A:HOH503 1.9 35.4 0.5
O12 A:EKA407 2.0 28.2 0.5
O11 A:EKD404 2.0 28.2 0.4
OD1 A:ASP190 2.0 25.9 1.0
O A:HOH510 2.0 36.6 1.0
O A:HOH617 2.1 32.9 1.0
O A:HOH518 2.2 25.3 1.0
O05 A:EKA407 2.5 35.9 0.5
C03 A:EKA407 2.9 28.9 0.5
C03 A:EKD404 2.9 28.9 0.4
CG A:ASP190 3.0 26.4 1.0
N04 A:EKD404 3.1 32.7 0.4
N04 A:EKA407 3.1 32.7 0.5
OD2 A:ASP190 3.5 22.3 1.0
OE2 B:GLU230 3.7 34.8 0.5
MG A:MG401 3.7 22.2 1.0
NZ A:LYS130 3.9 33.5 1.0
OE1 B:GLU226 4.0 37.6 0.6
O A:HOH549 4.1 24.8 1.0
OE2 A:GLU194 4.1 24.5 1.0
OE1 B:GLU230 4.2 36.8 0.6
CB A:ASP190 4.2 24.3 1.0
C02 A:EKD404 4.3 27.9 0.4
C02 A:EKA407 4.3 27.9 0.5
O A:HOH602 4.3 20.2 1.0
CD B:GLU230 4.3 34.4 0.5
OE2 B:GLU226 4.4 36.1 0.5
C5N A:NAP403 4.5 26.6 0.3
C05 A:EKD404 4.5 32.5 0.4
C5N A:NAP403 4.5 26.8 0.7
O A:PRO129 4.5 26.1 1.0
C06 A:EKA407 4.6 32.6 0.5
CE A:LYS130 4.6 31.1 1.0
CA A:ASP190 4.6 23.1 1.0
O A:ASP190 4.6 21.3 1.0
CD B:GLU226 4.6 33.4 0.4
C4N A:NAP403 4.7 27.3 0.3
C4N A:NAP403 4.7 27.3 0.7
O12 A:EKD404 4.7 25.3 0.4
O13 A:EKA407 4.7 25.1 0.5
CD A:LYS130 4.9 32.2 1.0
CA A:LYS130 5.0 28.1 1.0

Magnesium binding site 3 out of 4 in 6c55

Go back to Magnesium Binding Sites List in 6c55
Magnesium binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3


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 Reductosimerrase with Hydroxyoxamate Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:42.2
occ:1.00
 O A:HOH502 1.9 43.6 1.0
OD1 B:ASP190 2.1 35.0 1.0
O11 A:EKD406 2.2 47.8 0.9
O B:HOH526 2.3 32.5 1.0
O A:HOH628 2.4 33.9 1.0
O A:HOH507 2.5 54.1 1.0
N04 A:EKD406 2.8 60.5 0.9
C03 A:EKD406 2.9 52.5 0.9
OE2 A:GLU230 2.9 48.5 0.5
CG B:ASP190 3.1 30.3 1.0
OE2 A:GLU226 3.6 37.8 0.6
OD2 B:ASP190 3.7 28.9 1.0
MG B:MG401 3.7 31.9 1.0
CD A:GLU230 3.8 46.5 0.5
NZ B:LYS130 3.9 38.1 1.0
OE1 A:GLU230 4.0 52.2 0.8
C05 A:EKD406 4.1 59.7 0.9
O B:HOH537 4.2 25.8 1.0
C06 A:EKD406 4.2 56.8 0.9
OE1 A:GLU226 4.3 35.4 0.7
O A:HOH591 4.3 29.4 1.0
OE2 B:GLU194 4.3 31.4 1.0
CB B:ASP190 4.3 25.2 1.0
C02 A:EKD406 4.3 44.4 0.9
CD A:GLU226 4.3 33.3 0.5
C10 A:EKD406 4.7 58.6 0.9
C5N B:NAP402 4.7 38.2 1.0
CE B:LYS130 4.8 37.7 1.0
CA B:ASP190 4.8 23.5 1.0
O B:PRO129 4.8 31.7 1.0
C4N B:NAP402 4.8 34.9 1.0
O B:ASP190 4.9 21.0 1.0
O01 A:EKD406 4.9 37.7 0.9

Magnesium binding site 4 out of 4 in 6c55

Go back to Magnesium Binding Sites List in 6c55
Magnesium binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductosimerrase with Hydroxyoxamate Inhibitor 3


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 Reductosimerrase with Hydroxyoxamate Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:31.9
occ:1.00
 O B:HOH522 2.0 26.7 1.0
O11 A:EKD406 2.0 47.8 0.9
O A:HOH591 2.1 29.4 1.0
OD2 B:ASP190 2.1 28.9 1.0
O01 A:EKD406 2.2 37.7 0.9
OE2 B:GLU194 2.4 31.4 1.0
C03 A:EKD406 2.6 52.5 0.9
C02 A:EKD406 2.7 44.4 0.9
CG B:ASP190 3.1 30.3 1.0
CD B:GLU194 3.3 29.1 1.0
OD1 B:ASP190 3.3 35.0 1.0
OE1 B:GLU194 3.4 28.5 1.0
MG A:MG405 3.7 42.2 1.0
O A:HOH628 3.8 33.9 1.0
N04 A:EKD406 3.9 60.5 0.9
O12 A:EKD406 3.9 40.3 0.9
O B:HOH537 4.3 25.8 1.0
OG A:SER251 4.3 25.8 1.0
NE2 B:HIS107 4.4 30.3 1.0
CB B:ASP190 4.5 25.2 1.0
O2D B:NAP402 4.5 26.8 1.0
O B:ASP190 4.5 21.0 1.0
CE1 B:HIS107 4.6 25.4 1.0
O B:HOH526 4.6 32.5 1.0
CD2 B:HIS107 4.6 26.9 1.0
CG B:GLU194 4.7 27.0 1.0
CB A:ALA254 4.7 28.9 1.0
ND1 B:HIS107 4.8 28.2 1.0
C B:ASP190 4.8 24.6 1.0
CG B:HIS107 4.9 28.6 1.0
C05 A:EKD406 5.0 59.7 0.9
C6N B:NAP402 5.0 32.9 1.0

Reference:

A.Kandale, K.M.Patel, S.Zheng, L.You, L.W.Guddat, G.Schenk, M.Schmbri, R.P.Mcgeary. Design, Synthesis, in Vitro Activity and Crystallisation of Novel N-Isopropyl-N-Hydroxyoxamate Derivatives As Ketol-Acid Reductoisomerase (Kari) Inhibitors To Be Published.
Page generated: Mon Sep 30 20:09:07 2024

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