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Magnesium in PDB 6c5n: Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1, PDB code: 6c5n was solved by A.Kandale, K.M.Patel, S.Zheng, L.You, L.W.Guddat, G.Schenk, M.A.Schembri, R.P.Mcgeary, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.61 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.480, 80.394, 67.304, 90.00, 90.13, 90.00
R / Rfree (%) 15.5 / 19.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1 (pdb code 6c5n). 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 with Hydroxyoxamate Inhibitor 1, PDB code: 6c5n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6c5n

Go back to Magnesium Binding Sites List in 6c5n
Magnesium binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1


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 with Hydroxyoxamate Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:11.8
occ:1.00
 OD1 A:ASP190 2.0 12.4 1.0
O A:HOH557 2.1 9.7 1.0
O A:HOH706 2.1 11.7 1.0
O10 A:81B405 2.1 9.8 0.6
O11 A:81B405 2.1 10.0 0.6
O01 A:EN4404 2.2 10.9 0.4
O11 A:EN4404 2.2 11.7 0.4
OE2 A:GLU194 2.2 10.1 1.0
C03 A:81B405 2.7 11.0 0.6
C03 A:EN4404 2.8 11.4 0.4
C02 A:81B405 2.8 11.3 0.6
C02 A:EN4404 2.8 11.2 0.4
CG A:ASP190 3.0 11.4 1.0
CD A:GLU194 3.1 11.0 1.0
OE1 A:GLU194 3.4 10.4 1.0
OD2 A:ASP190 3.4 12.4 1.0
MG A:MG403 3.7 12.3 1.0
O B:HOH597 3.9 15.1 1.0
O01 A:81B405 4.0 11.1 0.6
N04 A:81B405 4.0 14.7 0.6
O12 A:EN4404 4.0 11.1 0.4
N04 A:EN4404 4.1 12.3 0.4
O A:HOH590 4.2 11.4 1.0
OG B:SER251 4.2 9.6 1.0
NE2 A:HIS107 4.2 10.3 1.0
CE1 A:HIS107 4.3 14.2 1.0
CB A:ASP190 4.4 8.6 1.0
O2D A:NDP401 4.5 10.0 1.0
O A:HOH595 4.5 13.4 1.0
CD2 A:HIS107 4.5 10.0 1.0
O A:ASP190 4.5 10.8 1.0
CG A:GLU194 4.5 9.5 1.0
ND1 A:HIS107 4.6 11.8 1.0
O05 A:EN4404 4.6 12.3 0.4
CB B:ALA254 4.6 9.0 1.0
CG A:HIS107 4.7 14.0 1.0
C A:ASP190 4.7 11.7 1.0
CB A:GLU194 4.9 8.4 1.0

Magnesium binding site 2 out of 4 in 6c5n

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Magnesium binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1


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 with Hydroxyoxamate Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:12.3
occ:1.00
 OD2 A:ASP190 1.9 12.4 1.0
O10 A:81B405 2.0 9.8 0.6
O A:HOH595 2.1 13.4 1.0
O11 A:EN4404 2.1 11.7 0.4
O B:HOH549 2.1 13.8 1.0
O05 A:EN4404 2.1 12.3 0.4
O B:HOH597 2.2 15.1 1.0
O A:HOH501 2.3 16.7 0.4
C03 A:81B405 2.8 11.0 0.6
C03 A:EN4404 2.8 11.4 0.4
N04 A:EN4404 2.9 12.3 0.4
N04 A:81B405 2.9 14.7 0.6
CG A:ASP190 3.0 11.4 1.0
OD1 A:ASP190 3.4 12.4 1.0
MG A:MG402 3.7 11.8 1.0
NZ A:LYS130 4.0 12.9 1.0
OE1 B:GLU230 4.0 13.3 0.8
OE2 B:GLU230 4.1 14.8 1.0
OE2 A:GLU194 4.1 10.1 1.0
OE1 B:GLU226 4.1 14.9 0.9
O A:HOH590 4.1 11.4 1.0
OE2 B:GLU226 4.1 10.8 0.8
CB A:ASP190 4.2 8.6 1.0
C02 A:81B405 4.2 11.3 0.6
C02 A:EN4404 4.3 11.2 0.4
C06 A:EN4404 4.3 14.3 0.4
C05 A:81B405 4.3 14.5 0.6
O A:HOH706 4.4 11.7 1.0
O A:PRO129 4.5 11.6 1.0
CD B:GLU230 4.5 11.0 0.6
CE A:LYS130 4.5 13.5 1.0
C5N A:NDP401 4.6 13.3 1.0
C4N A:NDP401 4.6 9.9 1.0
CD B:GLU226 4.6 8.2 0.6
CA A:ASP190 4.7 9.7 1.0
O A:ASP190 4.7 10.8 1.0
O11 A:81B405 4.7 10.0 0.6
C09 A:81B405 4.7 13.7 0.6
O01 A:EN4404 4.8 10.9 0.4
C07 A:EN4404 4.8 13.8 0.4
CA A:LYS130 4.9 11.3 1.0
C06 A:81B405 5.0 13.4 0.6
CD A:LYS130 5.0 12.7 1.0

Magnesium binding site 3 out of 4 in 6c5n

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Magnesium binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1


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 with Hydroxyoxamate Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:13.2
occ:1.00
 OD1 B:ASP190 2.0 15.0 1.0
O10 B:81B402 2.1 12.8 0.6
O05 B:EN4401 2.1 17.4 0.4
O11 B:EN4401 2.1 12.7 0.4
O B:HOH519 2.1 14.0 1.0
O A:HOH527 2.2 14.1 1.0
O B:HOH575 2.2 13.8 1.0
O B:HOH501 2.3 17.5 0.6
C03 B:81B402 2.9 12.8 0.6
C03 B:EN4401 2.9 12.8 0.4
N04 B:EN4401 2.9 16.3 0.4
N04 B:81B402 3.0 16.4 0.6
CG B:ASP190 3.0 12.9 1.0
OD2 B:ASP190 3.5 11.5 1.0
MG B:MG405 3.7 11.2 1.0
OE2 A:GLU230 4.0 17.0 1.0
NZ B:LYS130 4.0 14.6 1.0
OE1 A:GLU230 4.1 16.4 0.9
OE2 B:GLU194 4.1 11.4 1.0
OE1 A:GLU226 4.1 15.2 0.8
O B:HOH602 4.2 11.9 1.0
OE2 A:GLU226 4.2 16.0 1.0
CB B:ASP190 4.3 12.1 1.0
C02 B:81B402 4.3 14.4 0.6
C02 B:EN4401 4.3 14.3 0.4
C05 B:81B402 4.4 14.3 0.6
C06 B:EN4401 4.4 14.3 0.4
O B:HOH697 4.4 11.7 1.0
O B:PRO129 4.4 13.2 1.0
CD A:GLU230 4.5 11.7 0.8
CE B:LYS130 4.5 13.7 1.0
C4N B:NDP403 4.6 15.2 1.0
C5N B:NDP403 4.6 13.1 1.0
CD A:GLU226 4.6 10.6 0.6
O01 B:81B402 4.6 10.5 0.6
CA B:ASP190 4.7 11.0 1.0
C09 B:81B402 4.7 18.8 0.6
O B:ASP190 4.7 11.0 1.0
O12 B:EN4401 4.8 11.3 0.4
CA B:LYS130 4.9 11.2 1.0
C07 B:EN4401 4.9 18.7 0.4

Magnesium binding site 4 out of 4 in 6c5n

Go back to Magnesium Binding Sites List in 6c5n
Magnesium binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase with Hydroxyoxamate Inhibitor 1


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 with Hydroxyoxamate Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:11.2
occ:1.00
 O01 B:81B402 2.0 10.5 0.6
OD2 B:ASP190 2.0 11.5 1.0
O B:HOH571 2.1 10.6 1.0
O11 B:EN4401 2.1 12.7 0.4
O B:HOH697 2.1 11.7 1.0
O10 B:81B402 2.1 12.8 0.6
O12 B:EN4401 2.2 11.3 0.4
OE2 B:GLU194 2.2 11.4 1.0
C03 B:EN4401 2.7 12.8 0.4
C03 B:81B402 2.8 12.8 0.6
C02 B:81B402 2.8 14.4 0.6
C02 B:EN4401 2.8 14.3 0.4
CG B:ASP190 3.1 12.9 1.0
CD B:GLU194 3.1 11.5 1.0
OE1 B:GLU194 3.4 10.9 1.0
OD1 B:ASP190 3.4 15.0 1.0
MG B:MG404 3.7 13.2 1.0
O B:HOH519 3.9 14.0 1.0
N04 B:EN4401 4.0 16.3 0.4
O11 B:81B402 4.0 13.3 0.6
O01 B:EN4401 4.1 13.2 0.4
N04 B:81B402 4.1 16.4 0.6
O B:HOH602 4.2 11.9 1.0
OG A:SER251 4.2 13.7 1.0
NE2 B:HIS107 4.3 12.2 1.0
CE1 B:HIS107 4.3 12.3 1.0
CB B:ASP190 4.4 12.1 1.0
O2D B:NDP403 4.5 11.6 1.0
O B:HOH575 4.5 13.8 1.0
CD2 B:HIS107 4.5 12.4 1.0
O05 B:EN4401 4.5 17.4 0.4
CG B:GLU194 4.5 10.7 1.0
ND1 B:HIS107 4.5 12.3 1.0
O B:ASP190 4.6 11.0 1.0
CG B:HIS107 4.6 10.8 1.0
CB A:ALA254 4.7 9.2 1.0
C B:ASP190 4.8 10.1 1.0
CB B:GLU194 5.0 10.2 1.0
C4N B:NDP403 5.0 15.2 1.0

Reference:

A.Kandale, K.M.Patel, S.Zheng, L.You, L.W.Guddat, G.Schenk, M.A.Schembri, R.P.Mcgeary. Design, Synthesis, in Vitro Activity and Crystallisation of Novel N-Isopropyl-N-Hydroxyoxamate Derivatives As Ketol-Acid Reductosiomerase (Kari) Inhibitor To Be Published.
Page generated: Mon Sep 30 20:09:39 2024

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