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Magnesium in PDB 5w3k: Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd

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

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

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd, PDB code: 5w3k was solved by K.M.Patel, D.Teran, S.Zheng, A.Kandale, M.Schembri, R.P.Mcgeary, G.Schenk, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.55 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.941, 80.773, 66.748, 90.00, 92.49, 90.00
R / Rfree (%) 16 / 18.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd (pdb code 5w3k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd, PDB code: 5w3k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5w3k

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Magnesium binding site 1 out of 6 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd


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 Nadph, MG2+ and Cpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:12.8
occ:1.00
 OD1 A:ASP190 2.0 12.8 1.0
O B:HOH537 2.0 12.0 1.0
O09 B:9TY401 2.1 12.3 1.0
O01 B:9TY401 2.1 12.6 1.0
O A:HOH574 2.1 11.7 1.0
O B:HOH559 2.2 13.2 1.0
C02 B:9TY401 2.4 13.0 1.0
CG A:ASP190 2.9 13.6 1.0
OD2 A:ASP190 3.3 11.9 1.0
MG A:MG403 3.7 12.6 1.0
OE2 B:GLU230 3.8 14.4 1.0
NZ A:LYS130 3.9 14.9 1.0
C03 B:9TY401 3.9 10.2 1.0
OE1 B:GLU226 3.9 16.9 1.0
O A:HOH608 4.1 11.6 1.0
OE2 B:GLU226 4.1 15.6 1.0
OE2 A:GLU194 4.2 11.3 1.0
CB A:ASP190 4.2 12.0 1.0
OE1 B:GLU230 4.2 13.0 1.0
CE A:LYS130 4.2 15.0 1.0
O A:HOH664 4.4 12.9 1.0
CD B:GLU230 4.4 12.5 1.0
CD B:GLU226 4.5 15.0 1.0
CA A:ASP190 4.5 14.1 1.0
O A:PRO129 4.5 13.1 1.0
O A:ASP190 4.6 12.0 1.0
C5N A:NDP406 4.6 13.8 0.4
C4N A:NDP406 4.7 12.0 0.4
CA A:LYS130 4.7 12.9 1.0
C08 B:9TY401 4.8 15.1 1.0
O05 B:9TY401 4.8 11.8 1.0
C07 B:9TY401 4.8 13.2 1.0
C04 B:9TY401 4.8 11.3 1.0
CD A:LYS130 4.9 14.1 1.0
C A:ASP190 4.9 11.3 1.0
C5N A:NDP406 4.9 12.3 0.6
C4N A:NDP406 4.9 12.5 0.6
N A:GLY131 5.0 11.9 1.0

Magnesium binding site 2 out of 6 in 5w3k

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Magnesium binding site 2 out of 6 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd


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 Nadph, MG2+ and Cpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:12.6
occ:1.00
 O09 B:9TY401 2.0 12.3 1.0
O A:HOH531 2.0 12.1 1.0
O05 B:9TY401 2.1 11.8 1.0
OD2 A:ASP190 2.1 11.9 1.0
OE2 A:GLU194 2.1 11.3 1.0
O A:HOH664 2.2 12.9 1.0
C02 B:9TY401 3.0 13.0 1.0
C04 B:9TY401 3.1 11.3 1.0
CD A:GLU194 3.1 10.0 1.0
CG A:ASP190 3.2 13.6 1.0
OE1 A:GLU194 3.4 12.1 1.0
C03 B:9TY401 3.5 10.2 1.0
OD1 A:ASP190 3.6 12.8 1.0
MG A:MG402 3.7 12.8 1.0
O B:HOH559 3.9 13.2 1.0
O01 B:9TY401 4.1 12.6 1.0
O A:HOH608 4.2 11.6 1.0
OG B:SER251 4.2 12.2 1.0
O06 B:9TY401 4.3 12.7 1.0
CB A:ASP190 4.4 12.0 1.0
CG A:GLU194 4.5 10.4 1.0
O A:HOH574 4.5 11.7 1.0
O2D A:NDP406 4.5 13.0 0.6
NE2 A:HIS107 4.5 13.4 1.0
CE1 A:HIS107 4.5 15.1 1.0
O A:ASP190 4.5 12.0 1.0
C4N A:NDP406 4.6 12.0 0.4
CB B:ALA254 4.6 12.8 1.0
O2D A:NDP406 4.7 13.0 0.4
C5N A:NDP406 4.7 13.8 0.4
C08 B:9TY401 4.7 15.1 1.0
CD2 A:HIS107 4.7 12.3 1.0
ND1 A:HIS107 4.8 12.8 1.0
C A:ASP190 4.8 11.3 1.0
CB A:GLU194 4.9 11.3 1.0
CG A:HIS107 4.9 12.3 1.0
C6N A:NDP406 4.9 13.3 0.4
C4N A:NDP406 4.9 12.5 0.6

Magnesium binding site 3 out of 6 in 5w3k

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Magnesium binding site 3 out of 6 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd


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 Nadph, MG2+ and Cpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:25.8
occ:1.00
 O A:HOH543 2.1 30.0 1.0
O A:ALA73 2.3 19.7 1.0
O A:VAL70 2.3 22.9 1.0
O A:HOH654 2.4 22.7 1.0
O A:LYS71 2.5 25.1 1.0
C A:LYS71 3.2 24.2 1.0
OD1 A:ASN101 3.2 23.7 1.0
C A:ALA73 3.4 17.2 1.0
N A:ALA73 3.4 22.2 1.0
C A:VAL70 3.5 26.3 1.0
CA A:LYS71 3.7 27.3 1.0
ND2 A:ASN101 3.8 22.2 1.0
CG A:ASN101 3.8 24.6 1.0
C A:GLN72 3.9 27.2 1.0
CA A:ALA73 4.0 19.1 1.0
N A:GLN72 4.0 20.7 1.0
N A:LYS71 4.1 23.8 1.0
O A:HOH716 4.1 34.1 1.0
O A:ASN96 4.4 22.5 1.0
O A:GLN72 4.4 25.6 1.0
OE2 A:GLU98 4.5 31.7 1.0
CD A:GLU98 4.5 41.0 1.0
CA A:GLN72 4.5 21.7 1.0
N A:ASP74 4.5 16.3 1.0
OE1 A:GLU98 4.7 44.5 1.0
CD1 A:ILE76 4.7 23.0 1.0
CA A:VAL70 4.7 18.6 1.0
CB A:ALA73 4.8 22.7 1.0
CG A:GLU98 4.9 30.3 1.0
CG1 A:VAL70 5.0 20.1 1.0
CB A:GLU98 5.0 26.9 1.0
CA A:ASP74 5.0 16.3 1.0

Magnesium binding site 4 out of 6 in 5w3k

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Magnesium binding site 4 out of 6 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd


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 Nadph, MG2+ and Cpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:49.4
occ:1.00
 O A:HOH781 2.8 27.2 1.0
O A:ASN39 3.0 21.9 1.0
O A:HOH644 3.4 44.6 1.0
OH A:TYR41 3.8 22.9 1.0
CB A:ASN39 3.9 18.6 1.0
CE2 A:TYR41 4.0 24.2 1.0
CZ A:TYR41 4.1 22.0 1.0
C A:ASN39 4.1 17.3 1.0
CG A:ASN39 4.2 26.8 1.0
OD1 A:ASN39 4.2 22.5 1.0
O A:HOH806 4.3 40.4 1.0
CA A:ASN39 4.4 19.4 1.0
O A:HOH593 4.6 20.6 1.0
OD2 A:ASP13 4.7 26.1 1.0
CD2 A:TYR41 4.8 17.8 1.0

Magnesium binding site 5 out of 6 in 5w3k

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Magnesium binding site 5 out of 6 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd


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 Nadph, MG2+ and Cpd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:13.1
occ:1.00
 OD1 B:ASP190 1.9 13.5 1.0
O A:HOH519 2.0 12.0 1.0
O06 A:9TY401 2.0 10.8 1.0
O A:HOH568 2.1 12.5 1.0
O05 A:9TY401 2.1 11.9 1.0
O B:HOH565 2.1 11.6 1.0
C04 A:9TY401 2.4 10.7 1.0
CG B:ASP190 2.9 11.2 1.0
OD2 B:ASP190 3.3 11.7 1.0
MG B:MG403 3.7 12.1 1.0
OE2 A:GLU230 3.8 13.2 1.0
NZ B:LYS130 3.9 11.0 1.0
C03 A:9TY401 3.9 11.6 1.0
OE1 A:GLU226 4.0 14.9 1.0
O B:HOH627 4.1 11.9 1.0
OE2 A:GLU226 4.1 15.2 1.0
CB B:ASP190 4.1 12.4 1.0
OE2 B:GLU194 4.2 11.3 1.0
OE1 A:GLU230 4.2 12.2 1.0
CE B:LYS130 4.3 14.3 1.0
O B:HOH690 4.4 11.2 1.0
CA B:ASP190 4.4 11.1 1.0
CD A:GLU226 4.5 13.4 1.0
CD A:GLU230 4.5 13.5 1.0
O B:PRO129 4.5 12.1 1.0
O B:ASP190 4.6 12.8 1.0
CA B:LYS130 4.7 12.1 1.0
C07 A:9TY401 4.8 11.3 1.0
O01 A:9TY401 4.8 12.6 1.0
CD B:LYS130 4.8 12.8 1.0
C02 A:9TY401 4.8 11.4 1.0
C08 A:9TY401 4.8 12.8 1.0
C4N B:NDP404 4.8 11.5 1.0
C5N B:NDP404 4.9 12.4 1.0
C B:ASP190 4.9 11.6 1.0

Magnesium binding site 6 out of 6 in 5w3k

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Magnesium binding site 6 out of 6 in the Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex Nadph, MG2+ and Cpd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:12.1
occ:1.00
 O06 A:9TY401 2.0 10.8 1.0
O B:HOH543 2.0 12.8 1.0
O B:HOH690 2.1 11.2 1.0
OD2 B:ASP190 2.1 11.7 1.0
O01 A:9TY401 2.1 12.6 1.0
OE2 B:GLU194 2.1 11.3 1.0
C04 A:9TY401 3.1 10.7 1.0
C02 A:9TY401 3.1 11.4 1.0
CD B:GLU194 3.1 13.8 1.0
CG B:ASP190 3.2 11.2 1.0
OE1 B:GLU194 3.4 11.8 1.0
C03 A:9TY401 3.5 11.6 1.0
OD1 B:ASP190 3.6 13.5 1.0
MG B:MG402 3.7 13.1 1.0
O A:HOH568 3.9 12.5 1.0
O05 A:9TY401 4.2 11.9 1.0
O09 A:9TY401 4.2 12.7 1.0
O B:HOH627 4.2 11.9 1.0
OG A:SER251 4.2 11.4 1.0
CB B:ASP190 4.4 12.4 1.0
NE2 B:HIS107 4.5 13.4 1.0
CG B:GLU194 4.5 10.9 1.0
O2D B:NDP404 4.5 13.1 1.0
O B:HOH565 4.5 11.6 1.0
CE1 B:HIS107 4.5 16.5 1.0
O B:ASP190 4.6 12.8 1.0
CB A:ALA254 4.6 11.6 1.0
CD2 B:HIS107 4.7 11.8 1.0
C4N B:NDP404 4.7 11.5 1.0
C07 A:9TY401 4.7 11.3 1.0
ND1 B:HIS107 4.8 14.4 1.0
C B:ASP190 4.8 11.6 1.0
CG B:HIS107 4.9 12.8 1.0
CB B:GLU194 4.9 10.7 1.0
C5N B:NDP404 4.9 12.4 1.0

Reference:

K.M.Patel, D.Teran, S.Zheng, A.Kandale, M.Garcia, Y.Lv, M.A.Schembri, R.P.Mcgeary, G.Schenk, L.W.Guddat. Crystal Structures of Staphylococcus Aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues That Have Biocidal Activity. Chemistry V. 23 18289 2017.
ISSN: ISSN 1521-3765
PubMed: 28975665
DOI: 10.1002/CHEM.201704481
Page generated: Mon Sep 30 06:28:13 2024

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