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
|