Magnesium in PDB 5etq: S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution
Protein crystallography data
The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution, PDB code: 5etq
was solved by
M.L.Dennis,
T.S.Peat,
J.D.Swarbrick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.76 /
1.96
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.630,
68.200,
52.820,
90.00,
106.05,
90.00
|
R / Rfree (%)
|
18.2 /
21.6
|
Other elements in 5etq:
The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution
(pdb code 5etq). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution, PDB code: 5etq:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5etq
Go back to
Magnesium Binding Sites List in 5etq
Magnesium binding site 1 out
of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg201
b:12.3
occ:1.00
|
O2B
|
A:APC203
|
2.0
|
13.5
|
1.0
|
O3G
|
A:APC203
|
2.1
|
10.9
|
1.0
|
O
|
A:HOH342
|
2.1
|
12.6
|
1.0
|
OD2
|
A:ASP97
|
2.1
|
7.5
|
1.0
|
OD2
|
A:ASP95
|
2.1
|
6.4
|
1.0
|
O
|
A:HOH355
|
2.2
|
11.1
|
1.0
|
CG
|
A:ASP97
|
3.0
|
7.2
|
1.0
|
CG
|
A:ASP95
|
3.1
|
7.0
|
1.0
|
PB
|
A:APC203
|
3.2
|
11.3
|
1.0
|
PG
|
A:APC203
|
3.2
|
12.9
|
1.0
|
OD1
|
A:ASP97
|
3.2
|
7.0
|
1.0
|
O3B
|
A:APC203
|
3.3
|
12.2
|
1.0
|
MG
|
A:MG202
|
3.4
|
11.0
|
1.0
|
OD1
|
A:ASP95
|
3.5
|
6.5
|
1.0
|
O1B
|
A:APC203
|
3.8
|
12.2
|
1.0
|
O
|
A:HOH345
|
3.9
|
11.8
|
1.0
|
O2G
|
A:APC203
|
3.9
|
13.1
|
1.0
|
O
|
A:HOH354
|
4.0
|
22.2
|
1.0
|
O
|
A:HOH360
|
4.1
|
16.9
|
1.0
|
N11
|
A:YH2204
|
4.3
|
13.7
|
1.0
|
NH1
|
A:ARG121
|
4.4
|
7.5
|
1.0
|
O1G
|
A:APC203
|
4.4
|
10.9
|
1.0
|
CB
|
A:ASP97
|
4.4
|
7.1
|
1.0
|
CB
|
A:ASP95
|
4.4
|
6.8
|
1.0
|
O
|
A:HOH327
|
4.5
|
6.3
|
1.0
|
C3A
|
A:APC203
|
4.7
|
10.4
|
1.0
|
NE2
|
A:HIS115
|
4.7
|
9.1
|
1.0
|
NH1
|
A:ARG92
|
4.7
|
18.8
|
1.0
|
S12
|
A:YH2204
|
4.8
|
18.2
|
1.0
|
O2A
|
A:APC203
|
4.9
|
9.5
|
1.0
|
C10
|
A:YH2204
|
5.0
|
17.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5etq
Go back to
Magnesium Binding Sites List in 5etq
Magnesium binding site 2 out
of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:11.0
occ:1.00
|
O
|
A:HOH327
|
2.0
|
6.3
|
1.0
|
O2A
|
A:APC203
|
2.0
|
9.5
|
1.0
|
O
|
A:HOH310
|
2.0
|
9.1
|
1.0
|
OD1
|
A:ASP95
|
2.1
|
6.5
|
1.0
|
OD1
|
A:ASP97
|
2.1
|
7.0
|
1.0
|
O2B
|
A:APC203
|
2.2
|
13.5
|
1.0
|
PB
|
A:APC203
|
3.0
|
11.3
|
1.0
|
CG
|
A:ASP95
|
3.1
|
7.0
|
1.0
|
PA
|
A:APC203
|
3.2
|
12.1
|
1.0
|
CG
|
A:ASP97
|
3.2
|
7.2
|
1.0
|
OD2
|
A:ASP95
|
3.4
|
6.4
|
1.0
|
MG
|
A:MG201
|
3.4
|
12.3
|
1.0
|
C3A
|
A:APC203
|
3.5
|
10.4
|
1.0
|
OD2
|
A:ASP97
|
3.6
|
7.5
|
1.0
|
O5'
|
A:APC203
|
3.6
|
11.8
|
1.0
|
OE2
|
A:GLU78
|
4.1
|
9.2
|
1.0
|
O1B
|
A:APC203
|
4.2
|
12.2
|
1.0
|
O
|
A:VAL96
|
4.2
|
6.9
|
1.0
|
O
|
A:HOH311
|
4.3
|
25.9
|
1.0
|
O3B
|
A:APC203
|
4.3
|
12.2
|
1.0
|
NH1
|
A:ARG83
|
4.4
|
8.2
|
1.0
|
CB
|
A:ASP95
|
4.5
|
6.8
|
1.0
|
O
|
A:HOH301
|
4.5
|
21.6
|
1.0
|
CB
|
A:ASP97
|
4.5
|
7.1
|
1.0
|
C
|
A:VAL96
|
4.6
|
7.6
|
1.0
|
N3
|
A:APC203
|
4.6
|
15.1
|
1.0
|
C2
|
A:APC203
|
4.6
|
13.0
|
1.0
|
O1A
|
A:APC203
|
4.6
|
12.0
|
1.0
|
O3G
|
A:APC203
|
4.6
|
10.9
|
1.0
|
O
|
A:HOH342
|
4.6
|
12.6
|
1.0
|
N
|
A:VAL96
|
4.7
|
7.4
|
1.0
|
NH2
|
A:ARG83
|
4.7
|
7.8
|
1.0
|
O2G
|
A:APC203
|
4.7
|
13.1
|
1.0
|
CA
|
A:ASP97
|
4.7
|
7.2
|
1.0
|
N
|
A:ASP97
|
4.8
|
8.3
|
1.0
|
PG
|
A:APC203
|
4.9
|
12.9
|
1.0
|
CA
|
A:ASP95
|
4.9
|
6.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5etq
Go back to
Magnesium Binding Sites List in 5etq
Magnesium binding site 3 out
of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg201
b:14.1
occ:1.00
|
O1A
|
B:APC203
|
2.0
|
14.1
|
1.0
|
O2B
|
B:APC203
|
2.1
|
11.2
|
1.0
|
O
|
B:HOH309
|
2.1
|
11.6
|
1.0
|
O
|
B:HOH341
|
2.1
|
9.9
|
1.0
|
OD1
|
B:ASP97
|
2.1
|
5.6
|
1.0
|
OD1
|
B:ASP95
|
2.1
|
4.8
|
1.0
|
CG
|
B:ASP95
|
3.1
|
6.1
|
1.0
|
PB
|
B:APC203
|
3.1
|
13.8
|
1.0
|
PA
|
B:APC203
|
3.2
|
14.1
|
1.0
|
CG
|
B:ASP97
|
3.2
|
5.8
|
1.0
|
C3A
|
B:APC203
|
3.4
|
13.1
|
1.0
|
OD2
|
B:ASP95
|
3.4
|
6.3
|
1.0
|
MG
|
B:MG202
|
3.6
|
13.3
|
1.0
|
OD2
|
B:ASP97
|
3.7
|
6.4
|
1.0
|
O5'
|
B:APC203
|
3.7
|
16.9
|
1.0
|
O1B
|
B:APC203
|
3.9
|
14.1
|
1.0
|
OE2
|
B:GLU78
|
4.1
|
10.6
|
1.0
|
O
|
B:VAL96
|
4.2
|
5.8
|
1.0
|
O
|
B:HOH301
|
4.2
|
22.7
|
1.0
|
NH1
|
B:ARG83
|
4.3
|
13.6
|
1.0
|
O3B
|
B:APC203
|
4.5
|
13.4
|
1.0
|
CB
|
B:ASP95
|
4.5
|
6.1
|
1.0
|
O2A
|
B:APC203
|
4.5
|
14.2
|
1.0
|
CB
|
B:ASP97
|
4.5
|
6.3
|
1.0
|
C
|
B:VAL96
|
4.6
|
5.6
|
1.0
|
O
|
B:HOH313
|
4.6
|
19.3
|
1.0
|
N3
|
B:APC203
|
4.6
|
15.7
|
1.0
|
C2
|
B:APC203
|
4.6
|
11.5
|
1.0
|
N
|
B:VAL96
|
4.6
|
6.9
|
1.0
|
O1G
|
B:APC203
|
4.7
|
10.2
|
1.0
|
O
|
B:HOH329
|
4.7
|
12.3
|
1.0
|
CA
|
B:ASP97
|
4.7
|
6.2
|
1.0
|
O2G
|
B:APC203
|
4.8
|
13.5
|
1.0
|
N
|
B:ASP97
|
4.8
|
6.3
|
1.0
|
NH2
|
B:ARG83
|
4.8
|
10.2
|
1.0
|
CA
|
B:ASP95
|
4.9
|
6.7
|
1.0
|
PG
|
B:APC203
|
4.9
|
14.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5etq
Go back to
Magnesium Binding Sites List in 5etq
Magnesium binding site 4 out
of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg202
b:13.3
occ:1.00
|
O1G
|
B:APC203
|
2.0
|
10.2
|
1.0
|
O
|
B:HOH348
|
2.1
|
12.0
|
1.0
|
O
|
B:HOH329
|
2.1
|
12.3
|
1.0
|
O2B
|
B:APC203
|
2.1
|
11.2
|
1.0
|
OD2
|
B:ASP97
|
2.2
|
6.4
|
1.0
|
OD2
|
B:ASP95
|
2.2
|
6.3
|
1.0
|
CG
|
B:ASP97
|
3.1
|
5.8
|
1.0
|
PB
|
B:APC203
|
3.1
|
13.8
|
1.0
|
PG
|
B:APC203
|
3.2
|
14.0
|
1.0
|
CG
|
B:ASP95
|
3.2
|
6.1
|
1.0
|
OD1
|
B:ASP97
|
3.3
|
5.6
|
1.0
|
O3B
|
B:APC203
|
3.3
|
13.4
|
1.0
|
MG
|
B:MG201
|
3.6
|
14.1
|
1.0
|
OD1
|
B:ASP95
|
3.6
|
4.8
|
1.0
|
O1B
|
B:APC203
|
3.8
|
14.1
|
1.0
|
O
|
B:HOH326
|
3.9
|
10.5
|
1.0
|
O2G
|
B:APC203
|
4.0
|
13.5
|
1.0
|
O
|
B:HOH347
|
4.1
|
12.3
|
1.0
|
O
|
B:HOH350
|
4.1
|
23.5
|
1.0
|
NH1
|
B:ARG121
|
4.2
|
6.6
|
1.0
|
N11
|
B:YH2204
|
4.3
|
14.7
|
1.0
|
O3G
|
B:APC203
|
4.3
|
11.4
|
1.0
|
CB
|
B:ASP95
|
4.5
|
6.1
|
1.0
|
CB
|
B:ASP97
|
4.5
|
6.3
|
1.0
|
NE2
|
B:HIS115
|
4.6
|
11.6
|
1.0
|
C3A
|
B:APC203
|
4.7
|
13.1
|
1.0
|
O
|
B:HOH341
|
4.7
|
9.9
|
1.0
|
NH1
|
B:ARG92
|
4.8
|
14.8
|
1.0
|
S12
|
B:YH2204
|
4.8
|
18.5
|
1.0
|
O1A
|
B:APC203
|
4.9
|
14.1
|
1.0
|
C10
|
B:YH2204
|
5.0
|
17.9
|
1.0
|
|
Reference:
M.L.Dennis,
N.P.Pitcher,
M.D.Lee,
A.J.Debono,
Z.C.Wang,
J.R.Harjani,
R.Rahmani,
B.Cleary,
T.S.Peat,
J.B.Baell,
J.D.Swarbrick.
Structural Basis For the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase From Staphylococcus Aureus and Escherichia Coli. J.Med.Chem. V. 59 5248 2016.
ISSN: ISSN 0022-2623
PubMed: 27094768
DOI: 10.1021/ACS.JMEDCHEM.6B00002
Page generated: Sun Sep 29 03:55:38 2024
|