Magnesium in PDB 7uy4: Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp
Enzymatic activity of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp
All present enzymatic activity of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp:
2.7.7.47;
Protein crystallography data
The structure of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp, PDB code: 7uy4
was solved by
S.M.Reeve,
R.E.Lee,
N.Das,
S.Jayaraman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.43 /
1.98
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.043,
106.958,
114.148,
90,
90,
90
|
R / Rfree (%)
|
17.8 /
22.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp
(pdb code 7uy4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp, PDB code: 7uy4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7uy4
Go back to
Magnesium Binding Sites List in 7uy4
Magnesium binding site 1 out
of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:36.3
occ:1.00
|
OD1
|
A:ASP45
|
2.0
|
28.1
|
1.0
|
OD2
|
A:ASP43
|
2.1
|
31.7
|
1.0
|
OE1
|
A:GLU83
|
2.1
|
34.3
|
1.0
|
O
|
A:HOH449
|
2.2
|
34.7
|
1.0
|
O2A
|
A:ANP301
|
2.2
|
41.6
|
1.0
|
O11
|
A:SMI302
|
2.2
|
38.7
|
1.0
|
CD
|
A:GLU83
|
2.9
|
40.8
|
1.0
|
CG
|
A:ASP45
|
3.0
|
37.3
|
1.0
|
CG
|
A:ASP43
|
3.1
|
34.2
|
1.0
|
PA
|
A:ANP301
|
3.2
|
56.9
|
1.0
|
OE2
|
A:GLU83
|
3.3
|
38.0
|
1.0
|
OD2
|
A:ASP45
|
3.4
|
34.4
|
1.0
|
OD1
|
A:ASP43
|
3.4
|
35.4
|
1.0
|
O5'
|
A:ANP301
|
3.5
|
50.7
|
1.0
|
C11
|
A:SMI302
|
3.6
|
43.9
|
1.0
|
MG
|
A:MG304
|
3.7
|
34.1
|
1.0
|
O
|
A:HOH431
|
3.7
|
39.5
|
1.0
|
N10
|
A:SMI302
|
3.8
|
40.6
|
1.0
|
O
|
A:HOH433
|
3.9
|
36.5
|
1.0
|
O1A
|
A:ANP301
|
3.9
|
53.1
|
1.0
|
C10
|
A:SMI302
|
4.0
|
38.4
|
1.0
|
CG
|
A:GLU83
|
4.1
|
37.4
|
1.0
|
CB
|
A:GLU83
|
4.1
|
34.0
|
1.0
|
CB
|
A:ASP45
|
4.2
|
26.6
|
1.0
|
C12
|
A:SMI302
|
4.4
|
35.9
|
1.0
|
CB
|
A:ASP43
|
4.4
|
32.0
|
1.0
|
O
|
A:HOH480
|
4.5
|
40.2
|
1.0
|
C1M
|
A:SMI302
|
4.6
|
36.8
|
1.0
|
O3A
|
A:ANP301
|
4.6
|
44.8
|
1.0
|
O2B
|
A:SMI302
|
4.6
|
42.6
|
1.0
|
CA
|
A:ASP45
|
4.8
|
28.0
|
1.0
|
C5'
|
A:ANP301
|
4.9
|
44.0
|
1.0
|
O2B
|
A:ANP301
|
4.9
|
38.6
|
1.0
|
O1G
|
A:ANP301
|
4.9
|
37.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7uy4
Go back to
Magnesium Binding Sites List in 7uy4
Magnesium binding site 2 out
of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:34.1
occ:1.00
|
O2B
|
A:ANP301
|
2.0
|
38.6
|
1.0
|
OD2
|
A:ASP45
|
2.0
|
34.4
|
1.0
|
OD1
|
A:ASP43
|
2.1
|
35.4
|
1.0
|
O
|
A:HOH429
|
2.1
|
35.5
|
1.0
|
O1G
|
A:ANP301
|
2.2
|
37.9
|
1.0
|
O2A
|
A:ANP301
|
2.2
|
41.6
|
1.0
|
CG
|
A:ASP45
|
3.0
|
37.3
|
1.0
|
CG
|
A:ASP43
|
3.1
|
34.2
|
1.0
|
PB
|
A:ANP301
|
3.1
|
40.6
|
1.0
|
PG
|
A:ANP301
|
3.3
|
37.5
|
1.0
|
PA
|
A:ANP301
|
3.3
|
56.9
|
1.0
|
OD1
|
A:ASP45
|
3.4
|
28.1
|
1.0
|
O3A
|
A:ANP301
|
3.5
|
44.8
|
1.0
|
N3B
|
A:ANP301
|
3.5
|
41.9
|
1.0
|
OD2
|
A:ASP43
|
3.6
|
31.7
|
1.0
|
MG
|
A:MG303
|
3.7
|
36.3
|
1.0
|
OG
|
A:SER32
|
3.9
|
32.1
|
1.0
|
O
|
A:ASP43
|
3.9
|
30.4
|
1.0
|
O
|
A:HOH480
|
4.0
|
40.2
|
1.0
|
O3G
|
A:ANP301
|
4.0
|
31.0
|
1.0
|
N
|
A:SER32
|
4.1
|
35.1
|
1.0
|
O
|
A:HOH431
|
4.1
|
39.5
|
1.0
|
O1A
|
A:ANP301
|
4.1
|
53.1
|
1.0
|
N
|
A:ASP43
|
4.2
|
31.4
|
1.0
|
O
|
A:HOH411
|
4.2
|
32.7
|
1.0
|
CB
|
A:ASP45
|
4.4
|
26.6
|
1.0
|
C
|
A:ASP43
|
4.4
|
35.8
|
1.0
|
CB
|
A:ASP43
|
4.4
|
32.0
|
1.0
|
O1B
|
A:ANP301
|
4.5
|
47.3
|
1.0
|
O2G
|
A:ANP301
|
4.5
|
36.5
|
1.0
|
CA
|
A:ASP43
|
4.5
|
34.8
|
1.0
|
O5'
|
A:ANP301
|
4.6
|
50.7
|
1.0
|
CB
|
A:SER32
|
4.6
|
37.5
|
1.0
|
CA
|
A:GLY31
|
4.7
|
32.1
|
1.0
|
O
|
A:HOH449
|
4.8
|
34.7
|
1.0
|
C
|
A:GLY31
|
4.9
|
33.4
|
1.0
|
N
|
A:ASP45
|
4.9
|
33.2
|
1.0
|
O11
|
A:SMI302
|
4.9
|
38.7
|
1.0
|
CA
|
A:SER32
|
5.0
|
35.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7uy4
Go back to
Magnesium Binding Sites List in 7uy4
Magnesium binding site 3 out
of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:45.7
occ:1.00
|
OD1
|
B:ASP43
|
1.9
|
41.6
|
1.0
|
O2B
|
B:ANP301
|
2.0
|
45.6
|
1.0
|
O
|
B:HOH413
|
2.1
|
35.2
|
1.0
|
OD2
|
B:ASP45
|
2.1
|
37.0
|
1.0
|
O1G
|
B:ANP301
|
2.1
|
41.8
|
1.0
|
O2A
|
B:ANP301
|
2.3
|
44.8
|
1.0
|
CG
|
B:ASP43
|
3.0
|
39.1
|
1.0
|
CG
|
B:ASP45
|
3.0
|
43.1
|
1.0
|
PB
|
B:ANP301
|
3.2
|
47.4
|
1.0
|
OD1
|
B:ASP45
|
3.3
|
36.0
|
1.0
|
PA
|
B:ANP301
|
3.4
|
51.8
|
1.0
|
PG
|
B:ANP301
|
3.4
|
45.3
|
1.0
|
O3A
|
B:ANP301
|
3.5
|
42.8
|
1.0
|
OD2
|
B:ASP43
|
3.5
|
40.7
|
1.0
|
MG
|
B:MG304
|
3.6
|
44.7
|
1.0
|
N3B
|
B:ANP301
|
3.7
|
45.7
|
1.0
|
O
|
B:ASP43
|
3.8
|
37.2
|
1.0
|
OG
|
B:SER32
|
3.9
|
39.1
|
1.0
|
O
|
B:HOH417
|
4.0
|
41.1
|
1.0
|
O1A
|
B:ANP301
|
4.0
|
46.7
|
1.0
|
O
|
B:HOH419
|
4.0
|
38.5
|
1.0
|
N
|
B:ASP43
|
4.1
|
40.5
|
1.0
|
O
|
B:HOH504
|
4.1
|
51.0
|
1.0
|
N
|
B:SER32
|
4.1
|
37.6
|
1.0
|
O3G
|
B:ANP301
|
4.1
|
45.3
|
1.0
|
CB
|
B:ASP43
|
4.2
|
43.7
|
1.0
|
C
|
B:ASP43
|
4.3
|
41.2
|
1.0
|
CB
|
B:ASP45
|
4.3
|
37.8
|
1.0
|
CA
|
B:ASP43
|
4.4
|
38.9
|
1.0
|
O2G
|
B:ANP301
|
4.5
|
46.6
|
1.0
|
O1B
|
B:ANP301
|
4.5
|
48.2
|
1.0
|
CB
|
B:SER32
|
4.6
|
37.6
|
1.0
|
CA
|
B:GLY31
|
4.6
|
40.5
|
1.0
|
O5'
|
B:ANP301
|
4.7
|
49.5
|
1.0
|
O
|
B:HOH479
|
4.8
|
41.8
|
1.0
|
N
|
B:ASP45
|
4.8
|
37.2
|
1.0
|
O11
|
B:SMI302
|
4.9
|
47.3
|
1.0
|
C
|
B:GLY31
|
4.9
|
38.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7uy4
Go back to
Magnesium Binding Sites List in 7uy4
Magnesium binding site 4 out
of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:44.7
occ:1.00
|
O
|
B:HOH479
|
2.0
|
41.8
|
1.0
|
OD2
|
B:ASP43
|
2.1
|
40.7
|
1.0
|
OD1
|
B:ASP45
|
2.1
|
36.0
|
1.0
|
O11
|
B:SMI302
|
2.2
|
47.3
|
1.0
|
OE1
|
B:GLU83
|
2.2
|
41.8
|
1.0
|
O2A
|
B:ANP301
|
2.2
|
44.8
|
1.0
|
CD
|
B:GLU83
|
3.0
|
39.9
|
1.0
|
CG
|
B:ASP45
|
3.1
|
43.1
|
1.0
|
CG
|
B:ASP43
|
3.1
|
39.1
|
1.0
|
PA
|
B:ANP301
|
3.1
|
51.8
|
1.0
|
OE2
|
B:GLU83
|
3.3
|
43.0
|
1.0
|
OD1
|
B:ASP43
|
3.4
|
41.6
|
1.0
|
C11
|
B:SMI302
|
3.4
|
48.2
|
1.0
|
OD2
|
B:ASP45
|
3.5
|
37.0
|
1.0
|
O1A
|
B:ANP301
|
3.6
|
46.7
|
1.0
|
O5'
|
B:ANP301
|
3.6
|
49.5
|
1.0
|
O
|
B:HOH417
|
3.6
|
41.1
|
1.0
|
N10
|
B:SMI302
|
3.6
|
43.5
|
1.0
|
MG
|
B:MG303
|
3.6
|
45.7
|
1.0
|
C10
|
B:SMI302
|
3.8
|
43.1
|
1.0
|
CG
|
B:GLU83
|
4.2
|
41.9
|
1.0
|
O
|
B:HOH496
|
4.2
|
38.1
|
1.0
|
CB
|
B:GLU83
|
4.2
|
35.7
|
1.0
|
CB
|
B:ASP45
|
4.3
|
37.8
|
1.0
|
C12
|
B:SMI302
|
4.4
|
44.2
|
1.0
|
CB
|
B:ASP43
|
4.4
|
43.7
|
1.0
|
C1M
|
B:SMI302
|
4.5
|
40.7
|
1.0
|
O3A
|
B:ANP301
|
4.6
|
42.8
|
1.0
|
O2B
|
B:SMI302
|
4.6
|
40.7
|
1.0
|
O
|
B:HOH504
|
4.7
|
51.0
|
1.0
|
O2B
|
B:ANP301
|
4.8
|
45.6
|
1.0
|
O1G
|
B:ANP301
|
4.9
|
41.8
|
1.0
|
C5'
|
B:ANP301
|
4.9
|
53.7
|
1.0
|
CA
|
B:ASP45
|
4.9
|
37.6
|
1.0
|
|
Reference:
N.Das,
S.M.Reeve,
R.E.Lee.
Characterization of the Spectinomycin Deactivating Enzyme Ant-3,9 To Be Published.
Page generated: Thu Oct 3 10:17:15 2024
|