Magnesium in PDB 5iqc: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Protein crystallography data
The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1, PDB code: 5iqc
was solved by
S.J.Caldwell,
A.M.Berghuis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
90.44 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.780,
98.890,
93.860,
90.00,
105.51,
90.00
|
R / Rfree (%)
|
17.9 /
22.9
|
Other elements in 5iqc:
The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
(pdb code 5iqc). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1, PDB code: 5iqc:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 5iqc
Go back to
Magnesium Binding Sites List in 5iqc
Magnesium binding site 1 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg700
b:30.4
occ:1.00
|
O2G
|
A:GNP500
|
1.5
|
44.8
|
0.6
|
O2A
|
A:GNP500
|
1.9
|
44.8
|
1.0
|
O
|
A:HOH901
|
2.0
|
34.0
|
0.4
|
OD2
|
A:ASP393
|
2.1
|
38.2
|
1.0
|
O
|
A:HOH900
|
2.1
|
35.4
|
1.0
|
NE2
|
A:HIS379
|
2.1
|
47.5
|
1.0
|
O1B
|
A:GNP500
|
2.4
|
40.1
|
0.4
|
PG
|
A:GNP500
|
2.8
|
46.5
|
0.6
|
CE1
|
A:HIS379
|
3.0
|
45.3
|
1.0
|
CG
|
A:ASP393
|
3.1
|
42.1
|
1.0
|
CD2
|
A:HIS379
|
3.1
|
46.4
|
1.0
|
PA
|
A:GNP500
|
3.2
|
43.3
|
1.0
|
O3G
|
A:GNP500
|
3.3
|
46.2
|
0.6
|
N3B
|
A:GNP500
|
3.5
|
43.7
|
0.6
|
PB
|
A:GNP500
|
3.5
|
38.7
|
0.4
|
CB
|
A:ASP393
|
3.5
|
41.0
|
1.0
|
O
|
A:HOH904
|
3.7
|
48.8
|
0.4
|
O3A
|
A:GNP500
|
3.7
|
40.5
|
0.4
|
MG
|
A:MG702
|
3.7
|
51.1
|
1.0
|
O3A
|
A:GNP500
|
3.7
|
42.5
|
0.6
|
O
|
A:HOH1029
|
3.7
|
50.1
|
1.0
|
O2B
|
A:GNP500
|
3.8
|
43.6
|
0.6
|
PB
|
A:GNP500
|
3.9
|
40.5
|
0.6
|
O1G
|
A:GNP500
|
3.9
|
47.4
|
0.6
|
O1A
|
A:GNP500
|
4.0
|
40.0
|
1.0
|
O
|
A:HOH924
|
4.1
|
26.4
|
0.4
|
ND1
|
A:HIS379
|
4.2
|
44.2
|
1.0
|
O2B
|
A:GNP500
|
4.2
|
37.9
|
0.4
|
OD1
|
A:ASP393
|
4.2
|
41.5
|
1.0
|
CG
|
A:HIS379
|
4.2
|
43.7
|
1.0
|
O5'
|
A:GNP500
|
4.4
|
40.0
|
1.0
|
ND2
|
A:ASN378
|
4.6
|
55.1
|
1.0
|
C5'
|
A:GNP500
|
4.6
|
41.0
|
1.0
|
O
|
A:HOH902
|
4.6
|
42.2
|
1.0
|
O3'
|
A:GNP500
|
4.7
|
45.7
|
1.0
|
O3G
|
A:GNP500
|
4.7
|
38.5
|
0.4
|
OD2
|
A:ASP374
|
4.8
|
42.4
|
1.0
|
N3B
|
A:GNP500
|
4.8
|
39.4
|
0.4
|
|
Magnesium binding site 2 out
of 9 in 5iqc
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Magnesium Binding Sites List in 5iqc
Magnesium binding site 2 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg702
b:51.1
occ:1.00
|
O3G
|
A:GNP500
|
1.8
|
38.5
|
0.4
|
O
|
A:HOH903
|
1.8
|
55.8
|
1.0
|
O3G
|
A:GNP500
|
1.9
|
46.2
|
0.6
|
OD2
|
A:ASP393
|
2.0
|
38.2
|
1.0
|
O
|
A:HOH904
|
2.0
|
48.8
|
0.4
|
O2B
|
A:GNP500
|
2.1
|
43.6
|
0.6
|
OD1
|
A:ASP393
|
2.2
|
41.5
|
1.0
|
O
|
A:HOH902
|
2.3
|
42.2
|
1.0
|
CG
|
A:ASP393
|
2.4
|
42.1
|
1.0
|
O1B
|
A:GNP500
|
3.0
|
40.1
|
0.4
|
PG
|
A:GNP500
|
3.0
|
40.1
|
0.4
|
PG
|
A:GNP500
|
3.2
|
46.5
|
0.6
|
O1G
|
A:GNP500
|
3.2
|
41.1
|
0.4
|
PB
|
A:GNP500
|
3.4
|
40.5
|
0.6
|
O
|
A:HOH901
|
3.5
|
34.0
|
0.4
|
O
|
A:HOH911
|
3.6
|
58.0
|
1.0
|
N3B
|
A:GNP500
|
3.6
|
43.7
|
0.6
|
MG
|
A:MG700
|
3.7
|
30.4
|
1.0
|
N3B
|
A:GNP500
|
3.7
|
39.4
|
0.4
|
O2G
|
A:GNP500
|
3.7
|
44.8
|
0.6
|
PB
|
A:GNP500
|
3.8
|
38.7
|
0.4
|
CB
|
A:ASP393
|
3.9
|
41.0
|
1.0
|
NZ
|
A:LYS226
|
4.1
|
52.4
|
1.0
|
O2G
|
A:GNP500
|
4.2
|
41.0
|
0.4
|
O3A
|
A:GNP500
|
4.3
|
40.5
|
0.4
|
O1G
|
A:GNP500
|
4.3
|
47.4
|
0.6
|
OD2
|
A:ASP374
|
4.3
|
42.4
|
1.0
|
O1B
|
A:GNP500
|
4.3
|
40.9
|
0.6
|
O3A
|
A:GNP500
|
4.4
|
42.5
|
0.6
|
O2A
|
A:GNP500
|
4.4
|
44.8
|
1.0
|
C19
|
A:51G600
|
4.4
|
68.7
|
1.0
|
O
|
A:HOH924
|
4.5
|
26.4
|
0.4
|
O1A
|
A:GNP500
|
4.5
|
40.0
|
1.0
|
CA
|
A:GLY395
|
4.6
|
48.3
|
1.0
|
OD2
|
A:ASP396
|
4.6
|
47.8
|
1.0
|
PA
|
A:GNP500
|
4.7
|
43.3
|
1.0
|
N
|
A:GLY395
|
4.7
|
45.8
|
1.0
|
N
|
A:51G600
|
4.8
|
64.8
|
1.0
|
CA
|
A:ASP393
|
4.8
|
40.1
|
1.0
|
CE1
|
A:HIS379
|
4.8
|
45.3
|
1.0
|
O
|
A:ASP393
|
4.8
|
37.5
|
1.0
|
NE2
|
A:HIS379
|
4.9
|
47.5
|
1.0
|
C
|
A:ASP393
|
5.0
|
38.2
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 5iqc
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Magnesium Binding Sites List in 5iqc
Magnesium binding site 3 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg700
b:29.5
occ:1.00
|
O
|
B:HOH900
|
1.7
|
40.2
|
1.0
|
O1A
|
B:GNP500
|
1.7
|
34.6
|
1.0
|
O1G
|
B:GNP500
|
1.7
|
52.5
|
0.8
|
O
|
B:HOH901
|
1.9
|
32.4
|
0.2
|
OD2
|
B:ASP393
|
2.2
|
42.6
|
1.0
|
NE2
|
B:HIS379
|
2.2
|
36.2
|
1.0
|
O2B
|
B:GNP500
|
2.5
|
36.1
|
0.2
|
PG
|
B:GNP500
|
3.0
|
58.4
|
0.8
|
PA
|
B:GNP500
|
3.1
|
40.7
|
1.0
|
CE1
|
B:HIS379
|
3.1
|
35.1
|
1.0
|
CD2
|
B:HIS379
|
3.1
|
34.2
|
1.0
|
CG
|
B:ASP393
|
3.2
|
41.7
|
1.0
|
N3B
|
B:GNP500
|
3.2
|
52.4
|
0.8
|
PB
|
B:GNP500
|
3.5
|
36.4
|
0.2
|
CB
|
B:ASP393
|
3.6
|
40.8
|
1.0
|
O3A
|
B:GNP500
|
3.6
|
37.1
|
0.2
|
O3A
|
B:GNP500
|
3.7
|
43.4
|
0.8
|
O3G
|
B:GNP500
|
3.8
|
61.1
|
0.8
|
PB
|
B:GNP500
|
3.8
|
47.3
|
0.8
|
O
|
B:HOH925
|
3.8
|
40.8
|
1.0
|
O1B
|
B:GNP500
|
3.8
|
50.2
|
0.8
|
O
|
B:HOH904
|
3.9
|
51.1
|
0.2
|
MG
|
B:MG702
|
4.0
|
52.5
|
1.0
|
O2A
|
B:GNP500
|
4.0
|
36.4
|
1.0
|
O5'
|
B:GNP500
|
4.1
|
38.3
|
1.0
|
O
|
B:HOH924
|
4.1
|
26.2
|
0.2
|
O2G
|
B:GNP500
|
4.2
|
62.1
|
0.8
|
O1B
|
B:GNP500
|
4.2
|
37.2
|
0.2
|
ND1
|
B:HIS379
|
4.2
|
32.5
|
1.0
|
O3'
|
B:GNP500
|
4.2
|
38.4
|
1.0
|
CG
|
B:HIS379
|
4.3
|
31.6
|
1.0
|
OD1
|
B:ASP393
|
4.3
|
40.9
|
1.0
|
C5'
|
B:GNP500
|
4.6
|
41.3
|
1.0
|
ND2
|
B:ASN378
|
4.6
|
50.5
|
1.0
|
C3'
|
B:GNP500
|
4.7
|
39.8
|
1.0
|
O3G
|
B:GNP500
|
4.8
|
34.5
|
0.2
|
O
|
B:HOH902
|
4.9
|
47.6
|
1.0
|
OD2
|
B:ASP374
|
4.9
|
38.9
|
1.0
|
N3B
|
B:GNP500
|
4.9
|
37.9
|
0.2
|
|
Magnesium binding site 4 out
of 9 in 5iqc
Go back to
Magnesium Binding Sites List in 5iqc
Magnesium binding site 4 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg702
b:52.5
occ:1.00
|
O
|
B:HOH903
|
1.9
|
44.7
|
1.0
|
O
|
B:HOH904
|
1.9
|
51.1
|
0.2
|
O
|
B:HOH902
|
2.1
|
47.6
|
1.0
|
O3G
|
B:GNP500
|
2.2
|
34.5
|
0.2
|
OD2
|
B:ASP393
|
2.2
|
42.6
|
1.0
|
O3G
|
B:GNP500
|
2.2
|
61.1
|
0.8
|
O1B
|
B:GNP500
|
2.2
|
50.2
|
0.8
|
OD1
|
B:ASP393
|
2.3
|
40.9
|
1.0
|
CG
|
B:ASP393
|
2.6
|
41.7
|
1.0
|
O2B
|
B:GNP500
|
3.2
|
36.1
|
0.2
|
PG
|
B:GNP500
|
3.3
|
36.8
|
0.2
|
O2G
|
B:GNP500
|
3.4
|
38.3
|
0.2
|
PG
|
B:GNP500
|
3.4
|
58.4
|
0.8
|
O1G
|
B:GNP500
|
3.7
|
52.5
|
0.8
|
PB
|
B:GNP500
|
3.7
|
47.3
|
0.8
|
O
|
B:HOH901
|
3.8
|
32.4
|
0.2
|
N3B
|
B:GNP500
|
3.9
|
52.4
|
0.8
|
MG
|
B:MG700
|
4.0
|
29.5
|
1.0
|
O
|
B:HOH911
|
4.0
|
52.2
|
1.0
|
N3B
|
B:GNP500
|
4.0
|
37.9
|
0.2
|
PB
|
B:GNP500
|
4.0
|
36.4
|
0.2
|
OD2
|
B:ASP374
|
4.1
|
38.9
|
1.0
|
CB
|
B:ASP393
|
4.1
|
40.8
|
1.0
|
O
|
B:HOH1299
|
4.2
|
53.4
|
1.0
|
O
|
B:HOH1083
|
4.2
|
41.4
|
1.0
|
OD2
|
B:ASP396
|
4.2
|
56.0
|
1.0
|
O
|
B:HOH924
|
4.3
|
26.2
|
0.2
|
NZ
|
B:LYS226
|
4.4
|
45.1
|
1.0
|
O3A
|
B:GNP500
|
4.5
|
37.1
|
0.2
|
CA
|
B:GLY395
|
4.5
|
46.4
|
1.0
|
O1A
|
B:GNP500
|
4.5
|
34.6
|
1.0
|
O3A
|
B:GNP500
|
4.5
|
43.4
|
0.8
|
C19
|
B:51G600
|
4.6
|
86.3
|
1.0
|
O2B
|
B:GNP500
|
4.6
|
50.3
|
0.8
|
O2G
|
B:GNP500
|
4.6
|
62.1
|
0.8
|
O1G
|
B:GNP500
|
4.6
|
37.7
|
0.2
|
N
|
B:GLY395
|
4.6
|
39.4
|
1.0
|
CE1
|
B:HIS379
|
4.8
|
35.1
|
1.0
|
O
|
B:ASP393
|
4.8
|
38.4
|
1.0
|
O2A
|
B:GNP500
|
4.8
|
36.4
|
1.0
|
CG
|
B:ASP396
|
4.8
|
43.9
|
1.0
|
PA
|
B:GNP500
|
4.8
|
40.7
|
1.0
|
C
|
B:GLY395
|
4.9
|
49.1
|
1.0
|
CA
|
B:ASP393
|
4.9
|
40.5
|
1.0
|
NE2
|
B:HIS379
|
4.9
|
36.2
|
1.0
|
O
|
B:HOH951
|
5.0
|
26.3
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 5iqc
Go back to
Magnesium Binding Sites List in 5iqc
Magnesium binding site 5 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg700
b:37.1
occ:1.00
|
O2G
|
C:GNP500
|
1.7
|
57.9
|
0.5
|
O
|
C:HOH900
|
1.8
|
48.3
|
1.0
|
O2A
|
C:GNP500
|
1.9
|
49.7
|
1.0
|
O
|
C:HOH901
|
2.0
|
45.2
|
0.6
|
OD2
|
C:ASP393
|
2.2
|
38.5
|
1.0
|
NE2
|
C:HIS379
|
2.3
|
47.0
|
1.0
|
O1B
|
C:GNP500
|
2.3
|
45.8
|
0.6
|
PG
|
C:GNP500
|
2.9
|
59.5
|
0.5
|
N3B
|
C:GNP500
|
3.2
|
56.3
|
0.5
|
CE1
|
C:HIS379
|
3.2
|
47.3
|
1.0
|
PA
|
C:GNP500
|
3.2
|
49.2
|
1.0
|
CG
|
C:ASP393
|
3.2
|
39.7
|
1.0
|
CD2
|
C:HIS379
|
3.2
|
44.0
|
1.0
|
PB
|
C:GNP500
|
3.5
|
44.7
|
0.6
|
O2B
|
C:GNP500
|
3.6
|
52.6
|
0.5
|
O3A
|
C:GNP500
|
3.7
|
51.5
|
0.5
|
CB
|
C:ASP393
|
3.7
|
37.0
|
1.0
|
O3A
|
C:GNP500
|
3.7
|
47.7
|
0.6
|
PB
|
C:GNP500
|
3.8
|
52.6
|
0.5
|
O
|
C:HOH904
|
3.9
|
42.5
|
0.6
|
O3G
|
C:GNP500
|
3.9
|
57.9
|
0.5
|
O1G
|
C:GNP500
|
3.9
|
61.4
|
0.5
|
MG
|
C:MG702
|
4.0
|
54.2
|
1.0
|
O5'
|
C:GNP500
|
4.1
|
46.3
|
1.0
|
O1A
|
C:GNP500
|
4.2
|
49.5
|
1.0
|
O
|
C:HOH1260
|
4.2
|
53.1
|
1.0
|
ND1
|
C:HIS379
|
4.3
|
43.6
|
1.0
|
OD1
|
C:ASP393
|
4.3
|
41.3
|
1.0
|
O
|
C:HOH924
|
4.3
|
46.5
|
0.6
|
O2B
|
C:GNP500
|
4.3
|
47.3
|
0.6
|
CG
|
C:HIS379
|
4.4
|
42.5
|
1.0
|
O3'
|
C:GNP500
|
4.4
|
53.9
|
1.0
|
O3G
|
C:GNP500
|
4.6
|
48.0
|
0.6
|
ND2
|
C:ASN378
|
4.6
|
60.6
|
1.0
|
C5'
|
C:GNP500
|
4.7
|
47.7
|
1.0
|
N3B
|
C:GNP500
|
4.8
|
46.2
|
0.6
|
O
|
C:HOH902
|
4.9
|
47.0
|
1.0
|
C3'
|
C:GNP500
|
4.9
|
53.6
|
1.0
|
OD2
|
C:ASP374
|
4.9
|
42.5
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 5iqc
Go back to
Magnesium Binding Sites List in 5iqc
Magnesium binding site 6 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:54.2
occ:1.00
|
O
|
C:HOH903
|
1.9
|
48.5
|
1.0
|
O3G
|
C:GNP500
|
1.9
|
48.0
|
0.6
|
O
|
C:HOH904
|
2.0
|
42.5
|
0.6
|
O2B
|
C:GNP500
|
2.1
|
52.6
|
0.5
|
OD2
|
C:ASP393
|
2.2
|
38.5
|
1.0
|
O
|
C:HOH902
|
2.2
|
47.0
|
1.0
|
OD1
|
C:ASP393
|
2.2
|
41.3
|
1.0
|
O3G
|
C:GNP500
|
2.3
|
57.9
|
0.5
|
CG
|
C:ASP393
|
2.5
|
39.7
|
1.0
|
PG
|
C:GNP500
|
3.1
|
48.1
|
0.6
|
O1G
|
C:GNP500
|
3.1
|
48.2
|
0.6
|
PG
|
C:GNP500
|
3.3
|
59.5
|
0.5
|
O1B
|
C:GNP500
|
3.5
|
45.8
|
0.6
|
PB
|
C:GNP500
|
3.5
|
52.6
|
0.5
|
O2G
|
C:GNP500
|
3.5
|
57.9
|
0.5
|
O
|
C:HOH901
|
3.7
|
45.2
|
0.6
|
N3B
|
C:GNP500
|
3.8
|
56.3
|
0.5
|
O
|
C:HOH911
|
4.0
|
59.9
|
1.0
|
MG
|
C:MG700
|
4.0
|
37.1
|
1.0
|
N3B
|
C:GNP500
|
4.0
|
46.2
|
0.6
|
CB
|
C:ASP393
|
4.1
|
37.0
|
1.0
|
OD2
|
C:ASP374
|
4.1
|
42.5
|
1.0
|
O2G
|
C:GNP500
|
4.2
|
47.4
|
0.6
|
O
|
C:HOH1083
|
4.2
|
52.0
|
1.0
|
OD2
|
C:ASP396
|
4.2
|
55.8
|
1.0
|
PB
|
C:GNP500
|
4.2
|
44.7
|
0.6
|
NZ
|
C:LYS226
|
4.3
|
47.4
|
1.0
|
O1B
|
C:GNP500
|
4.3
|
50.9
|
0.5
|
CA
|
C:GLY395
|
4.4
|
48.2
|
1.0
|
N
|
C:GLY395
|
4.5
|
44.2
|
1.0
|
O3A
|
C:GNP500
|
4.6
|
51.5
|
0.5
|
O2A
|
C:GNP500
|
4.6
|
49.7
|
1.0
|
O1G
|
C:GNP500
|
4.6
|
61.4
|
0.5
|
O3A
|
C:GNP500
|
4.7
|
47.7
|
0.6
|
O
|
C:ASP393
|
4.8
|
39.1
|
1.0
|
CE1
|
C:HIS379
|
4.8
|
47.3
|
1.0
|
CA
|
C:ASP393
|
4.9
|
40.4
|
1.0
|
CG
|
C:ASP396
|
4.9
|
51.4
|
1.0
|
C
|
C:GLY395
|
4.9
|
49.9
|
1.0
|
PA
|
C:GNP500
|
4.9
|
49.2
|
1.0
|
NE2
|
C:HIS379
|
4.9
|
47.0
|
1.0
|
O1A
|
C:GNP500
|
4.9
|
49.5
|
1.0
|
O
|
C:HOH951
|
5.0
|
42.6
|
1.0
|
O
|
C:HOH924
|
5.0
|
46.5
|
0.6
|
|
Magnesium binding site 7 out
of 9 in 5iqc
Go back to
Magnesium Binding Sites List in 5iqc
Magnesium binding site 7 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg800
b:64.2
occ:1.00
|
O
|
C:HOH1636
|
2.2
|
38.5
|
1.0
|
OD1
|
C:ASN385
|
2.2
|
62.2
|
1.0
|
O
|
C:HOH1637
|
2.3
|
37.0
|
1.0
|
CG
|
C:ASN385
|
3.2
|
60.8
|
1.0
|
ND2
|
C:ASN385
|
3.6
|
60.6
|
1.0
|
O
|
C:GLY384
|
4.4
|
69.4
|
1.0
|
C
|
C:GLY384
|
4.4
|
62.1
|
1.0
|
N
|
C:ASN385
|
4.5
|
63.0
|
1.0
|
CB
|
C:ASN385
|
4.6
|
59.4
|
1.0
|
CA
|
C:ASN385
|
4.8
|
62.0
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 5iqc
Go back to
Magnesium Binding Sites List in 5iqc
Magnesium binding site 8 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg700
b:38.9
occ:1.00
|
O2G
|
D:GNP500
|
1.6
|
53.7
|
1.0
|
O2A
|
D:GNP500
|
1.7
|
51.2
|
1.0
|
O
|
D:HOH900
|
1.8
|
50.1
|
1.0
|
NE2
|
D:HIS379
|
2.1
|
52.2
|
1.0
|
OD2
|
D:ASP393
|
2.2
|
48.0
|
1.0
|
PG
|
D:GNP500
|
2.9
|
62.0
|
1.0
|
CE1
|
D:HIS379
|
3.1
|
54.3
|
1.0
|
CD2
|
D:HIS379
|
3.1
|
53.1
|
1.0
|
PA
|
D:GNP500
|
3.1
|
51.1
|
1.0
|
N3B
|
D:GNP500
|
3.1
|
54.8
|
1.0
|
CG
|
D:ASP393
|
3.1
|
47.5
|
1.0
|
CB
|
D:ASP393
|
3.5
|
47.9
|
1.0
|
O1G
|
D:GNP500
|
3.6
|
61.9
|
1.0
|
O
|
D:HOH925
|
3.7
|
46.6
|
1.0
|
O3A
|
D:GNP500
|
3.8
|
54.3
|
1.0
|
PB
|
D:GNP500
|
3.9
|
55.2
|
1.0
|
O1A
|
D:GNP500
|
3.9
|
48.2
|
1.0
|
MG
|
D:MG702
|
4.0
|
67.3
|
1.0
|
O1B
|
D:GNP500
|
4.0
|
59.9
|
1.0
|
O3G
|
D:GNP500
|
4.1
|
57.4
|
1.0
|
ND1
|
D:HIS379
|
4.1
|
55.0
|
1.0
|
CG
|
D:HIS379
|
4.2
|
51.5
|
1.0
|
O5'
|
D:GNP500
|
4.2
|
53.3
|
1.0
|
OD1
|
D:ASP393
|
4.3
|
45.4
|
1.0
|
O3'
|
D:GNP500
|
4.3
|
49.1
|
1.0
|
C5'
|
D:GNP500
|
4.5
|
54.5
|
1.0
|
ND2
|
D:ASN378
|
4.6
|
61.2
|
1.0
|
O
|
D:HOH1119
|
4.6
|
44.9
|
1.0
|
O
|
D:HOH902
|
4.7
|
58.7
|
1.0
|
C3'
|
D:GNP500
|
4.7
|
52.8
|
1.0
|
OD2
|
D:ASP374
|
4.9
|
50.4
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 5iqc
Go back to
Magnesium Binding Sites List in 5iqc
Magnesium binding site 9 out
of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg702
b:67.3
occ:1.00
|
O1G
|
D:GNP500
|
1.9
|
61.9
|
1.0
|
O
|
D:HOH903
|
2.0
|
53.4
|
1.0
|
O1B
|
D:GNP500
|
2.1
|
59.9
|
1.0
|
O
|
D:HOH902
|
2.1
|
58.7
|
1.0
|
OD2
|
D:ASP393
|
2.3
|
48.0
|
1.0
|
OD1
|
D:ASP393
|
2.4
|
45.4
|
1.0
|
CG
|
D:ASP393
|
2.6
|
47.5
|
1.0
|
PG
|
D:GNP500
|
3.2
|
62.0
|
1.0
|
PB
|
D:GNP500
|
3.4
|
55.2
|
1.0
|
N3B
|
D:GNP500
|
3.6
|
54.8
|
1.0
|
O2G
|
D:GNP500
|
3.9
|
53.7
|
1.0
|
O
|
D:HOH911
|
3.9
|
49.8
|
1.0
|
MG
|
D:MG700
|
4.0
|
38.9
|
1.0
|
NZ
|
D:LYS226
|
4.1
|
53.9
|
1.0
|
CB
|
D:ASP393
|
4.2
|
47.9
|
1.0
|
O2B
|
D:GNP500
|
4.2
|
61.4
|
1.0
|
O3G
|
D:GNP500
|
4.3
|
57.4
|
1.0
|
OD2
|
D:ASP374
|
4.4
|
50.4
|
1.0
|
OD2
|
D:ASP396
|
4.4
|
55.6
|
1.0
|
O3A
|
D:GNP500
|
4.4
|
54.3
|
1.0
|
O
|
D:HOH909
|
4.5
|
47.6
|
1.0
|
O2A
|
D:GNP500
|
4.5
|
51.2
|
1.0
|
O
|
D:HOH925
|
4.5
|
46.6
|
1.0
|
CA
|
D:GLY395
|
4.5
|
50.5
|
1.0
|
N
|
D:GLY395
|
4.7
|
46.9
|
1.0
|
PA
|
D:GNP500
|
4.8
|
51.1
|
1.0
|
O1A
|
D:GNP500
|
4.8
|
48.2
|
1.0
|
C
|
D:GLY395
|
4.9
|
50.1
|
1.0
|
CG
|
D:ASP396
|
5.0
|
50.0
|
1.0
|
CA
|
D:ASP393
|
5.0
|
46.6
|
1.0
|
O
|
D:ASP393
|
5.0
|
42.4
|
1.0
|
|
Reference:
S.J.Caldwell,
Y.Huang,
A.M.Berghuis.
Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase Aph(2)-Ia. Structure V. 24 935 2016.
ISSN: ISSN 0969-2126
PubMed: 27161980
DOI: 10.1016/J.STR.2016.04.002
Page generated: Sun Sep 29 16:49:21 2024
|