Magnesium in PDB 5iqb: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Kanamycin A
Protein crystallography data
The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Kanamycin A, PDB code: 5iqb
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)
|
90.13 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.430,
99.220,
93.510,
90.00,
105.46,
90.00
|
R / Rfree (%)
|
16.7 /
21.1
|
Other elements in 5iqb:
The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Kanamycin A 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 Kanamycin A
(pdb code 5iqb). 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 Kanamycin A, PDB code: 5iqb:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 5iqb
Go back to
Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg700
b:35.5
occ:1.00
|
O
|
A:HOH900
|
1.9
|
41.6
|
1.0
|
O1A
|
A:GNP500
|
2.0
|
44.6
|
1.0
|
OD2
|
A:ASP393
|
2.1
|
34.1
|
1.0
|
O2G
|
A:GNP500
|
2.1
|
42.8
|
0.2
|
N3B
|
A:GNP500
|
2.2
|
42.2
|
0.2
|
NE2
|
A:HIS379
|
2.2
|
39.8
|
1.0
|
O
|
A:HOH901
|
2.2
|
43.5
|
0.8
|
O1B
|
A:GNP500
|
2.3
|
49.1
|
0.8
|
PG
|
A:GNP500
|
2.6
|
43.1
|
0.2
|
CE1
|
A:HIS379
|
3.0
|
40.4
|
1.0
|
CG
|
A:ASP393
|
3.2
|
35.9
|
1.0
|
PA
|
A:GNP500
|
3.3
|
41.2
|
1.0
|
PB
|
A:GNP500
|
3.3
|
42.5
|
0.2
|
CD2
|
A:HIS379
|
3.3
|
41.9
|
1.0
|
PB
|
A:GNP500
|
3.4
|
46.5
|
0.8
|
O3A
|
A:GNP500
|
3.6
|
42.3
|
0.2
|
O3A
|
A:GNP500
|
3.6
|
43.5
|
0.8
|
O2B
|
A:GNP500
|
3.7
|
40.7
|
0.2
|
O1G
|
A:GNP500
|
3.7
|
42.9
|
0.2
|
CB
|
A:ASP393
|
3.7
|
34.4
|
1.0
|
O
|
A:HOH904
|
3.7
|
38.0
|
0.8
|
O3G
|
A:GNP500
|
3.8
|
41.9
|
0.2
|
MG
|
A:MG702
|
3.8
|
46.9
|
1.0
|
O
|
A:HOH1221
|
3.9
|
58.5
|
1.0
|
O2A
|
A:GNP500
|
4.1
|
37.5
|
1.0
|
O2B
|
A:GNP500
|
4.1
|
43.4
|
0.8
|
ND1
|
A:HIS379
|
4.2
|
37.4
|
1.0
|
O
|
A:HOH972
|
4.3
|
57.6
|
1.0
|
OD1
|
A:ASP393
|
4.3
|
35.8
|
1.0
|
CG
|
A:HIS379
|
4.4
|
36.4
|
1.0
|
ND2
|
A:ASN378
|
4.4
|
54.4
|
1.0
|
O5'
|
A:GNP500
|
4.4
|
43.6
|
1.0
|
O3G
|
A:GNP500
|
4.4
|
45.8
|
0.8
|
O3'
|
A:GNP500
|
4.5
|
46.9
|
1.0
|
O1B
|
A:GNP500
|
4.6
|
41.2
|
0.2
|
N3B
|
A:GNP500
|
4.7
|
43.8
|
0.8
|
C5'
|
A:GNP500
|
4.7
|
43.0
|
1.0
|
O
|
A:HOH903
|
4.8
|
42.0
|
1.0
|
OD2
|
A:ASP374
|
4.8
|
46.4
|
1.0
|
O13
|
A:KAN600
|
4.9
|
49.5
|
1.0
|
C3'
|
A:GNP500
|
4.9
|
45.6
|
1.0
|
O
|
A:HOH924
|
5.0
|
49.5
|
0.8
|
|
Magnesium binding site 2 out
of 9 in 5iqb
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Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg702
b:46.9
occ:1.00
|
O
|
A:HOH904
|
1.8
|
38.0
|
0.8
|
O3G
|
A:GNP500
|
1.8
|
45.8
|
0.8
|
O
|
A:HOH902
|
2.0
|
56.7
|
1.0
|
O2B
|
A:GNP500
|
2.1
|
40.7
|
0.2
|
OD2
|
A:ASP393
|
2.2
|
34.1
|
1.0
|
OD1
|
A:ASP393
|
2.2
|
35.8
|
1.0
|
O
|
A:HOH903
|
2.3
|
42.0
|
1.0
|
CG
|
A:ASP393
|
2.4
|
35.9
|
1.0
|
O3G
|
A:GNP500
|
2.8
|
41.9
|
0.2
|
PG
|
A:GNP500
|
3.1
|
45.4
|
0.8
|
O1G
|
A:GNP500
|
3.3
|
49.0
|
0.8
|
O1B
|
A:GNP500
|
3.4
|
49.1
|
0.8
|
O
|
A:HOH926
|
3.4
|
32.8
|
0.8
|
PB
|
A:GNP500
|
3.4
|
42.5
|
0.2
|
PG
|
A:GNP500
|
3.5
|
43.1
|
0.2
|
O2G
|
A:GNP500
|
3.5
|
42.8
|
0.2
|
N3B
|
A:GNP500
|
3.6
|
42.2
|
0.2
|
MG
|
A:MG700
|
3.8
|
35.5
|
1.0
|
O
|
A:HOH901
|
3.9
|
43.5
|
0.8
|
CB
|
A:ASP393
|
4.0
|
34.4
|
1.0
|
N3B
|
A:GNP500
|
4.0
|
43.8
|
0.8
|
PB
|
A:GNP500
|
4.1
|
46.5
|
0.8
|
OD2
|
A:ASP374
|
4.2
|
46.4
|
1.0
|
O2G
|
A:GNP500
|
4.2
|
50.8
|
0.8
|
O1B
|
A:GNP500
|
4.2
|
41.2
|
0.2
|
O
|
A:HOH909
|
4.3
|
51.9
|
0.2
|
NZ
|
A:LYS226
|
4.3
|
47.6
|
1.0
|
O3A
|
A:GNP500
|
4.4
|
43.5
|
0.8
|
CA
|
A:GLY395
|
4.4
|
39.7
|
1.0
|
O3A
|
A:GNP500
|
4.4
|
42.3
|
0.2
|
N4
|
A:KAN600
|
4.5
|
50.9
|
1.0
|
N
|
A:GLY395
|
4.5
|
38.7
|
1.0
|
O1A
|
A:GNP500
|
4.6
|
44.6
|
1.0
|
O2A
|
A:GNP500
|
4.7
|
37.5
|
1.0
|
OD1
|
A:ASP396
|
4.7
|
49.1
|
1.0
|
CA
|
A:ASP393
|
4.7
|
35.0
|
1.0
|
O
|
A:ASP393
|
4.8
|
34.8
|
1.0
|
CE1
|
A:HIS379
|
4.8
|
40.4
|
1.0
|
PA
|
A:GNP500
|
4.9
|
41.2
|
1.0
|
O1G
|
A:GNP500
|
4.9
|
42.9
|
0.2
|
C
|
A:GLY395
|
4.9
|
42.6
|
1.0
|
O
|
A:HOH924
|
4.9
|
49.5
|
0.8
|
C
|
A:ASP393
|
4.9
|
36.2
|
1.0
|
O
|
A:HOH951
|
4.9
|
38.5
|
1.0
|
CG
|
A:ASP396
|
4.9
|
45.0
|
1.0
|
OD2
|
A:ASP396
|
4.9
|
47.9
|
1.0
|
NE2
|
A:HIS379
|
4.9
|
39.8
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 5iqb
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Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg700
b:33.2
occ:1.00
|
O
|
B:HOH900
|
1.6
|
39.1
|
1.0
|
O1A
|
B:GNP500
|
1.9
|
40.2
|
1.0
|
O2G
|
B:GNP500
|
2.0
|
45.9
|
0.4
|
O
|
B:HOH901
|
2.0
|
50.5
|
0.6
|
OD2
|
B:ASP393
|
2.1
|
40.3
|
1.0
|
NE2
|
B:HIS379
|
2.2
|
39.2
|
1.0
|
O1B
|
B:GNP500
|
2.4
|
41.6
|
0.6
|
CE1
|
B:HIS379
|
3.0
|
39.7
|
1.0
|
PG
|
B:GNP500
|
3.1
|
48.4
|
0.4
|
CG
|
B:ASP393
|
3.1
|
41.5
|
1.0
|
CD2
|
B:HIS379
|
3.2
|
40.5
|
1.0
|
N3B
|
B:GNP500
|
3.2
|
44.3
|
0.4
|
PA
|
B:GNP500
|
3.2
|
42.0
|
1.0
|
PB
|
B:GNP500
|
3.5
|
42.4
|
0.6
|
CB
|
B:ASP393
|
3.6
|
42.3
|
1.0
|
O3A
|
B:GNP500
|
3.7
|
42.3
|
0.4
|
O2B
|
B:GNP500
|
3.7
|
41.5
|
0.4
|
PB
|
B:GNP500
|
3.7
|
43.0
|
0.4
|
O3A
|
B:GNP500
|
3.7
|
42.3
|
0.6
|
MG
|
B:MG702
|
3.9
|
44.5
|
1.0
|
O2A
|
B:GNP500
|
4.1
|
41.0
|
1.0
|
ND1
|
B:HIS379
|
4.2
|
37.2
|
1.0
|
O3G
|
B:GNP500
|
4.2
|
48.5
|
0.4
|
O1G
|
B:GNP500
|
4.2
|
44.9
|
0.4
|
OD1
|
B:ASP393
|
4.2
|
43.4
|
1.0
|
CG
|
B:HIS379
|
4.2
|
38.1
|
1.0
|
O3'
|
B:GNP500
|
4.3
|
42.9
|
1.0
|
O5'
|
B:GNP500
|
4.3
|
43.5
|
1.0
|
O2B
|
B:GNP500
|
4.3
|
40.9
|
0.6
|
O
|
B:HOH904
|
4.4
|
48.2
|
0.6
|
ND2
|
B:ASN378
|
4.4
|
52.7
|
1.0
|
C5'
|
B:GNP500
|
4.5
|
43.1
|
1.0
|
N3B
|
B:GNP500
|
4.8
|
43.3
|
0.6
|
O
|
B:HOH1260
|
4.8
|
61.4
|
1.0
|
O3G
|
B:GNP500
|
4.8
|
43.4
|
0.6
|
C3'
|
B:GNP500
|
4.8
|
44.5
|
1.0
|
O
|
B:HOH903
|
5.0
|
50.1
|
1.0
|
OD2
|
B:ASP374
|
5.0
|
45.7
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 5iqb
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Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg702
b:44.5
occ:1.00
|
O
|
B:HOH902
|
2.1
|
48.0
|
1.0
|
O3G
|
B:GNP500
|
2.1
|
43.4
|
0.6
|
O
|
B:HOH903
|
2.2
|
50.1
|
1.0
|
OD2
|
B:ASP393
|
2.2
|
40.3
|
1.0
|
O2B
|
B:GNP500
|
2.2
|
41.5
|
0.4
|
OD1
|
B:ASP393
|
2.2
|
43.4
|
1.0
|
O
|
B:HOH904
|
2.3
|
48.2
|
0.6
|
CG
|
B:ASP393
|
2.5
|
41.5
|
1.0
|
O3G
|
B:GNP500
|
2.7
|
48.5
|
0.4
|
PG
|
B:GNP500
|
3.2
|
46.1
|
0.6
|
O2G
|
B:GNP500
|
3.3
|
45.9
|
0.4
|
O1G
|
B:GNP500
|
3.4
|
46.3
|
0.6
|
O
|
B:HOH901
|
3.4
|
50.5
|
0.6
|
O1B
|
B:GNP500
|
3.4
|
41.6
|
0.6
|
PG
|
B:GNP500
|
3.5
|
48.4
|
0.4
|
PB
|
B:GNP500
|
3.7
|
43.0
|
0.4
|
O
|
B:HOH924
|
3.7
|
51.7
|
0.6
|
MG
|
B:MG700
|
3.9
|
33.2
|
1.0
|
N3B
|
B:GNP500
|
4.0
|
44.3
|
0.4
|
N3B
|
B:GNP500
|
4.0
|
43.3
|
0.6
|
CB
|
B:ASP393
|
4.0
|
42.3
|
1.0
|
OD2
|
B:ASP374
|
4.1
|
45.7
|
1.0
|
PB
|
B:GNP500
|
4.2
|
42.4
|
0.6
|
N4
|
B:KAN600
|
4.4
|
58.0
|
1.0
|
CA
|
B:GLY395
|
4.4
|
40.6
|
1.0
|
NZ
|
B:LYS226
|
4.5
|
51.8
|
1.0
|
O2G
|
B:GNP500
|
4.5
|
49.1
|
0.6
|
N
|
B:GLY395
|
4.6
|
39.7
|
1.0
|
O1B
|
B:GNP500
|
4.6
|
41.5
|
0.4
|
OD1
|
B:ASP396
|
4.6
|
55.1
|
1.0
|
O3A
|
B:GNP500
|
4.6
|
42.3
|
0.4
|
O1G
|
B:GNP500
|
4.7
|
44.9
|
0.4
|
O3A
|
B:GNP500
|
4.7
|
42.3
|
0.6
|
O
|
B:ASP393
|
4.7
|
40.7
|
1.0
|
OD2
|
B:ASP396
|
4.7
|
57.8
|
1.0
|
O1A
|
B:GNP500
|
4.7
|
40.2
|
1.0
|
CE1
|
B:HIS379
|
4.7
|
39.7
|
1.0
|
CG
|
B:ASP396
|
4.7
|
48.6
|
1.0
|
C
|
B:GLY395
|
4.7
|
44.1
|
1.0
|
O
|
B:HOH951
|
4.8
|
36.1
|
1.0
|
O13
|
B:KAN600
|
4.8
|
54.1
|
1.0
|
CA
|
B:ASP393
|
4.8
|
39.6
|
1.0
|
N
|
B:ASP396
|
4.9
|
41.6
|
1.0
|
NE2
|
B:HIS379
|
4.9
|
39.2
|
1.0
|
C
|
B:ASP393
|
5.0
|
39.0
|
1.0
|
O2A
|
B:GNP500
|
5.0
|
41.0
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 5iqb
Go back to
Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg700
b:37.2
occ:1.00
|
O
|
C:HOH900
|
1.8
|
41.3
|
1.0
|
O1A
|
C:GNP500
|
1.8
|
43.5
|
1.0
|
O2G
|
C:GNP500
|
1.8
|
51.6
|
0.3
|
O
|
C:HOH901
|
2.0
|
54.9
|
0.7
|
OD2
|
C:ASP393
|
2.1
|
41.8
|
1.0
|
NE2
|
C:HIS379
|
2.2
|
39.3
|
1.0
|
O1B
|
C:GNP500
|
2.3
|
39.6
|
0.7
|
N3B
|
C:GNP500
|
2.7
|
49.0
|
0.3
|
PG
|
C:GNP500
|
2.7
|
51.7
|
0.3
|
CE1
|
C:HIS379
|
3.1
|
38.7
|
1.0
|
PA
|
C:GNP500
|
3.1
|
48.0
|
1.0
|
CG
|
C:ASP393
|
3.2
|
42.7
|
1.0
|
CD2
|
C:HIS379
|
3.2
|
39.8
|
1.0
|
PB
|
C:GNP500
|
3.4
|
44.6
|
0.7
|
O2B
|
C:GNP500
|
3.5
|
47.7
|
0.3
|
PB
|
C:GNP500
|
3.5
|
49.0
|
0.3
|
O3A
|
C:GNP500
|
3.6
|
47.6
|
0.3
|
O3A
|
C:GNP500
|
3.6
|
45.9
|
0.7
|
CB
|
C:ASP393
|
3.7
|
40.0
|
1.0
|
O1G
|
C:GNP500
|
3.8
|
52.6
|
0.3
|
MG
|
C:MG702
|
3.8
|
49.1
|
1.0
|
O
|
C:HOH904
|
3.8
|
48.6
|
0.7
|
O2A
|
C:GNP500
|
3.9
|
45.0
|
1.0
|
O3G
|
C:GNP500
|
3.9
|
51.1
|
0.3
|
O2B
|
C:GNP500
|
4.1
|
42.9
|
0.7
|
ND1
|
C:HIS379
|
4.2
|
39.1
|
1.0
|
OD1
|
C:ASP393
|
4.3
|
43.6
|
1.0
|
O5'
|
C:GNP500
|
4.3
|
48.0
|
1.0
|
CG
|
C:HIS379
|
4.3
|
38.7
|
1.0
|
O
|
C:HOH924
|
4.4
|
60.5
|
0.7
|
ND2
|
C:ASN378
|
4.5
|
56.6
|
1.0
|
O3'
|
C:GNP500
|
4.5
|
54.5
|
1.0
|
O3G
|
C:GNP500
|
4.5
|
48.1
|
0.7
|
O
|
C:HOH1260
|
4.6
|
61.2
|
1.0
|
C5'
|
C:GNP500
|
4.7
|
45.9
|
1.0
|
N3B
|
C:GNP500
|
4.7
|
44.5
|
0.7
|
C3'
|
C:GNP500
|
4.9
|
51.2
|
1.0
|
O1B
|
C:GNP500
|
4.9
|
45.8
|
0.3
|
OD2
|
C:ASP374
|
5.0
|
43.8
|
1.0
|
O
|
C:HOH903
|
5.0
|
47.8
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 5iqb
Go back to
Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:49.1
occ:1.00
|
O3G
|
C:GNP500
|
1.8
|
48.1
|
0.7
|
O
|
C:HOH904
|
1.8
|
48.6
|
0.7
|
O
|
C:HOH902
|
1.9
|
45.3
|
1.0
|
O2B
|
C:GNP500
|
2.1
|
47.7
|
0.3
|
OD2
|
C:ASP393
|
2.1
|
41.8
|
1.0
|
OD1
|
C:ASP393
|
2.3
|
43.6
|
1.0
|
O
|
C:HOH903
|
2.3
|
47.8
|
1.0
|
O3G
|
C:GNP500
|
2.5
|
51.1
|
0.3
|
CG
|
C:ASP393
|
2.5
|
42.7
|
1.0
|
PG
|
C:GNP500
|
3.1
|
46.4
|
0.7
|
O1B
|
C:GNP500
|
3.2
|
39.6
|
0.7
|
O1G
|
C:GNP500
|
3.2
|
47.5
|
0.7
|
O2G
|
C:GNP500
|
3.2
|
51.6
|
0.3
|
PG
|
C:GNP500
|
3.2
|
51.7
|
0.3
|
PB
|
C:GNP500
|
3.5
|
49.0
|
0.3
|
O
|
C:HOH901
|
3.6
|
54.9
|
0.7
|
N3B
|
C:GNP500
|
3.7
|
49.0
|
0.3
|
MG
|
C:MG700
|
3.8
|
37.2
|
1.0
|
N3B
|
C:GNP500
|
3.9
|
44.5
|
0.7
|
PB
|
C:GNP500
|
3.9
|
44.6
|
0.7
|
CB
|
C:ASP393
|
4.1
|
40.0
|
1.0
|
OD2
|
C:ASP374
|
4.2
|
43.8
|
1.0
|
O2G
|
C:GNP500
|
4.3
|
52.6
|
0.7
|
O1B
|
C:GNP500
|
4.3
|
45.8
|
0.3
|
NZ
|
C:LYS226
|
4.3
|
48.7
|
1.0
|
N4
|
C:KAN600
|
4.4
|
68.6
|
1.0
|
O3A
|
C:GNP500
|
4.4
|
45.9
|
0.7
|
O3A
|
C:GNP500
|
4.5
|
47.6
|
0.3
|
O
|
C:HOH924
|
4.6
|
60.5
|
0.7
|
O1G
|
C:GNP500
|
4.6
|
52.6
|
0.3
|
O1A
|
C:GNP500
|
4.6
|
43.5
|
1.0
|
CA
|
C:GLY395
|
4.6
|
51.3
|
1.0
|
N
|
C:GLY395
|
4.7
|
46.5
|
1.0
|
CE1
|
C:HIS379
|
4.7
|
38.7
|
1.0
|
O2A
|
C:GNP500
|
4.7
|
45.0
|
1.0
|
O
|
C:HOH909
|
4.8
|
40.0
|
0.3
|
OD1
|
C:ASP396
|
4.8
|
54.1
|
1.0
|
O
|
C:ASP393
|
4.9
|
39.6
|
1.0
|
NE2
|
C:HIS379
|
4.9
|
39.3
|
1.0
|
PA
|
C:GNP500
|
4.9
|
48.0
|
1.0
|
CA
|
C:ASP393
|
4.9
|
41.6
|
1.0
|
OD2
|
C:ASP396
|
4.9
|
57.5
|
1.0
|
O13
|
C:KAN600
|
5.0
|
65.1
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 5iqb
Go back to
Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg800
b:76.1
occ:1.00
|
O
|
C:HOH1638
|
2.0
|
61.0
|
1.0
|
O
|
C:HOH1636
|
2.2
|
53.2
|
1.0
|
O
|
C:HOH1637
|
2.3
|
74.1
|
1.0
|
OD1
|
C:ASN385
|
2.5
|
86.4
|
1.0
|
CG
|
C:ASN385
|
3.3
|
82.4
|
1.0
|
ND2
|
C:ASN385
|
3.4
|
81.9
|
1.0
|
C
|
C:GLY384
|
4.6
|
77.0
|
1.0
|
N
|
C:ASN385
|
4.7
|
78.0
|
1.0
|
CB
|
C:ASN385
|
4.7
|
79.8
|
1.0
|
O
|
C:GLY384
|
4.8
|
81.2
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 5iqb
Go back to
Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg700
b:36.4
occ:1.00
|
O
|
D:HOH900
|
1.9
|
46.9
|
1.0
|
O1A
|
D:GNP500
|
1.9
|
53.8
|
1.0
|
O
|
D:HOH901
|
2.0
|
36.6
|
0.5
|
OD2
|
D:ASP393
|
2.1
|
54.8
|
1.0
|
NE2
|
D:HIS379
|
2.2
|
53.4
|
1.0
|
O1B
|
D:GNP500
|
2.3
|
51.6
|
0.5
|
N3B
|
D:GNP500
|
2.5
|
56.8
|
0.5
|
O2G
|
D:GNP500
|
2.5
|
57.7
|
0.5
|
CE1
|
D:HIS379
|
2.9
|
51.6
|
1.0
|
PG
|
D:GNP500
|
3.1
|
59.9
|
0.5
|
CG
|
D:ASP393
|
3.2
|
49.9
|
1.0
|
PA
|
D:GNP500
|
3.2
|
54.3
|
1.0
|
CD2
|
D:HIS379
|
3.2
|
49.4
|
1.0
|
PB
|
D:GNP500
|
3.3
|
58.0
|
0.5
|
PB
|
D:GNP500
|
3.5
|
60.2
|
0.5
|
O3A
|
D:GNP500
|
3.6
|
55.6
|
0.5
|
O3A
|
D:GNP500
|
3.6
|
57.1
|
0.5
|
CB
|
D:ASP393
|
3.7
|
49.5
|
1.0
|
O
|
D:HOH1119
|
3.9
|
58.5
|
1.0
|
MG
|
D:MG702
|
3.9
|
47.7
|
1.0
|
O
|
D:HOH904
|
4.0
|
51.5
|
0.5
|
O2B
|
D:GNP500
|
4.0
|
61.0
|
0.5
|
O2A
|
D:GNP500
|
4.0
|
47.5
|
1.0
|
ND1
|
D:HIS379
|
4.1
|
50.6
|
1.0
|
O2B
|
D:GNP500
|
4.1
|
59.6
|
0.5
|
O3G
|
D:GNP500
|
4.1
|
59.2
|
0.5
|
O1G
|
D:GNP500
|
4.2
|
57.7
|
0.5
|
OD1
|
D:ASP393
|
4.3
|
48.9
|
1.0
|
CG
|
D:HIS379
|
4.3
|
50.5
|
1.0
|
O3'
|
D:GNP500
|
4.3
|
47.0
|
1.0
|
O5'
|
D:GNP500
|
4.4
|
56.0
|
1.0
|
ND2
|
D:ASN378
|
4.4
|
62.5
|
1.0
|
O3G
|
D:GNP500
|
4.4
|
53.0
|
0.5
|
O13
|
D:KAN600
|
4.7
|
48.6
|
1.0
|
N3B
|
D:GNP500
|
4.7
|
56.9
|
0.5
|
C5'
|
D:GNP500
|
4.7
|
56.8
|
1.0
|
OD2
|
D:ASP374
|
4.7
|
48.3
|
1.0
|
O1B
|
D:GNP500
|
4.8
|
61.4
|
0.5
|
C3'
|
D:GNP500
|
4.8
|
53.4
|
1.0
|
O
|
D:HOH903
|
4.9
|
42.0
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 5iqb
Go back to
Magnesium Binding Sites List in 5iqb
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 Kanamycin A
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 Kanamycin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg702
b:47.7
occ:1.00
|
O3G
|
D:GNP500
|
1.9
|
53.0
|
0.5
|
O
|
D:HOH904
|
2.0
|
51.5
|
0.5
|
O
|
D:HOH902
|
2.0
|
48.5
|
1.0
|
O
|
D:HOH903
|
2.2
|
42.0
|
1.0
|
OD2
|
D:ASP393
|
2.4
|
54.8
|
1.0
|
O2B
|
D:GNP500
|
2.4
|
61.0
|
0.5
|
O3G
|
D:GNP500
|
2.4
|
59.2
|
0.5
|
OD1
|
D:ASP393
|
2.5
|
48.9
|
1.0
|
CG
|
D:ASP393
|
2.8
|
49.9
|
1.0
|
PG
|
D:GNP500
|
3.0
|
55.8
|
0.5
|
O1G
|
D:GNP500
|
3.0
|
55.0
|
0.5
|
O1B
|
D:GNP500
|
3.3
|
51.6
|
0.5
|
PG
|
D:GNP500
|
3.3
|
59.9
|
0.5
|
N3B
|
D:GNP500
|
3.5
|
56.8
|
0.5
|
PB
|
D:GNP500
|
3.5
|
60.2
|
0.5
|
O2G
|
D:GNP500
|
3.6
|
57.7
|
0.5
|
N3B
|
D:GNP500
|
3.9
|
56.9
|
0.5
|
O
|
D:HOH901
|
3.9
|
36.6
|
0.5
|
MG
|
D:MG700
|
3.9
|
36.4
|
1.0
|
OD2
|
D:ASP374
|
3.9
|
48.3
|
1.0
|
PB
|
D:GNP500
|
3.9
|
58.0
|
0.5
|
N4
|
D:KAN600
|
4.0
|
53.8
|
1.0
|
O2G
|
D:GNP500
|
4.2
|
55.1
|
0.5
|
CB
|
D:ASP393
|
4.3
|
49.5
|
1.0
|
OD1
|
D:ASP396
|
4.3
|
55.8
|
1.0
|
O
|
D:HOH1427
|
4.5
|
68.0
|
1.0
|
O3A
|
D:GNP500
|
4.5
|
55.6
|
0.5
|
O1B
|
D:GNP500
|
4.5
|
61.4
|
0.5
|
OD2
|
D:ASP396
|
4.5
|
54.3
|
1.0
|
O3A
|
D:GNP500
|
4.5
|
57.1
|
0.5
|
CA
|
D:GLY395
|
4.5
|
50.1
|
1.0
|
CG
|
D:ASP396
|
4.6
|
51.4
|
1.0
|
O13
|
D:KAN600
|
4.6
|
48.6
|
1.0
|
O1G
|
D:GNP500
|
4.7
|
57.7
|
0.5
|
NZ
|
D:LYS226
|
4.7
|
51.0
|
1.0
|
N
|
D:GLY395
|
4.7
|
46.9
|
1.0
|
C
|
D:GLY395
|
4.8
|
48.9
|
1.0
|
O1A
|
D:GNP500
|
4.8
|
53.8
|
1.0
|
CE1
|
D:HIS379
|
4.8
|
51.6
|
1.0
|
N
|
D:ASP396
|
4.9
|
48.4
|
1.0
|
O
|
D:HOH951
|
4.9
|
44.9
|
1.0
|
O
|
D:ASP393
|
4.9
|
43.8
|
1.0
|
CG
|
D:ASP374
|
5.0
|
47.8
|
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 16:49:15 2024
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