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Magnesium in PDB 5iqd: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin, PDB code: 5iqd 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) 90.26 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.220, 99.670, 93.400, 90.00, 104.90, 90.00
R / Rfree (%) 16.2 / 20.2

Other elements in 5iqd:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

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 Ribostamycin (pdb code 5iqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 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 Ribostamycin, PDB code: 5iqd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5iqd

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Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:35.5
occ:1.00
 O A:HOH900 1.9 37.3 1.0
O2A A:GNP500 2.0 31.7 1.0
OD2 A:ASP393 2.1 30.1 1.0
O A:HOH901 2.1 36.2 1.0
O2B A:GNP500 2.2 37.4 1.0
NE2 A:HIS379 2.3 29.0 1.0
CG A:ASP393 3.1 30.7 1.0
PA A:GNP500 3.2 32.0 1.0
CE1 A:HIS379 3.2 28.2 1.0
O3A A:GNP500 3.3 33.8 1.0
PB A:GNP500 3.3 36.7 1.0
CD2 A:HIS379 3.3 27.5 1.0
CB A:ASP393 3.6 29.5 1.0
MG A:MG702 3.8 37.1 1.0
O1A A:GNP500 4.0 29.9 1.0
O A:HOH924 4.0 40.1 1.0
O1B A:GNP500 4.0 38.0 1.0
O A:HOH904 4.1 37.4 1.0
O A:HOH1221 4.1 37.3 1.0
OD1 A:ASP393 4.2 31.1 1.0
O5' A:GNP500 4.4 32.7 1.0
ND1 A:HIS379 4.4 26.6 1.0
O3G A:GNP500 4.4 35.3 1.0
CG A:HIS379 4.4 26.6 1.0
N3B A:GNP500 4.6 37.3 1.0
C5' A:GNP500 4.7 34.5 1.0
O A:HOH972 4.7 55.9 1.0
O3' A:GNP500 4.8 35.8 1.0
OD2 A:ASP374 4.8 32.1 1.0
ND2 A:ASN378 4.9 45.9 1.0
O A:HOH902 4.9 34.8 1.0

Magnesium binding site 2 out of 8 in 5iqd

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Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:37.1
occ:1.00
 O A:HOH904 2.0 37.4 1.0
O3G A:GNP500 2.0 35.3 1.0
OD2 A:ASP393 2.1 30.1 1.0
OD1 A:ASP393 2.1 31.1 1.0
O A:HOH903 2.2 33.6 1.0
O A:HOH902 2.2 34.8 1.0
CG A:ASP393 2.4 30.7 1.0
PG A:GNP500 3.3 38.6 1.0
O2B A:GNP500 3.3 37.4 1.0
O A:HOH901 3.5 36.2 1.0
O2G A:GNP500 3.6 40.5 1.0
MG A:MG700 3.8 35.5 1.0
CB A:ASP393 3.9 29.5 1.0
OD2 A:ASP374 4.1 32.1 1.0
N3B A:GNP500 4.1 37.3 1.0
NZ A:LYS226 4.2 38.1 1.0
PB A:GNP500 4.2 36.7 1.0
O A:HOH1083 4.3 46.2 1.0
O3A A:GNP500 4.4 33.8 1.0
CA A:GLY395 4.4 34.6 1.0
O1G A:GNP500 4.4 39.0 1.0
O A:HOH911 4.5 50.3 1.0
N A:GLY395 4.5 32.7 1.0
O A:ASP393 4.6 30.4 1.0
O A:HOH924 4.6 40.1 1.0
CA A:ASP393 4.7 30.8 1.0
OD1 A:ASP396 4.7 40.2 1.0
C A:ASP393 4.8 30.1 1.0
OD2 A:ASP396 4.8 39.9 1.0
O2A A:GNP500 4.8 31.7 1.0
CG A:ASP396 4.9 37.3 1.0
CE1 A:HIS379 4.9 28.2 1.0
O A:HOH951 4.9 27.3 1.0
C A:GLY395 4.9 37.2 1.0
O1A A:GNP500 4.9 29.9 1.0
NE2 A:HIS379 4.9 29.0 1.0
N A:ASP396 4.9 34.3 1.0
PA A:GNP500 5.0 32.0 1.0

Magnesium binding site 3 out of 8 in 5iqd

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Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:30.4
occ:1.00
 O2G B:GNP500 1.7 31.0 0.5
O2A B:GNP500 1.9 29.9 1.0
O B:HOH900 2.0 37.1 1.0
OD2 B:ASP393 2.2 34.0 1.0
NE2 B:HIS379 2.2 30.6 1.0
O2B B:GNP500 2.3 31.2 0.5
O B:HOH901 2.4 28.9 0.5
PG B:GNP500 3.1 32.6 0.5
CD2 B:HIS379 3.1 31.5 1.0
CE1 B:HIS379 3.1 28.2 1.0
CG B:ASP393 3.2 33.3 1.0
PA B:GNP500 3.2 30.6 1.0
N3B B:GNP500 3.5 32.1 0.5
CB B:ASP393 3.6 33.2 1.0
O3A B:GNP500 3.6 31.1 0.5
PB B:GNP500 3.6 31.7 0.5
O3A B:GNP500 3.7 31.1 0.5
O2B B:GNP500 3.7 30.7 0.5
O3G B:GNP500 3.7 32.4 0.5
PB B:GNP500 3.8 31.6 0.5
MG B:MG702 3.9 36.5 1.0
O1A B:GNP500 4.1 29.3 1.0
ND1 B:HIS379 4.2 29.2 1.0
CG B:HIS379 4.2 30.4 1.0
O1G B:GNP500 4.2 33.5 0.5
OD1 B:ASP393 4.3 35.5 1.0
O1B B:GNP500 4.3 33.6 0.5
O5' B:GNP500 4.3 32.3 1.0
O3' B:GNP500 4.4 36.6 1.0
O B:HOH904 4.6 42.5 0.5
C5' B:GNP500 4.6 34.3 1.0
ND2 B:ASN378 4.7 44.4 1.0
O B:HOH902 4.8 39.0 1.0
O3G B:GNP500 4.9 31.9 0.5
OD2 B:ASP374 4.9 30.6 1.0
C3' B:GNP500 4.9 35.1 1.0
N3B B:GNP500 4.9 32.5 0.5
O B:HOH924 5.0 35.2 0.5

Magnesium binding site 4 out of 8 in 5iqd

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Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:36.5
occ:1.00
 O3G B:GNP500 1.9 31.9 0.5
O B:HOH904 2.0 42.5 0.5
O2B B:GNP500 2.1 30.7 0.5
O B:HOH903 2.1 37.0 1.0
OD2 B:ASP393 2.1 34.0 1.0
O B:HOH902 2.2 39.0 1.0
OD1 B:ASP393 2.2 35.5 1.0
O3G B:GNP500 2.3 32.4 0.5
CG B:ASP393 2.5 33.3 1.0
PG B:GNP500 3.1 33.0 0.5
O B:HOH901 3.1 28.9 0.5
O2B B:GNP500 3.1 31.2 0.5
O2G B:GNP500 3.3 34.8 0.5
PG B:GNP500 3.5 32.6 0.5
PB B:GNP500 3.6 31.6 0.5
O2G B:GNP500 3.8 31.0 0.5
N3B B:GNP500 3.9 32.5 0.5
N3B B:GNP500 3.9 32.1 0.5
MG B:MG700 3.9 30.4 1.0
PB B:GNP500 4.0 31.7 0.5
CB B:ASP393 4.0 33.2 1.0
NZ B:LYS226 4.2 41.5 1.0
OD2 B:ASP374 4.2 30.6 1.0
O1G B:GNP500 4.3 33.5 0.5
O1B B:GNP500 4.4 32.0 0.5
O3A B:GNP500 4.4 31.1 0.5
CA B:GLY395 4.5 37.6 1.0
O3A B:GNP500 4.5 31.1 0.5
N B:GLY395 4.6 36.0 1.0
O2A B:GNP500 4.7 29.9 1.0
O1G B:GNP500 4.7 33.5 0.5
O B:HOH1083 4.7 49.9 1.0
O B:ASP393 4.8 31.8 1.0
C B:GLY395 4.8 36.5 1.0
PA B:GNP500 4.8 30.6 1.0
OD1 B:ASP396 4.8 46.7 1.0
OD2 B:ASP396 4.8 46.4 1.0
CA B:ASP393 4.8 31.2 1.0
O1A B:GNP500 4.9 29.3 1.0
N B:ASP396 4.9 34.5 1.0
O B:HOH951 4.9 27.4 1.0
CG B:ASP396 4.9 40.0 1.0
CE1 B:HIS379 4.9 28.2 1.0
O B:HOH924 5.0 35.2 0.5
C B:ASP393 5.0 32.0 1.0

Magnesium binding site 5 out of 8 in 5iqd

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Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:34.4
occ:1.00
 O C:HOH900 1.8 37.6 1.0
O2A C:GNP500 1.9 37.8 1.0
O C:HOH901 2.2 39.6 1.0
O2B C:GNP500 2.2 40.6 1.0
OD2 C:ASP393 2.2 29.5 1.0
NE2 C:HIS379 2.3 31.4 1.0
PA C:GNP500 3.2 37.8 1.0
CD2 C:HIS379 3.2 31.0 1.0
CE1 C:HIS379 3.2 30.6 1.0
CG C:ASP393 3.3 30.4 1.0
PB C:GNP500 3.4 41.6 1.0
O3A C:GNP500 3.6 39.2 1.0
O C:HOH1124 3.6 68.7 1.0
CB C:ASP393 3.7 29.8 1.0
O C:HOH924 3.8 45.6 1.0
O1A C:GNP500 4.0 35.9 1.0
O1B C:GNP500 4.0 44.8 1.0
O C:HOH904 4.1 38.9 1.0
MG C:MG702 4.1 38.3 1.0
O C:HOH1221 4.1 45.2 1.0
O5' C:GNP500 4.2 39.4 1.0
O C:HOH1260 4.3 60.0 1.0
OD1 C:ASP393 4.4 31.2 1.0
ND1 C:HIS379 4.4 30.2 1.0
CG C:HIS379 4.4 30.3 1.0
O3G C:GNP500 4.5 38.9 1.0
C5' C:GNP500 4.6 41.0 1.0
O3' C:GNP500 4.6 41.9 1.0
ND2 C:ASN378 4.7 47.6 1.0
N3B C:GNP500 4.7 42.5 1.0
OD2 C:ASP374 4.9 38.0 1.0
C3' C:GNP500 4.9 40.5 1.0

Magnesium binding site 6 out of 8 in 5iqd

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Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:38.3
occ:1.00
 O C:HOH904 1.8 38.9 1.0
O3G C:GNP500 1.9 38.9 1.0
O C:HOH903 2.0 36.2 1.0
OD1 C:ASP393 2.2 31.2 1.0
O C:HOH902 2.2 34.0 1.0
OD2 C:ASP393 2.3 29.5 1.0
CG C:ASP393 2.6 30.4 1.0
PG C:GNP500 3.2 42.5 1.0
O2G C:GNP500 3.3 43.5 1.0
O2B C:GNP500 3.5 40.6 1.0
O C:HOH901 3.7 39.6 1.0
OD2 C:ASP374 4.1 38.0 1.0
CB C:ASP393 4.1 29.8 1.0
O C:HOH1083 4.1 50.4 1.0
MG C:MG700 4.1 34.4 1.0
N3B C:GNP500 4.2 42.5 1.0
NZ C:LYS226 4.2 39.9 1.0
O1G C:GNP500 4.3 42.5 1.0
PB C:GNP500 4.3 41.6 1.0
CA C:GLY395 4.4 40.3 1.0
O C:HOH911 4.4 56.5 1.0
N C:GLY395 4.5 37.3 1.0
OD1 C:ASP396 4.6 46.2 1.0
O3A C:GNP500 4.6 39.2 1.0
O C:ASP393 4.6 29.1 1.0
O C:HOH924 4.7 45.6 1.0
OD2 C:ASP396 4.7 40.4 1.0
CG C:ASP396 4.8 39.9 1.0
O C:HOH951 4.8 32.0 1.0
O2A C:GNP500 4.8 37.8 1.0
CA C:ASP393 4.9 31.0 1.0
C C:GLY395 4.9 40.1 1.0
C C:ASP393 4.9 31.5 1.0
N C:ASP396 4.9 38.6 1.0
O1A C:GNP500 5.0 35.9 1.0
CE1 C:HIS379 5.0 30.6 1.0

Magnesium binding site 7 out of 8 in 5iqd

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Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:31.8
occ:1.00
 O D:HOH901 1.7 51.1 0.3
O2G D:GNP500 1.9 44.4 0.7
O2A D:GNP500 1.9 35.0 1.0
O D:HOH900 2.1 46.0 1.0
NE2 D:HIS379 2.1 38.0 1.0
OD2 D:ASP393 2.3 37.8 1.0
O2B D:GNP500 2.4 39.5 0.3
CE1 D:HIS379 3.1 36.9 1.0
PG D:GNP500 3.1 45.9 0.7
CD2 D:HIS379 3.1 37.4 1.0
N3B D:GNP500 3.2 44.9 0.7
CG D:ASP393 3.3 36.8 1.0
PA D:GNP500 3.3 38.1 1.0
PB D:GNP500 3.5 40.1 0.3
O3G D:GNP500 3.7 46.7 0.7
O3A D:GNP500 3.7 38.5 0.3
CB D:ASP393 3.7 36.0 1.0
PB D:GNP500 3.7 44.4 0.7
O3A D:GNP500 3.8 40.3 0.7
O2B D:GNP500 3.8 41.8 0.7
O D:HOH904 3.9 38.0 0.3
MG D:MG702 4.1 43.5 1.0
O1B D:GNP500 4.1 41.5 0.3
O1A D:GNP500 4.2 35.6 1.0
ND1 D:HIS379 4.2 35.3 1.0
CG D:HIS379 4.2 36.1 1.0
O1G D:GNP500 4.3 48.9 0.7
O3' D:GNP500 4.3 38.0 1.0
O5' D:GNP500 4.3 38.1 1.0
O D:HOH924 4.4 61.7 0.3
OD1 D:ASP393 4.4 38.2 1.0
ND2 D:ASN378 4.5 53.8 1.0
C5' D:GNP500 4.6 39.6 1.0
O D:HOH1119 4.6 53.3 1.0
O3G D:GNP500 4.6 38.7 0.3
C3' D:GNP500 4.8 38.2 1.0
OD2 D:ASP374 4.9 33.0 1.0
N3B D:GNP500 4.9 40.8 0.3
O D:HOH902 5.0 36.2 1.0

Magnesium binding site 8 out of 8 in 5iqd

Go back to Magnesium Binding Sites List in 5iqd
Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin


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 Ribostamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:43.5
occ:1.00
 O3G D:GNP500 1.6 38.7 0.3
O D:HOH904 1.8 38.0 0.3
O D:HOH903 2.0 48.6 1.0
O D:HOH902 2.2 36.2 1.0
OD2 D:ASP393 2.2 37.8 1.0
OD1 D:ASP393 2.2 38.2 1.0
O3G D:GNP500 2.3 46.7 0.7
O2B D:GNP500 2.3 41.8 0.7
CG D:ASP393 2.5 36.8 1.0
PG D:GNP500 3.0 40.4 0.3
O2B D:GNP500 3.1 39.5 0.3
O2G D:GNP500 3.5 42.1 0.3
PG D:GNP500 3.6 45.9 0.7
PB D:GNP500 3.7 44.4 0.7
O D:HOH901 3.7 51.1 0.3
N3B D:GNP500 3.8 40.8 0.3
O2G D:GNP500 3.9 44.4 0.7
PB D:GNP500 3.9 40.1 0.3
O1G D:GNP500 4.0 41.2 0.3
N3B D:GNP500 4.0 44.9 0.7
CB D:ASP393 4.0 36.0 1.0
O D:HOH1299 4.0 59.9 0.7
MG D:MG700 4.1 31.8 1.0
OD2 D:ASP374 4.1 33.0 1.0
NZ D:LYS226 4.2 41.6 1.0
O D:HOH1083 4.3 56.0 1.0
O3A D:GNP500 4.4 38.5 0.3
CA D:GLY395 4.4 36.4 1.0
O1B D:GNP500 4.5 45.3 0.7
N D:GLY395 4.5 38.2 1.0
O2A D:GNP500 4.6 35.0 1.0
OD1 D:ASP396 4.6 49.0 1.0
O3A D:GNP500 4.7 40.3 0.7
C D:GLY395 4.7 37.7 1.0
O D:ASP393 4.7 34.8 1.0
O D:HOH951 4.7 33.7 1.0
OD2 D:ASP396 4.8 51.1 1.0
CG D:ASP396 4.8 45.4 1.0
N D:ASP396 4.8 35.9 1.0
CA D:ASP393 4.8 36.0 1.0
O D:HOH924 4.8 61.7 0.3
O1G D:GNP500 4.8 48.9 0.7
C D:ASP393 4.9 34.4 1.0
O D:HOH909 4.9 34.6 0.7
PA D:GNP500 4.9 38.1 1.0
CE1 D:HIS379 4.9 36.9 1.0
O1A D:GNP500 5.0 35.6 1.0
NE2 D:HIS379 5.0 38.0 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 16:49:29 2024

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