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Magnesium in PDB 5iqi: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant in Complex with Gmppnp and Magnesium

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant in Complex with Gmppnp and Magnesium, PDB code: 5iqi 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) 89.76 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.169, 99.740, 92.970, 90.00, 105.10, 90.00
R / Rfree (%) 16.7 / 21.1

Other elements in 5iqi:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant in Complex with Gmppnp and Magnesium 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) Y237F Mutant in Complex with Gmppnp and Magnesium (pdb code 5iqi). 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) Y237F Mutant in Complex with Gmppnp and Magnesium, PDB code: 5iqi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5iqi

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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) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:36.7
occ:1.00
 O A:HOH901 1.9 38.1 1.0
O A:HOH900 2.0 35.8 1.0
OD2 A:ASP393 2.0 31.3 1.0
O1A A:GNP500 2.1 38.2 1.0
O1B A:GNP500 2.2 46.3 1.0
NE2 A:HIS379 2.3 29.8 1.0
CG A:ASP393 3.1 31.2 1.0
CE1 A:HIS379 3.1 29.4 1.0
PB A:GNP500 3.2 45.9 1.0
PA A:GNP500 3.2 38.0 1.0
CD2 A:HIS379 3.3 28.9 1.0
O3A A:GNP500 3.5 41.9 1.0
O A:HOH904 3.6 63.3 1.0
CB A:ASP393 3.6 29.8 1.0
O A:HOH1221 3.6 65.6 1.0
MG A:MG702 3.7 52.9 1.0
O2B A:GNP500 4.1 48.8 1.0
O2A A:GNP500 4.2 36.6 1.0
OD1 A:ASP393 4.2 29.9 1.0
ND1 A:HIS379 4.3 28.7 1.0
O5' A:GNP500 4.3 39.0 1.0
CG A:HIS379 4.4 27.4 1.0
O3G A:GNP500 4.5 45.6 0.5
O A:HOH1287 4.5 71.3 1.0
O3' A:GNP500 4.6 39.3 1.0
N3B A:GNP500 4.7 47.7 1.0
O A:HOH902 4.7 42.4 1.0
ND2 A:ASN378 4.7 52.2 1.0
C5' A:GNP500 4.7 38.8 1.0
OD2 A:ASP374 4.8 35.8 1.0
C3' A:GNP500 4.9 37.8 1.0

Magnesium binding site 2 out of 8 in 5iqi

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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) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:52.9
occ:1.00
 O3G A:GNP500 1.7 45.6 0.5
O A:HOH903 1.9 51.0 1.0
O A:HOH904 2.0 63.3 1.0
OD2 A:ASP393 2.1 31.3 1.0
OD1 A:ASP393 2.3 29.9 1.0
O A:HOH902 2.3 42.4 1.0
CG A:ASP393 2.5 31.2 1.0
PG A:GNP500 2.7 50.4 0.5
O1G A:GNP500 2.8 50.0 0.5
O1B A:GNP500 3.3 46.3 1.0
PB A:GNP500 3.5 45.9 1.0
N3B A:GNP500 3.6 47.7 1.0
MG A:MG700 3.7 36.7 1.0
O A:HOH1705 3.8 47.3 1.0
O A:HOH901 3.9 38.1 1.0
CB A:ASP393 4.0 29.8 1.0
O A:HOH1083 4.1 72.3 1.0
NZ A:LYS226 4.1 42.2 1.0
O2G A:GNP500 4.2 48.5 0.5
O3A A:GNP500 4.2 41.9 1.0
OD2 A:ASP374 4.3 35.8 1.0
CA A:GLY395 4.4 35.7 1.0
N A:GLY395 4.6 32.2 1.0
O1A A:GNP500 4.7 38.2 1.0
PA A:GNP500 4.7 38.0 1.0
O2A A:GNP500 4.7 36.6 1.0
OD2 A:ASP396 4.7 47.6 1.0
CA A:ASP393 4.8 31.6 1.0
O A:ASP393 4.8 30.0 1.0
C A:GLY395 4.9 39.8 1.0
O2B A:GNP500 5.0 48.8 1.0
C A:ASP393 5.0 31.2 1.0

Magnesium binding site 3 out of 8 in 5iqi

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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) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:33.8
occ:1.00
 O B:HOH900 2.0 32.8 1.0
OD2 B:ASP393 2.0 36.2 1.0
O1A B:GNP500 2.1 36.0 1.0
O2G B:GNP500 2.1 45.8 0.5
O B:HOH901 2.2 29.8 0.5
N3B B:GNP500 2.3 43.7 1.0
NE2 B:HIS379 2.4 30.5 1.0
PG B:GNP500 2.7 47.6 0.5
CG B:ASP393 3.1 35.6 1.0
PA B:GNP500 3.2 37.9 1.0
CE1 B:HIS379 3.2 27.8 1.0
PB B:GNP500 3.3 45.6 1.0
CD2 B:HIS379 3.4 31.0 1.0
CB B:ASP393 3.6 35.9 1.0
O3A B:GNP500 3.6 42.6 1.0
O3G B:GNP500 3.7 47.0 0.5
MG B:MG702 3.7 48.6 1.0
O B:HOH904 3.7 38.3 0.5
O2B B:GNP500 3.8 46.2 1.0
O1G B:GNP500 4.0 46.1 0.5
O2A B:GNP500 4.1 38.3 1.0
OD1 B:ASP393 4.2 34.6 1.0
ND1 B:HIS379 4.3 28.0 1.0
O B:HOH1260 4.3 42.1 1.0
O5' B:GNP500 4.4 36.9 1.0
CG B:HIS379 4.4 29.0 1.0
C5' B:GNP500 4.5 35.9 1.0
O3' B:GNP500 4.5 35.7 1.0
O1B B:GNP500 4.6 47.9 1.0
O B:HOH902 4.6 35.3 1.0
O B:HOH921 4.7 43.7 0.5
ND2 B:ASN378 4.7 44.5 1.0
OD2 B:ASP374 4.8 31.7 1.0
C3' B:GNP500 4.9 35.6 1.0

Magnesium binding site 4 out of 8 in 5iqi

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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) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:48.6
occ:1.00
 O B:HOH904 1.9 38.3 0.5
O3G B:GNP500 2.0 47.0 0.5
O B:HOH902 2.0 35.3 1.0
OD2 B:ASP393 2.1 36.2 1.0
O B:HOH903 2.1 43.1 1.0
OD1 B:ASP393 2.2 34.6 1.0
O2B B:GNP500 2.3 46.2 1.0
CG B:ASP393 2.4 35.6 1.0
PG B:GNP500 3.1 47.6 0.5
O2G B:GNP500 3.5 45.8 0.5
PB B:GNP500 3.5 45.6 1.0
MG B:MG700 3.7 33.8 1.0
N3B B:GNP500 3.8 43.7 1.0
CB B:ASP393 4.0 35.9 1.0
OD2 B:ASP374 4.1 31.7 1.0
O B:HOH901 4.2 29.8 0.5
CA B:GLY395 4.3 32.9 1.0
NZ B:LYS226 4.4 46.8 1.0
O1G B:GNP500 4.4 46.1 0.5
O3A B:GNP500 4.5 42.6 1.0
OD2 B:ASP396 4.5 46.8 1.0
N B:GLY395 4.5 32.7 1.0
O1B B:GNP500 4.5 47.9 1.0
O B:ASP393 4.7 32.6 1.0
C B:GLY395 4.7 33.2 1.0
CG B:ASP396 4.8 42.6 1.0
CA B:ASP393 4.8 33.2 1.0
O1A B:GNP500 4.8 36.0 1.0
PA B:GNP500 4.9 37.9 1.0
O2A B:GNP500 4.9 38.3 1.0
OD1 B:ASP396 4.9 52.5 1.0
CE1 B:HIS379 4.9 27.8 1.0
N B:ASP396 4.9 31.3 1.0
C B:ASP393 4.9 32.8 1.0
O B:HOH951 4.9 26.4 1.0

Magnesium binding site 5 out of 8 in 5iqi

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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) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:38.5
occ:1.00
 O1A C:GNP500 1.8 35.2 1.0
O C:HOH900 1.9 38.9 1.0
O C:HOH901 2.0 34.4 1.0
OD2 C:ASP393 2.1 33.5 1.0
NE2 C:HIS379 2.3 30.4 1.0
O1B C:GNP500 2.3 42.5 1.0
PA C:GNP500 3.1 36.4 1.0
CG C:ASP393 3.1 34.2 1.0
CE1 C:HIS379 3.2 29.4 1.0
CD2 C:HIS379 3.2 29.8 1.0
PB C:GNP500 3.3 43.9 1.0
CB C:ASP393 3.6 32.8 1.0
O3A C:GNP500 3.6 38.4 1.0
O C:HOH921 3.8 55.1 1.0
MG C:MG702 4.0 50.0 1.0
O2A C:GNP500 4.0 35.9 1.0
O C:HOH904 4.0 52.0 1.0
O2B C:GNP500 4.1 49.3 1.0
O3G C:GNP500 4.2 44.2 0.5
OD1 C:ASP393 4.2 35.1 1.0
O C:HOH1260 4.2 40.7 1.0
O5' C:GNP500 4.3 36.8 1.0
ND1 C:HIS379 4.3 28.9 1.0
CG C:HIS379 4.4 28.8 1.0
O3' C:GNP500 4.6 41.2 1.0
ND2 C:ASN378 4.6 48.4 1.0
C5' C:GNP500 4.6 38.4 1.0
O C:HOH1221 4.8 62.7 1.0
N3B C:GNP500 4.8 46.9 1.0
OD2 C:ASP374 4.9 37.9 1.0
C3' C:GNP500 4.9 38.7 1.0
O C:HOH902 5.0 38.0 1.0

Magnesium binding site 6 out of 8 in 5iqi

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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) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:50.0
occ:1.00
 O3G C:GNP500 1.7 44.2 0.5
O C:HOH903 1.8 57.1 1.0
O C:HOH904 2.0 52.0 1.0
OD2 C:ASP393 2.3 33.5 1.0
OD1 C:ASP393 2.3 35.1 1.0
O C:HOH902 2.4 38.0 1.0
CG C:ASP393 2.6 34.2 1.0
PG C:GNP500 2.8 50.0 0.5
O1G C:GNP500 2.9 51.1 0.5
O1B C:GNP500 3.3 42.5 1.0
PB C:GNP500 3.8 43.9 1.0
O C:HOH901 3.9 34.4 1.0
N3B C:GNP500 3.9 46.9 1.0
MG C:MG700 4.0 38.5 1.0
O2G C:GNP500 4.0 52.5 0.5
CB C:ASP393 4.1 32.8 1.0
OD2 C:ASP374 4.3 37.9 1.0
CA C:GLY395 4.3 37.3 1.0
NZ C:LYS226 4.3 41.5 1.0
O C:HOH1083 4.3 55.3 1.0
O C:HOH921 4.4 55.1 1.0
O3A C:GNP500 4.5 38.4 1.0
N C:GLY395 4.5 35.0 1.0
OD2 C:ASP396 4.6 47.7 1.0
C C:GLY395 4.8 38.6 1.0
O1A C:GNP500 4.8 35.2 1.0
O C:ASP393 4.8 34.8 1.0
CA C:ASP393 4.9 34.1 1.0
PA C:GNP500 4.9 36.4 1.0
OD1 C:ASP396 4.9 53.7 1.0
CG C:ASP396 4.9 42.7 1.0
O2A C:GNP500 4.9 35.9 1.0
C C:ASP393 5.0 34.1 1.0

Magnesium binding site 7 out of 8 in 5iqi

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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) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:35.6
occ:1.00
 O D:HOH901 1.8 33.1 0.5
O1A D:GNP500 2.0 39.5 1.0
O D:HOH900 2.0 38.5 1.0
OD2 D:ASP393 2.2 40.4 1.0
O2G D:GNP500 2.2 53.3 0.5
N3B D:GNP500 2.3 48.9 1.0
NE2 D:HIS379 2.3 37.4 1.0
PG D:GNP500 2.7 56.4 0.5
CE1 D:HIS379 3.2 36.4 1.0
PA D:GNP500 3.2 42.0 1.0
CG D:ASP393 3.2 39.4 1.0
CD2 D:HIS379 3.3 36.2 1.0
PB D:GNP500 3.3 52.7 1.0
O3A D:GNP500 3.6 47.1 1.0
CB D:ASP393 3.6 38.9 1.0
O3G D:GNP500 3.7 56.1 0.5
MG D:MG702 3.8 50.0 1.0
O1G D:GNP500 3.9 57.0 0.5
O2B D:GNP500 3.9 52.2 1.0
O D:HOH904 4.2 63.7 0.5
O2A D:GNP500 4.3 41.4 1.0
O3' D:GNP500 4.3 38.2 1.0
ND1 D:HIS379 4.3 33.9 1.0
O D:HOH1119 4.3 55.1 1.0
O5' D:GNP500 4.3 41.8 1.0
OD1 D:ASP393 4.3 39.6 1.0
CG D:HIS379 4.4 35.6 1.0
O D:HOH921 4.5 43.9 0.5
C5' D:GNP500 4.5 41.0 1.0
ND2 D:ASN378 4.5 51.6 1.0
O D:HOH902 4.6 40.3 1.0
O1B D:GNP500 4.6 50.6 1.0
C3' D:GNP500 4.8 38.9 1.0
OD2 D:ASP374 4.8 38.2 1.0

Magnesium binding site 8 out of 8 in 5iqi

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Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant in Complex with Gmppnp and Magnesium


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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:50.0
occ:1.00
 OD2 D:ASP393 2.1 40.4 1.0
O3G D:GNP500 2.1 56.1 0.5
O2B D:GNP500 2.1 52.2 1.0
O D:HOH902 2.1 40.3 1.0
O D:HOH903 2.2 46.1 1.0
OD1 D:ASP393 2.2 39.6 1.0
O D:HOH904 2.4 63.7 0.5
CG D:ASP393 2.4 39.4 1.0
PG D:GNP500 3.1 56.4 0.5
PB D:GNP500 3.3 52.7 1.0
N3B D:GNP500 3.5 48.9 1.0
O2G D:GNP500 3.6 53.3 0.5
O D:HOH1083 3.6 69.4 1.0
MG D:MG700 3.8 35.6 1.0
O D:HOH911 3.9 34.0 0.5
CB D:ASP393 3.9 38.9 1.0
O D:HOH901 4.0 33.1 0.5
NZ D:LYS226 4.2 49.2 1.0
OD2 D:ASP374 4.3 38.2 1.0
O1B D:GNP500 4.3 50.6 1.0
O3A D:GNP500 4.3 47.1 1.0
O1G D:GNP500 4.5 57.0 0.5
CA D:GLY395 4.5 36.3 1.0
O1A D:GNP500 4.5 39.5 1.0
O D:HOH1501 4.6 60.3 1.0
N D:GLY395 4.6 35.9 1.0
PA D:GNP500 4.7 42.0 1.0
OD2 D:ASP396 4.7 50.2 1.0
CA D:ASP393 4.8 37.0 1.0
O D:ASP393 4.8 33.5 1.0
O2A D:GNP500 4.9 41.4 1.0
C D:GLY395 4.9 37.3 1.0
C D:ASP393 5.0 33.5 1.0
O D:HOH921 5.0 43.9 0.5

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 16:53:29 2024

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