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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp and Magnesium, PDB code: 5iqa 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) 56.04 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.170, 100.320, 94.060, 90.00, 105.00, 90.00
R / Rfree (%) 16.7 / 20.6

Other elements in 5iqa:

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

Magnesium binding site 1 out of 8 in 5iqa

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

b:33.6
occ:1.00
 O A:HOH900 1.9 31.3 1.0
O1A A:GNP500 2.1 33.1 1.0
O A:HOH901 2.1 36.3 1.0
OD2 A:ASP393 2.1 30.7 1.0
O1B A:GNP500 2.2 39.5 1.0
NE2 A:HIS379 2.2 32.2 1.0
CE1 A:HIS379 3.1 29.6 1.0
CG A:ASP393 3.2 32.4 1.0
PA A:GNP500 3.3 34.9 1.0
CD2 A:HIS379 3.3 31.0 1.0
PB A:GNP500 3.3 37.9 1.0
O3A A:GNP500 3.5 36.1 1.0
CB A:ASP393 3.7 31.1 1.0
MG A:MG702 4.0 37.2 1.0
O A:HOH904 4.0 40.3 1.0
O A:HOH1221 4.1 38.6 1.0
O2B A:GNP500 4.2 40.5 1.0
O2A A:GNP500 4.2 32.8 1.0
ND1 A:HIS379 4.2 30.0 1.0
OD1 A:ASP393 4.3 31.9 1.0
O A:HOH921 4.3 50.0 1.0
CG A:HIS379 4.4 28.6 1.0
O3G A:GNP500 4.4 37.3 1.0
O5' A:GNP500 4.5 35.1 1.0
N3B A:GNP500 4.6 39.5 1.0
OD2 A:ASP374 4.7 39.0 1.0
O A:HOH902 4.8 33.7 1.0
C5' A:GNP500 4.8 36.0 1.0
ND2 A:ASN378 4.9 58.2 1.0

Magnesium binding site 2 out of 8 in 5iqa

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

b:37.2
occ:1.00
 O3G A:GNP500 2.0 37.3 1.0
O A:HOH904 2.1 40.3 1.0
O A:HOH903 2.1 39.5 1.0
OD1 A:ASP393 2.2 31.9 1.0
O A:HOH902 2.3 33.7 1.0
OD2 A:ASP393 2.3 30.7 1.0
CG A:ASP393 2.6 32.4 1.0
PG A:GNP500 3.1 43.9 1.0
O1G A:GNP500 3.2 46.7 1.0
O1B A:GNP500 3.5 39.5 1.0
O A:HOH901 3.8 36.3 1.0
MG A:MG700 4.0 33.6 1.0
N3B A:GNP500 4.0 39.5 1.0
CB A:ASP393 4.1 31.1 1.0
OD2 A:ASP374 4.2 39.0 1.0
NZ A:LYS226 4.2 39.8 1.0
O A:HOH991 4.2 47.9 1.0
O A:HOH1083 4.2 51.2 1.0
PB A:GNP500 4.2 37.9 1.0
O2G A:GNP500 4.3 43.2 1.0
CA A:GLY395 4.3 39.3 1.0
N A:GLY395 4.4 36.5 1.0
OD1 A:ASP396 4.6 46.8 1.0
O3A A:GNP500 4.6 36.1 1.0
O A:ASP393 4.8 29.2 1.0
CG A:ASP396 4.8 40.8 1.0
OD2 A:ASP396 4.8 45.4 1.0
C A:GLY395 4.9 42.4 1.0
CA A:ASP393 4.9 31.9 1.0
O A:HOH951 4.9 29.0 1.0
N A:ASP396 4.9 35.3 1.0
O1A A:GNP500 4.9 33.1 1.0
C A:ASP393 4.9 31.6 1.0

Magnesium binding site 3 out of 8 in 5iqa

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

b:39.5
occ:1.00
 O2G B:GNP500 1.7 38.5 0.3
O B:HOH900 1.8 36.2 1.0
O1A B:GNP500 2.0 37.0 1.0
O B:HOH901 2.1 47.2 0.7
OD2 B:ASP393 2.1 32.7 1.0
O1B B:GNP500 2.2 41.3 0.7
NE2 B:HIS379 2.3 31.2 1.0
PG B:GNP500 2.9 38.7 0.3
CG B:ASP393 3.1 34.0 1.0
PA B:GNP500 3.1 37.9 1.0
CE1 B:HIS379 3.2 29.6 1.0
N3B B:GNP500 3.2 38.5 0.3
CD2 B:HIS379 3.3 33.2 1.0
O B:HOH904 3.4 59.0 0.7
PB B:GNP500 3.4 41.4 0.7
O2B B:GNP500 3.5 36.1 0.3
O3A B:GNP500 3.5 38.3 0.3
O3A B:GNP500 3.6 40.1 0.7
CB B:ASP393 3.6 35.3 1.0
O3G B:GNP500 3.6 37.5 0.3
PB B:GNP500 3.6 37.7 0.3
O2A B:GNP500 3.9 36.9 1.0
O B:HOH1260 4.0 47.9 1.0
MG B:MG702 4.1 48.0 1.0
O2B B:GNP500 4.1 43.8 0.7
O1G B:GNP500 4.1 41.1 0.3
OD1 B:ASP393 4.2 33.9 1.0
ND1 B:HIS379 4.3 30.5 1.0
CG B:HIS379 4.4 30.6 1.0
O5' B:GNP500 4.4 39.4 1.0
C5' B:GNP500 4.7 40.6 1.0
O B:HOH921 4.7 48.7 0.7
N3B B:GNP500 4.7 43.0 0.7
O B:HOH902 4.7 41.9 1.0
O3' B:GNP500 4.8 42.8 1.0
O3G B:GNP500 4.8 41.7 0.7
ND2 B:ASN378 4.9 55.7 1.0
OD2 B:ASP374 4.9 40.8 1.0

Magnesium binding site 4 out of 8 in 5iqa

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

b:48.0
occ:1.00
 O B:HOH904 1.8 59.0 0.7
O3G B:GNP500 1.9 41.7 0.7
O B:HOH903 1.9 44.9 1.0
OD1 B:ASP393 2.3 33.9 1.0
O B:HOH902 2.3 41.9 1.0
OD2 B:ASP393 2.3 32.7 1.0
O2B B:GNP500 2.4 36.1 0.3
O3G B:GNP500 2.5 37.5 0.3
CG B:ASP393 2.6 34.0 1.0
PG B:GNP500 3.1 44.2 0.7
O1G B:GNP500 3.1 44.9 0.7
O B:HOH924 3.3 53.1 0.3
O1B B:GNP500 3.5 41.3 0.7
O B:HOH901 3.7 47.2 0.7
PG B:GNP500 3.8 38.7 0.3
PB B:GNP500 3.8 37.7 0.3
N3B B:GNP500 4.0 43.0 0.7
O B:HOH1083 4.0 59.5 1.0
O B:HOH1299 4.1 66.2 1.0
MG B:MG700 4.1 39.5 1.0
CA B:GLY395 4.2 39.0 1.0
PB B:GNP500 4.2 41.4 0.7
O2G B:GNP500 4.2 38.5 0.3
N3B B:GNP500 4.2 38.5 0.3
CB B:ASP393 4.2 35.3 1.0
NZ B:LYS226 4.3 46.5 1.0
OD2 B:ASP374 4.3 40.8 1.0
O2G B:GNP500 4.4 45.2 0.7
N B:GLY395 4.4 38.0 1.0
OD1 B:ASP396 4.4 54.7 1.0
C B:GLY395 4.5 42.2 1.0
O1B B:GNP500 4.6 39.3 0.3
N B:ASP396 4.6 36.0 1.0
CG B:ASP396 4.6 46.4 1.0
O3A B:GNP500 4.7 40.1 0.7
OD2 B:ASP396 4.7 55.4 1.0
O B:HOH951 4.7 31.7 1.0
O B:ASP393 4.8 35.2 1.0
O B:HOH909 4.8 39.3 0.3
O3A B:GNP500 4.9 38.3 0.3
CA B:ASP393 4.9 34.5 1.0
O1G B:GNP500 5.0 41.1 0.3
O2A B:GNP500 5.0 36.9 1.0
C B:ASP393 5.0 34.4 1.0

Magnesium binding site 5 out of 8 in 5iqa

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

b:36.8
occ:1.00
 O1A C:GNP500 1.9 33.8 1.0
O C:HOH900 2.1 37.5 1.0
OD2 C:ASP393 2.1 38.2 1.0
O1B C:GNP500 2.1 35.8 1.0
O C:HOH901 2.2 33.0 1.0
NE2 C:HIS379 2.3 34.4 1.0
CG C:ASP393 3.1 34.1 1.0
PA C:GNP500 3.1 36.5 1.0
CE1 C:HIS379 3.2 35.7 1.0
PB C:GNP500 3.3 40.6 1.0
CD2 C:HIS379 3.4 34.2 1.0
O3A C:GNP500 3.5 36.3 1.0
CB C:ASP393 3.6 32.5 1.0
MG C:MG702 3.8 38.6 1.0
O2A C:GNP500 3.9 34.7 1.0
O C:HOH921 4.0 46.7 1.0
O C:HOH904 4.0 39.8 1.0
O3G C:GNP500 4.1 40.2 1.0
O C:HOH1260 4.1 44.5 1.0
OD1 C:ASP393 4.2 39.0 1.0
O2B C:GNP500 4.2 39.4 1.0
O C:HOH1221 4.2 48.5 1.0
ND1 C:HIS379 4.3 34.4 1.0
O5' C:GNP500 4.4 36.6 1.0
CG C:HIS379 4.5 34.8 1.0
N3B C:GNP500 4.5 41.1 1.0
OD2 C:ASP374 4.7 40.2 1.0
C5' C:GNP500 4.8 40.6 1.0
O C:HOH902 4.8 32.5 1.0
O3' C:GNP500 4.9 43.9 1.0
PG C:GNP500 4.9 44.2 1.0
ND2 C:ASN378 4.9 54.7 1.0

Magnesium binding site 6 out of 8 in 5iqa

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

b:38.6
occ:1.00
 O3G C:GNP500 1.9 40.2 1.0
O C:HOH904 2.0 39.8 1.0
O C:HOH903 2.1 44.2 1.0
OD2 C:ASP393 2.2 38.2 1.0
O C:HOH902 2.2 32.5 1.0
OD1 C:ASP393 2.3 39.0 1.0
CG C:ASP393 2.6 34.1 1.0
PG C:GNP500 3.1 44.2 1.0
O1G C:GNP500 3.1 45.1 1.0
O1B C:GNP500 3.5 35.8 1.0
O C:HOH901 3.5 33.0 1.0
MG C:MG700 3.8 36.8 1.0
N3B C:GNP500 4.1 41.1 1.0
CB C:ASP393 4.1 32.5 1.0
OD2 C:ASP374 4.2 40.2 1.0
O C:HOH1083 4.2 49.2 1.0
PB C:GNP500 4.2 40.6 1.0
O2G C:GNP500 4.3 45.4 1.0
NZ C:LYS226 4.3 41.0 1.0
CA C:GLY395 4.5 40.6 1.0
N C:GLY395 4.6 36.2 1.0
OD1 C:ASP396 4.6 52.6 1.0
O3A C:GNP500 4.7 36.3 1.0
OD2 C:ASP396 4.8 58.4 1.0
O1A C:GNP500 4.8 33.8 1.0
CG C:ASP396 4.8 50.1 1.0
O C:ASP393 4.8 34.2 1.0
O C:HOH991 4.8 59.5 1.0
CA C:ASP393 4.9 33.1 1.0
O C:HOH951 4.9 37.3 1.0
C C:GLY395 5.0 44.1 1.0
O C:HOH921 5.0 46.7 1.0
O2A C:GNP500 5.0 34.7 1.0

Magnesium binding site 7 out of 8 in 5iqa

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

b:45.9
occ:1.00
 O2G D:GNP500 1.8 54.8 0.5
O1A D:GNP500 1.9 42.1 1.0
O D:HOH901 1.9 55.1 0.5
O D:HOH900 2.1 53.3 1.0
OD2 D:ASP393 2.3 44.8 1.0
NE2 D:HIS379 2.3 44.3 1.0
O1B D:GNP500 2.5 47.9 0.5
PG D:GNP500 2.8 53.5 0.5
N3B D:GNP500 2.8 50.2 0.5
PA D:GNP500 3.1 46.3 1.0
CE1 D:HIS379 3.3 44.9 1.0
CD2 D:HIS379 3.3 42.7 1.0
CG D:ASP393 3.3 42.0 1.0
PB D:GNP500 3.4 48.8 0.5
O3A D:GNP500 3.5 47.4 0.5
PB D:GNP500 3.6 49.0 0.5
O3A D:GNP500 3.6 46.9 0.5
O3G D:GNP500 3.6 57.6 0.5
O2B D:GNP500 3.7 47.5 0.5
CB D:ASP393 3.7 43.8 1.0
O D:HOH904 3.8 51.3 0.5
O1G D:GNP500 3.9 54.6 0.5
O2A D:GNP500 4.0 42.0 1.0
MG D:MG702 4.0 57.1 1.0
O2B D:GNP500 4.3 51.0 0.5
O3' D:GNP500 4.3 49.0 1.0
O5' D:GNP500 4.3 45.6 1.0
ND1 D:HIS379 4.4 42.1 1.0
OD1 D:ASP393 4.4 45.1 1.0
CG D:HIS379 4.4 40.4 1.0
O D:HOH921 4.5 54.8 0.5
C5' D:GNP500 4.5 47.2 1.0
O3G D:GNP500 4.7 59.2 0.5
ND2 D:ASN378 4.7 63.8 1.0
C3' D:GNP500 4.7 45.8 1.0
N3B D:GNP500 4.8 53.4 0.5
OD2 D:ASP374 5.0 48.7 1.0
O D:HOH902 5.0 47.6 1.0
O1B D:GNP500 5.0 50.6 0.5

Magnesium binding site 8 out of 8 in 5iqa

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

b:57.1
occ:1.00
 O3G D:GNP500 1.9 59.2 0.5
O D:HOH904 2.1 51.3 0.5
O D:HOH903 2.1 58.4 1.0
O D:HOH902 2.2 47.6 1.0
O2B D:GNP500 2.2 47.5 0.5
OD2 D:ASP393 2.2 44.8 1.0
O3G D:GNP500 2.3 57.6 0.5
OD1 D:ASP393 2.4 45.1 1.0
CG D:ASP393 2.7 42.0 1.0
PG D:GNP500 3.0 54.9 0.5
O1G D:GNP500 3.0 56.5 0.5
O D:HOH924 3.2 50.1 0.5
O1B D:GNP500 3.3 47.9 0.5
PG D:GNP500 3.5 53.5 0.5
PB D:GNP500 3.5 49.0 0.5
O D:HOH901 3.6 55.1 0.5
O2G D:GNP500 3.8 54.8 0.5
N3B D:GNP500 3.8 50.2 0.5
N3B D:GNP500 3.9 53.4 0.5
PB D:GNP500 4.0 48.8 0.5
O D:HOH911 4.0 41.9 0.5
MG D:MG700 4.0 45.9 1.0
OD2 D:ASP374 4.1 48.7 1.0
CB D:ASP393 4.1 43.8 1.0
O2G D:GNP500 4.2 58.8 0.5
O1B D:GNP500 4.3 50.6 0.5
O3A D:GNP500 4.4 47.4 0.5
NZ D:LYS226 4.4 51.7 1.0
O3A D:GNP500 4.6 46.9 0.5
CA D:GLY395 4.6 43.3 1.0
OD1 D:ASP396 4.6 62.5 1.0
O D:HOH921 4.6 54.8 0.5
OD2 D:ASP396 4.7 62.4 1.0
O1G D:GNP500 4.7 54.6 0.5
N D:GLY395 4.7 44.0 1.0
CG D:ASP396 4.7 55.3 1.0
O1A D:GNP500 4.8 42.1 1.0
C D:GLY395 4.8 45.5 1.0
N D:ASP396 4.9 47.5 1.0
O D:ASP393 4.9 38.3 1.0
O2A D:GNP500 5.0 42.0 1.0
CE1 D:HIS379 5.0 44.9 1.0
O D:HOH951 5.0 37.3 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 16:48:51 2024

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