Atomistry » Magnesium » PDB 5ims-5iwa » 5iqi
Atomistry »
  Magnesium »
    PDB 5ims-5iwa »
      5iqi »

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

Go back to Magnesium Binding Sites List in 5iqi
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

Go back to Magnesium Binding Sites List in 5iqi
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

Go back to Magnesium Binding Sites List in 5iqi
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

Go back to Magnesium Binding Sites List in 5iqi
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

Go back to Magnesium Binding Sites List in 5iqi
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

Go back to Magnesium Binding Sites List in 5iqi
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

Go back to Magnesium Binding Sites List in 5iqi
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

Go back to Magnesium Binding Sites List in 5iqi
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

Last articles

Ca in 5S5Q
Ca in 5S5P
Ca in 5S5O
Ca in 5S5N
Ca in 5S5M
Ca in 5S5L
Ca in 5S5K
Ca in 5S5J
Ca in 5S5I
Ca in 5S5H
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy