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Magnesium in PDB 6cgd: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin

Enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin

All present enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin:
2.7.1.190;

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin, PDB code: 6cgd 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) 90.74 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.080, 100.220, 93.990, 90.00, 105.12, 90.00
R / Rfree (%) 17.2 / 20.9

Other elements in 6cgd:

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

Magnesium binding site 1 out of 8 in 6cgd

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Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:40.1
occ:1.00
 O A:HOH900 1.9 38.9 1.0
OD2 A:ASP393 2.0 34.8 1.0
O A:HOH901 2.1 41.2 1.0
O1B A:GNP500 2.1 44.2 1.0
O1A A:GNP500 2.1 40.8 1.0
NE2 A:HIS379 2.3 35.3 1.0
CE1 A:HIS379 3.1 34.4 1.0
CG A:ASP393 3.2 34.4 1.0
PA A:GNP500 3.2 38.6 1.0
PB A:GNP500 3.3 41.0 1.0
CD2 A:HIS379 3.4 32.4 1.0
O3A A:GNP500 3.4 38.4 1.0
CB A:ASP393 3.7 33.0 1.0
MG A:MG702 3.9 43.9 1.0
O A:HOH904 3.9 45.7 1.0
O A:HOH1221 4.0 41.7 1.0
N37 A:AKN600 4.1 54.7 0.6
O2A A:GNP500 4.1 35.7 1.0
O2B A:GNP500 4.1 40.8 1.0
OD1 A:ASP393 4.2 34.4 1.0
O A:HOH972 4.2 56.9 1.0
ND1 A:HIS379 4.3 33.3 1.0
O3G A:GNP500 4.3 40.9 1.0
CG A:HIS379 4.4 32.4 1.0
O5' A:GNP500 4.5 39.1 1.0
C38 A:AKN600 4.5 58.9 0.6
N3B A:GNP500 4.6 40.0 1.0
O A:HOH902 4.7 40.5 1.0
C39 A:AKN600 4.7 57.5 0.6
O A:HOH921 4.7 40.8 1.0
ND2 A:ASN378 4.8 66.5 1.0
C5' A:GNP500 4.8 40.2 1.0
O3' A:GNP500 4.8 46.3 1.0
OD2 A:ASP374 4.8 41.8 1.0
PG A:GNP500 5.0 44.9 1.0

Magnesium binding site 2 out of 8 in 6cgd

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Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:43.9
occ:1.00
 OD1 A:ASP393 1.9 34.4 1.0
O A:HOH903 2.1 44.0 1.0
O A:HOH902 2.1 40.5 1.0
O A:HOH904 2.2 45.7 1.0
O3G A:GNP500 2.2 40.9 1.0
OD2 A:ASP393 2.2 34.8 1.0
CG A:ASP393 2.4 34.4 1.0
PG A:GNP500 3.3 44.9 1.0
O A:HOH921 3.6 40.8 1.0
O1G A:GNP500 3.6 43.7 1.0
O1B A:GNP500 3.6 44.2 1.0
O A:HOH901 3.8 41.2 1.0
CB A:ASP393 3.9 33.0 1.0
MG A:MG700 3.9 40.1 1.0
NZ A:LYS226 4.1 37.8 1.0
N25 A:AKN600 4.2 53.4 0.6
OD2 A:ASP374 4.2 41.8 1.0
CA A:GLY395 4.2 38.0 1.0
N A:GLY395 4.2 37.8 1.0
N3B A:GNP500 4.3 40.0 1.0
PB A:GNP500 4.4 41.0 1.0
O A:ASP393 4.4 34.3 1.0
OD1 A:ASP396 4.5 44.5 1.0
O A:HOH991 4.5 52.2 1.0
O2G A:GNP500 4.6 46.1 1.0
O3A A:GNP500 4.6 38.4 1.0
CA A:ASP393 4.6 33.4 1.0
C A:ASP393 4.7 33.9 1.0
O A:HOH951 4.7 30.4 1.0
C A:GLY395 4.7 41.4 1.0
CG A:ASP396 4.8 39.8 1.0
N A:ASP396 4.8 36.9 1.0
CE1 A:HIS379 4.9 34.4 1.0
O1A A:GNP500 4.9 40.8 1.0
OD2 A:ASP396 4.9 40.6 1.0
O2A A:GNP500 5.0 35.7 1.0

Magnesium binding site 3 out of 8 in 6cgd

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Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:36.2
occ:1.00
 O B:HOH900 1.8 34.5 1.0
O2G B:GNP500 2.0 33.8 0.3
O1A B:GNP500 2.0 33.5 1.0
OD2 B:ASP393 2.1 37.4 1.0
O B:HOH901 2.2 38.6 0.7
NE2 B:HIS379 2.2 34.0 1.0
O1B B:GNP500 2.2 32.7 0.7
CE1 B:HIS379 3.1 31.4 1.0
CG B:ASP393 3.1 38.3 1.0
CD2 B:HIS379 3.2 35.0 1.0
PA B:GNP500 3.2 35.7 1.0
PG B:GNP500 3.3 35.3 0.3
N3B B:GNP500 3.3 35.2 0.3
PB B:GNP500 3.5 37.0 0.7
CB B:ASP393 3.6 38.8 1.0
O3A B:GNP500 3.6 35.2 0.3
O3A B:GNP500 3.6 36.2 0.7
O2B B:GNP500 3.6 32.2 0.3
O B:HOH904 3.6 33.4 0.7
PB B:GNP500 3.7 34.5 0.3
MG B:MG702 3.8 47.2 1.0
O B:HOH1260 3.9 43.4 1.0
O2A B:GNP500 4.1 31.1 1.0
ND1 B:HIS379 4.2 31.6 1.0
O3G B:GNP500 4.2 36.6 0.3
OD1 B:ASP393 4.2 39.8 1.0
O2B B:GNP500 4.2 39.0 0.7
CG B:HIS379 4.3 32.8 1.0
O1G B:GNP500 4.3 35.9 0.3
O5' B:GNP500 4.4 38.5 1.0
C5' B:GNP500 4.6 39.2 1.0
O B:HOH902 4.6 40.7 1.0
O3' B:GNP500 4.7 40.3 1.0
ND2 B:ASN378 4.7 55.1 1.0
N3B B:GNP500 4.7 37.9 0.7
O3G B:GNP500 4.8 37.7 0.7
OD2 B:ASP374 4.9 39.8 1.0
C3' B:GNP500 5.0 39.2 1.0

Magnesium binding site 4 out of 8 in 6cgd

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Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:47.2
occ:1.00
 O B:HOH904 1.8 33.4 0.7
O B:HOH903 2.0 37.2 1.0
O3G B:GNP500 2.1 37.7 0.7
OD2 B:ASP393 2.1 37.4 1.0
O2B B:GNP500 2.2 32.2 0.3
O B:HOH902 2.2 40.7 1.0
OD1 B:ASP393 2.3 39.8 1.0
CG B:ASP393 2.5 38.3 1.0
O1G B:GNP500 3.0 38.0 0.7
PG B:GNP500 3.0 39.5 0.7
O3G B:GNP500 3.0 36.6 0.3
O1B B:GNP500 3.2 32.7 0.7
O B:HOH924 3.4 21.2 0.3
O B:HOH901 3.5 38.6 0.7
O2G B:GNP500 3.6 33.8 0.3
PB B:GNP500 3.6 34.5 0.3
PG B:GNP500 3.7 35.3 0.3
MG B:MG700 3.8 36.2 1.0
N3B B:GNP500 3.8 37.9 0.7
PB B:GNP500 4.0 37.0 0.7
N3B B:GNP500 4.0 35.2 0.3
CB B:ASP393 4.1 38.8 1.0
NZ B:LYS226 4.2 39.5 1.0
OD2 B:ASP374 4.2 39.8 1.0
O3A B:GNP500 4.4 36.2 0.7
CA B:GLY395 4.4 38.7 1.0
O2G B:GNP500 4.4 40.7 0.7
O1B B:GNP500 4.5 33.8 0.3
O3A B:GNP500 4.5 35.2 0.3
O B:HOH1083 4.6 60.4 1.0
N B:GLY395 4.6 37.8 1.0
OD1 B:ASP396 4.6 48.0 1.0
O1A B:GNP500 4.7 33.5 1.0
O B:HOH909 4.8 24.8 0.3
C B:GLY395 4.9 40.6 1.0
O2A B:GNP500 4.9 31.1 1.0
O B:ASP393 4.9 34.9 1.0
CG B:ASP396 4.9 40.3 1.0
PA B:GNP500 4.9 35.7 1.0
CE1 B:HIS379 4.9 31.4 1.0
CA B:ASP393 4.9 35.5 1.0
OD2 B:ASP396 5.0 44.9 1.0

Magnesium binding site 5 out of 8 in 6cgd

Go back to Magnesium Binding Sites List in 6cgd
Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:40.2
occ:1.00
 O C:HOH900 1.9 38.9 1.0
O1A C:GNP500 2.0 36.2 1.0
OD2 C:ASP393 2.1 34.2 1.0
O1B C:GNP500 2.2 37.6 1.0
O C:HOH901 2.3 38.7 1.0
NE2 C:HIS379 2.3 32.0 1.0
PA C:GNP500 3.1 36.3 1.0
CE1 C:HIS379 3.2 30.8 1.0
CG C:ASP393 3.2 33.3 1.0
CD2 C:HIS379 3.3 31.3 1.0
PB C:GNP500 3.3 39.6 1.0
O3A C:GNP500 3.5 37.9 1.0
CB C:ASP393 3.7 32.1 1.0
O C:HOH921 3.8 50.1 1.0
O2A C:GNP500 4.0 37.2 1.0
O C:HOH904 4.0 45.9 1.0
O C:HOH1260 4.0 45.2 1.0
O C:HOH1221 4.1 51.7 1.0
O2B C:GNP500 4.1 37.7 1.0
MG C:MG702 4.2 42.6 1.0
O5' C:GNP500 4.3 41.5 1.0
ND1 C:HIS379 4.3 31.0 1.0
OD1 C:ASP393 4.3 36.0 1.0
O3G C:GNP500 4.4 42.2 1.0
CG C:HIS379 4.4 30.3 1.0
O3' C:GNP500 4.6 46.4 1.0
N3B C:GNP500 4.7 37.9 1.0
ND2 C:ASN378 4.7 62.1 1.0
C5' C:GNP500 4.8 40.4 1.0
O C:HOH902 4.9 32.3 1.0
C3' C:GNP500 4.9 43.0 1.0
OD2 C:ASP374 4.9 39.0 1.0

Magnesium binding site 6 out of 8 in 6cgd

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Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:42.6
occ:1.00
 O C:HOH904 2.0 45.9 1.0
O C:HOH903 2.0 46.5 1.0
O3G C:GNP500 2.0 42.2 1.0
O C:HOH902 2.2 32.3 1.0
OD1 C:ASP393 2.2 36.0 1.0
OD2 C:ASP393 2.4 34.2 1.0
CG C:ASP393 2.7 33.3 1.0
PG C:GNP500 3.1 45.3 1.0
O1G C:GNP500 3.1 45.6 1.0
O1B C:GNP500 3.7 37.6 1.0
O C:HOH901 3.7 38.7 1.0
O C:HOH1083 4.0 46.5 1.0
CB C:ASP393 4.2 32.1 1.0
OD2 C:ASP374 4.2 39.0 1.0
N3B C:GNP500 4.2 37.9 1.0
MG C:MG700 4.2 40.2 1.0
O C:HOH991 4.2 47.7 1.0
NZ C:LYS226 4.2 35.7 1.0
CA C:GLY395 4.3 40.7 1.0
O2G C:GNP500 4.3 44.3 1.0
PB C:GNP500 4.4 39.6 1.0
OD1 C:ASP396 4.4 49.4 1.0
N C:GLY395 4.4 37.1 1.0
CG C:ASP396 4.7 43.8 1.0
O C:ASP393 4.7 34.2 1.0
O3A C:GNP500 4.7 37.9 1.0
OD2 C:ASP396 4.8 46.1 1.0
C C:GLY395 4.8 43.3 1.0
N C:ASP396 4.8 38.4 1.0
CA C:ASP393 4.9 31.7 1.0
O C:HOH951 4.9 35.6 1.0
C C:ASP393 5.0 35.1 1.0

Magnesium binding site 7 out of 8 in 6cgd

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Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:40.5
occ:1.00
 O D:HOH900 1.8 48.1 1.0
O1A D:GNP500 2.0 40.8 1.0
O2G D:GNP500 2.0 50.1 0.5
O D:HOH901 2.1 54.3 0.5
NE2 D:HIS379 2.2 44.3 1.0
OD2 D:ASP393 2.2 45.2 1.0
O1B D:GNP500 2.4 43.5 0.5
N3B D:GNP500 3.0 49.9 0.5
PG D:GNP500 3.1 49.0 0.5
CE1 D:HIS379 3.1 42.5 1.0
CD2 D:HIS379 3.2 42.6 1.0
CG D:ASP393 3.3 45.1 1.0
PA D:GNP500 3.3 44.5 1.0
PB D:GNP500 3.5 47.6 0.5
PB D:GNP500 3.6 50.7 0.5
O3A D:GNP500 3.7 45.8 0.5
O36 D:AKN600 3.7 63.7 0.6
CB D:ASP393 3.7 44.2 1.0
O3A D:GNP500 3.7 46.9 0.5
O2B D:GNP500 3.7 44.8 0.5
O D:HOH904 3.9 35.9 0.5
MG D:MG702 3.9 46.5 1.0
O3G D:GNP500 3.9 51.5 0.5
O2A D:GNP500 4.2 39.0 1.0
ND1 D:HIS379 4.2 41.2 1.0
O1G D:GNP500 4.2 48.6 0.5
CG D:HIS379 4.3 41.8 1.0
O2B D:GNP500 4.3 48.3 0.5
O3' D:GNP500 4.3 47.8 1.0
OD1 D:ASP393 4.3 44.6 1.0
O5' D:GNP500 4.5 47.1 1.0
ND2 D:ASN378 4.5 57.0 1.0
N25 D:AKN600 4.6 72.5 0.6
C5' D:GNP500 4.6 49.1 1.0
O D:HOH902 4.7 42.7 1.0
C3' D:GNP500 4.8 48.9 1.0
C35 D:AKN600 4.9 69.0 0.6
OD2 D:ASP374 4.9 45.4 1.0
N3B D:GNP500 4.9 47.0 0.5

Magnesium binding site 8 out of 8 in 6cgd

Go back to Magnesium Binding Sites List in 6cgd
Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin


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

b:46.5
occ:1.00
 O D:HOH904 1.8 35.9 0.5
O2B D:GNP500 2.0 44.8 0.5
O D:HOH903 2.0 48.2 1.0
OD2 D:ASP393 2.2 45.2 1.0
O D:HOH902 2.3 42.7 1.0
OD1 D:ASP393 2.3 44.6 1.0
O3G D:GNP500 2.5 48.8 0.5
CG D:ASP393 2.6 45.1 1.0
O3G D:GNP500 2.6 51.5 0.5
O1G D:GNP500 2.7 43.4 0.5
PG D:GNP500 3.0 45.7 0.5
O1B D:GNP500 3.0 43.5 0.5
O D:HOH924 3.4 43.5 0.5
PB D:GNP500 3.4 50.7 0.5
O D:HOH901 3.5 54.3 0.5
PG D:GNP500 3.6 49.0 0.5
O2G D:GNP500 3.7 50.1 0.5
N25 D:AKN600 3.7 72.5 0.6
N3B D:GNP500 3.7 47.0 0.5
N3B D:GNP500 3.8 49.9 0.5
PB D:GNP500 3.8 47.6 0.5
MG D:MG700 3.9 40.5 1.0
CB D:ASP393 4.1 44.2 1.0
NZ D:LYS226 4.1 47.2 1.0
O1B D:GNP500 4.3 48.2 0.5
OD2 D:ASP374 4.3 45.4 1.0
O3A D:GNP500 4.3 45.8 0.5
O3A D:GNP500 4.4 46.9 0.5
O2G D:GNP500 4.5 49.9 0.5
CA D:GLY395 4.5 44.4 1.0
O D:HOH909 4.6 42.2 0.5
O1A D:GNP500 4.6 40.8 1.0
N D:GLY395 4.7 44.5 1.0
OD1 D:ASP396 4.7 58.5 1.0
PA D:GNP500 4.8 44.5 1.0
O2A D:GNP500 4.8 39.0 1.0
O1G D:GNP500 4.9 48.6 0.5
C D:GLY395 4.9 46.9 1.0
CA D:ASP393 4.9 42.8 1.0
O D:ASP393 4.9 41.3 1.0
CG D:ASP396 5.0 51.7 1.0
CE1 D:HIS379 5.0 42.5 1.0

Reference:

S.J.Caldwell, A.M.Berghuis. Plasticity of Aminoglycoside Binding to Antibiotic Kinase Aph(2′′)-Ia. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 29661878
DOI: 10.1128/AAC.00202-18
Page generated: Wed Aug 13 04:14:03 2025

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