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Magnesium in PDB 6cey: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties, PDB code: 6cey 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) 90.73 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.250, 100.240, 94.010, 90.00, 105.17, 90.00
R / Rfree (%) 17.1 / 21.6

Other elements in 6cey:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties 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 Lividomycin Moieties (pdb code 6cey). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties, PDB code: 6cey:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6cey

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Magnesium binding site 1 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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

b:37.1
occ:1.00
 O2G A:GNP500 1.5 44.1 0.5
O A:HOH901 1.5 47.9 0.5
O A:HOH900 1.6 48.2 1.0
O1A A:GNP500 1.9 47.4 1.0
NE2 A:HIS379 2.0 44.3 1.0
OD2 A:ASP393 2.1 41.8 1.0
O1B A:GNP500 2.7 46.6 0.5
PG A:GNP500 3.0 44.2 0.5
CE1 A:HIS379 3.0 42.2 1.0
CD2 A:HIS379 3.0 46.3 1.0
CG A:ASP393 3.2 43.5 1.0
PA A:GNP500 3.3 43.7 1.0
N3B A:GNP500 3.5 44.7 0.5
O3G A:GNP500 3.5 44.6 0.5
CB A:ASP393 3.6 41.7 1.0
O3A A:GNP500 3.6 44.0 0.5
O3A A:GNP500 3.7 43.8 0.5
PB A:GNP500 3.8 44.1 0.5
MG A:MG702 3.9 55.3 1.0
PB A:GNP500 3.9 44.3 0.5
O2B A:GNP500 3.9 45.0 0.5
ND1 A:HIS379 4.1 42.2 1.0
O2A A:GNP500 4.1 41.1 1.0
CG A:HIS379 4.1 41.4 1.0
O1G A:GNP500 4.1 44.4 0.5
OD1 A:ASP393 4.3 42.1 1.0
O2B A:GNP500 4.3 42.2 0.5
O5' A:GNP500 4.4 44.8 1.0
O A:HOH1221 4.5 51.9 1.0
O3' A:GNP500 4.5 49.6 1.0
ND2 A:ASN378 4.6 64.0 1.0
C5' A:GNP500 4.6 46.4 1.0
O A:HOH904 4.7 46.3 0.5
C3' A:GNP500 4.8 48.4 1.0
O3G A:GNP500 4.8 46.1 0.5
OD2 A:ASP374 4.9 56.2 1.0

Magnesium binding site 2 out of 9 in 6cey

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Magnesium binding site 2 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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

b:55.3
occ:1.00
 O3G A:GNP500 1.8 46.1 0.5
O A:HOH903 1.9 53.3 1.0
OD1 A:ASP393 2.1 42.1 1.0
O2B A:GNP500 2.1 45.0 0.5
OD2 A:ASP393 2.1 41.8 1.0
O A:HOH904 2.1 46.3 0.5
O3G A:GNP500 2.1 44.6 0.5
CG A:ASP393 2.3 43.5 1.0
O A:HOH902 2.4 50.2 1.0
O1B A:GNP500 2.8 46.6 0.5
PG A:GNP500 3.3 45.3 0.5
PG A:GNP500 3.3 44.2 0.5
PB A:GNP500 3.3 44.3 0.5
O A:HOH901 3.3 47.9 0.5
N3B A:GNP500 3.6 44.7 0.5
O2G A:GNP500 3.7 44.1 0.5
PB A:GNP500 3.8 44.1 0.5
O1G A:GNP500 3.8 44.2 0.5
N3B A:GNP500 3.9 44.4 0.5
MG A:MG700 3.9 37.1 1.0
CB A:ASP393 3.9 41.7 1.0
O2G A:GNP500 4.0 47.1 0.5
OD2 A:ASP374 4.2 56.2 1.0
O3A A:GNP500 4.2 43.8 0.5
O1B A:GNP500 4.2 44.4 0.5
NZ A:LYS226 4.2 54.9 1.0
O3A A:GNP500 4.3 44.0 0.5
O1A A:GNP500 4.4 47.4 1.0
CA A:GLY395 4.5 48.8 1.0
O2A A:GNP500 4.5 41.1 1.0
O1G A:GNP500 4.6 44.4 0.5
N A:GLY395 4.6 46.0 1.0
PA A:GNP500 4.6 43.7 1.0
CA A:ASP393 4.7 42.5 1.0
OD2 A:ASP396 4.7 62.9 1.0
O A:ASP393 4.7 43.0 1.0
CE1 A:HIS379 4.8 42.2 1.0
NE2 A:HIS379 4.8 44.3 1.0
O A:HOH951 4.9 42.4 1.0
C A:ASP393 4.9 43.5 1.0

Magnesium binding site 3 out of 9 in 6cey

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Magnesium binding site 3 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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

b:26.8
occ:1.00
 O B:HOH900 1.5 46.5 1.0
O2G B:GNP500 1.5 47.4 1.0
O1A B:GNP500 1.8 42.1 1.0
NE2 B:HIS379 2.0 39.7 1.0
OD2 B:ASP393 2.2 45.9 1.0
CD2 B:HIS379 2.9 41.7 1.0
CE1 B:HIS379 3.0 37.0 1.0
PG B:GNP500 3.0 50.5 1.0
CG B:ASP393 3.2 43.7 1.0
PA B:GNP500 3.2 41.9 1.0
N3B B:GNP500 3.3 47.7 1.0
CB B:ASP393 3.6 44.4 1.0
O3G B:GNP500 3.8 52.0 1.0
MG B:MG702 3.9 50.0 1.0
O3A B:GNP500 3.9 42.9 1.0
PB B:GNP500 4.0 43.5 1.0
O2A B:GNP500 4.0 39.7 1.0
ND1 B:HIS379 4.1 34.7 1.0
O2B B:GNP500 4.1 44.4 1.0
CG B:HIS379 4.1 39.0 1.0
O3' B:GNP500 4.2 41.1 1.0
OD1 B:ASP393 4.2 43.3 1.0
O1G B:GNP500 4.3 50.3 1.0
O5' B:GNP500 4.3 44.2 1.0
ND2 B:ASN378 4.5 62.0 1.0
C5' B:GNP500 4.6 44.4 1.0
C3' B:GNP500 4.8 43.6 1.0
OD2 B:ASP374 4.9 47.6 1.0

Magnesium binding site 4 out of 9 in 6cey

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Magnesium binding site 4 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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

b:50.0
occ:1.00
 O3G B:GNP500 1.8 52.0 1.0
O B:HOH903 1.9 54.9 1.0
OD2 B:ASP393 2.0 45.9 1.0
OD1 B:ASP393 2.2 43.3 1.0
O B:HOH902 2.2 44.4 1.0
O2B B:GNP500 2.3 44.4 1.0
CG B:ASP393 2.4 43.7 1.0
PG B:GNP500 3.1 50.5 1.0
O B:HOH924 3.3 56.8 0.5
O2G B:GNP500 3.5 47.4 1.0
PB B:GNP500 3.6 43.5 1.0
N3B B:GNP500 3.6 47.7 1.0
MG B:MG700 3.9 26.8 1.0
CB B:ASP393 4.0 44.4 1.0
OD2 B:ASP374 4.0 47.6 1.0
O1B B:GNP500 4.2 44.2 1.0
O1G B:GNP500 4.3 50.3 1.0
O B:HOH1299 4.3 63.6 1.0
O1A B:GNP500 4.4 42.1 1.0
NZ B:LYS226 4.4 46.2 1.0
O3A B:GNP500 4.4 42.9 1.0
OD2 B:ASP396 4.5 63.9 1.0
CA B:GLY395 4.5 45.4 1.0
N B:GLY395 4.6 44.0 1.0
O2A B:GNP500 4.7 39.7 1.0
CE1 B:HIS379 4.7 37.0 1.0
PA B:GNP500 4.7 41.9 1.0
NE2 B:HIS379 4.8 39.7 1.0
O B:HOH951 4.8 39.0 1.0
O B:ASP393 4.8 39.4 1.0
CA B:ASP393 4.8 43.3 1.0
CG B:ASP396 4.8 59.8 1.0
C B:GLY395 4.9 46.2 1.0
C B:ASP393 5.0 41.0 1.0
OD1 B:ASP396 5.0 64.9 1.0

Magnesium binding site 5 out of 9 in 6cey

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Magnesium binding site 5 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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

b:33.2
occ:1.00
 O C:HOH900 1.6 46.2 1.0
O C:HOH901 1.8 72.3 0.6
O1A C:GNP500 1.8 40.3 1.0
NE2 C:HIS379 2.0 42.0 1.0
O2G C:GNP500 2.0 43.6 0.4
OD2 C:ASP393 2.1 53.1 1.0
O1B C:GNP500 2.9 43.0 0.6
N3B C:GNP500 3.0 41.4 0.4
CE1 C:HIS379 3.0 43.0 1.0
PG C:GNP500 3.0 41.7 0.4
CD2 C:HIS379 3.0 44.5 1.0
CG C:ASP393 3.2 49.6 1.0
PA C:GNP500 3.3 43.6 1.0
PB C:GNP500 3.7 42.3 0.4
CB C:ASP393 3.7 46.8 1.0
O2B C:GNP500 3.8 43.3 0.4
O3A C:GNP500 3.8 42.8 0.4
O3G C:GNP500 3.9 45.2 0.4
PB C:GNP500 3.9 44.0 0.6
O3A C:GNP500 4.0 43.3 0.6
ND1 C:HIS379 4.1 41.6 1.0
O C:HOH904 4.1 52.3 0.6
O1G C:GNP500 4.1 43.2 0.4
MG C:MG702 4.1 51.7 1.0
CG C:HIS379 4.1 42.3 1.0
O2A C:GNP500 4.2 40.4 1.0
O2B C:GNP500 4.2 41.9 0.6
OD1 C:ASP393 4.4 49.6 1.0
O C:HOH1287 4.4 52.8 0.6
O5' C:GNP500 4.4 44.3 1.0
ND2 C:ASN378 4.5 68.5 1.0
O3' C:GNP500 4.6 52.4 1.0
O C:HOH1221 4.7 75.0 1.0
C5' C:GNP500 4.7 47.3 1.0
OD2 C:ASP374 4.8 50.7 1.0
O3G C:GNP500 4.9 51.2 0.6
C3' C:GNP500 4.9 48.8 1.0

Magnesium binding site 6 out of 9 in 6cey

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Magnesium binding site 6 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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

b:51.7
occ:1.00
 O C:HOH903 1.8 77.5 1.0
O2B C:GNP500 1.9 43.3 0.4
O3G C:GNP500 1.9 51.2 0.6
O C:HOH904 2.1 52.3 0.6
O3G C:GNP500 2.2 45.2 0.4
OD1 C:ASP393 2.4 49.6 1.0
OD2 C:ASP393 2.4 53.1 1.0
O C:HOH902 2.5 47.4 1.0
CG C:ASP393 2.7 49.6 1.0
O1B C:GNP500 2.9 43.0 0.6
PG C:GNP500 3.3 50.0 0.6
O1G C:GNP500 3.3 49.5 0.6
PG C:GNP500 3.3 41.7 0.4
PB C:GNP500 3.4 42.3 0.4
O C:HOH901 3.5 72.3 0.6
O2G C:GNP500 3.6 43.6 0.4
N3B C:GNP500 3.7 41.4 0.4
PB C:GNP500 4.0 44.0 0.6
N3B C:GNP500 4.1 46.7 0.6
MG C:MG700 4.1 33.2 1.0
OD2 C:ASP374 4.2 50.7 1.0
O1B C:GNP500 4.3 43.3 0.4
CB C:ASP393 4.3 46.8 1.0
NZ C:LYS226 4.3 46.8 1.0
O2G C:GNP500 4.5 52.6 0.6
O3A C:GNP500 4.5 42.8 0.4
O1G C:GNP500 4.6 43.2 0.4
CA C:GLY395 4.6 54.4 1.0
O1A C:GNP500 4.6 40.3 1.0
OD2 C:ASP396 4.6 60.6 1.0
O3A C:GNP500 4.7 43.3 0.6
N C:GLY395 4.7 51.4 1.0
O C:HOH1287 4.7 52.8 0.6
CG C:ASP396 4.9 61.3 1.0
OD1 C:ASP396 4.9 65.4 1.0
O C:HOH909 4.9 53.6 0.4
O2A C:GNP500 4.9 40.4 1.0
PA C:GNP500 4.9 43.6 1.0

Magnesium binding site 7 out of 9 in 6cey

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Magnesium binding site 7 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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 Lividomycin Moieties within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg800

b:73.8
occ:1.00
 O C:HOH1637 2.4 60.0 1.0
O C:HOH1638 2.6 59.7 1.0
OD1 C:ASN385 2.6 68.2 1.0
O C:HOH1636 2.6 68.8 1.0
CG C:ASN385 3.8 67.8 1.0
ND2 C:ASN385 4.5 68.6 1.0
O C:GLY384 4.7 71.7 1.0
CB C:ASN385 5.0 65.8 1.0

Magnesium binding site 8 out of 9 in 6cey

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Magnesium binding site 8 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


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

b:29.7
occ:1.00
 O D:HOH900 1.6 47.1 1.0
O2G D:GNP500 1.6 52.6 1.0
O1A D:GNP500 1.8 45.9 1.0
NE2 D:HIS379 1.9 52.2 1.0
OD2 D:ASP393 1.9 57.0 1.0
CE1 D:HIS379 2.9 51.1 1.0
CD2 D:HIS379 2.9 52.6 1.0
CG D:ASP393 3.0 53.8 1.0
PG D:GNP500 3.1 55.3 1.0
PA D:GNP500 3.2 46.1 1.0
CB D:ASP393 3.5 54.0 1.0
N3B D:GNP500 3.5 51.8 1.0
O3G D:GNP500 3.7 58.1 1.0
O2B D:GNP500 3.8 52.4 1.0
O3A D:GNP500 3.9 51.1 1.0
MG D:MG702 3.9 58.0 1.0
ND1 D:HIS379 4.0 49.4 1.0
PB D:GNP500 4.0 51.2 1.0
CG D:HIS379 4.0 51.0 1.0
O2A D:GNP500 4.1 43.1 1.0
OD1 D:ASP393 4.1 52.7 1.0
O1G D:GNP500 4.3 55.7 1.0
O3' D:GNP500 4.4 48.5 1.0
O5' D:GNP500 4.4 48.4 1.0
ND2 D:ASN378 4.6 85.6 1.0
C5' D:GNP500 4.7 50.3 1.0
O D:HOH902 4.7 52.3 1.0
OD2 D:ASP374 4.7 52.6 1.0
C3' D:GNP500 4.8 52.1 1.0
CA D:ASP393 5.0 52.4 1.0

Magnesium binding site 9 out of 9 in 6cey

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Magnesium binding site 9 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:58.0
occ:1.00
 O D:HOH903 1.8 56.1 1.0
O3G D:GNP500 2.0 58.1 1.0
O D:HOH902 2.1 52.3 1.0
O2B D:GNP500 2.2 52.4 1.0
OD1 D:ASP393 2.2 52.7 1.0
OD2 D:ASP393 2.3 57.0 1.0
CG D:ASP393 2.6 53.8 1.0
PG D:GNP500 3.2 55.3 1.0
PB D:GNP500 3.5 51.2 1.0
N3B D:GNP500 3.6 51.8 1.0
O2G D:GNP500 3.7 52.6 1.0
O D:HOH911 3.8 36.6 0.5
MG D:MG700 3.9 29.7 1.0
CB D:ASP393 4.1 54.0 1.0
OD2 D:ASP374 4.1 52.6 1.0
O1B D:GNP500 4.2 49.8 1.0
NZ D:LYS226 4.3 58.0 1.0
O1G D:GNP500 4.3 55.7 1.0
CA D:GLY395 4.4 53.8 1.0
OD2 D:ASP396 4.5 66.3 1.0
O3A D:GNP500 4.5 51.1 1.0
O1A D:GNP500 4.5 45.9 1.0
N D:GLY395 4.5 52.3 1.0
O D:HOH924 4.6 37.3 0.5
C53 D:LIV600 4.7 89.0 0.5
CG D:ASP396 4.7 64.2 1.0
C D:GLY395 4.8 56.0 1.0
PA D:GNP500 4.8 46.1 1.0
O D:ASP393 4.8 48.3 1.0
O2A D:GNP500 4.8 43.1 1.0
O D:HOH951 4.8 58.4 1.0
CA D:ASP393 4.9 52.4 1.0
CE1 D:HIS379 4.9 51.1 1.0
N D:ASP396 4.9 57.6 1.0
OD1 D:ASP396 4.9 70.8 1.0
O53 D:LIV600 4.9 86.4 0.5
NE2 D:HIS379 5.0 52.2 1.0
C D:ASP393 5.0 50.0 1.0
O D:HOH909 5.0 51.1 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: Mon Sep 30 20:33:18 2024

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