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

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin, PDB code: 6cgg 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) 90.14 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.330, 99.780, 93.510, 90.00, 105.43, 90.00
R / Rfree (%) 17.8 / 22.3

Other elements in 6cgg:

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

Magnesium binding site 1 out of 8 in 6cgg

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


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

b:46.0
occ:1.00
 O A:HOH901 1.8 44.6 1.0
O2A A:GNP500 2.0 42.1 1.0
O A:HOH900 2.0 45.3 1.0
OD2 A:ASP393 2.1 43.4 1.0
NE2 A:HIS379 2.4 45.6 1.0
O2B A:GNP500 2.6 51.0 1.0
PA A:GNP500 3.1 42.5 1.0
CG A:ASP393 3.2 41.8 1.0
PB A:GNP500 3.3 48.3 1.0
CE1 A:HIS379 3.3 43.5 1.0
O3A A:GNP500 3.4 44.7 1.0
CD2 A:HIS379 3.4 45.0 1.0
MG A:MG702 3.5 47.9 1.0
CB A:ASP393 3.7 40.3 1.0
O A:HOH1221 3.8 45.4 1.0
O1B A:GNP500 3.8 49.6 1.0
O A:HOH904 4.1 52.1 1.0
O1A A:GNP500 4.1 39.9 1.0
O A:HOH921 4.2 48.5 1.0
OD1 A:ASP393 4.3 41.6 1.0
O5' A:GNP500 4.4 43.2 1.0
ND1 A:HIS379 4.5 43.2 1.0
CG A:HIS379 4.5 42.0 1.0
C5' A:GNP500 4.5 44.7 1.0
N3B A:GNP500 4.6 48.9 1.0
O3G A:GNP500 4.7 49.5 1.0
O A:HOH902 4.8 37.3 1.0
O3' A:GNP500 4.9 42.1 1.0

Magnesium binding site 2 out of 8 in 6cgg

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


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

b:47.9
occ:1.00
 O3G A:GNP500 1.9 49.5 1.0
OD2 A:ASP393 1.9 43.4 1.0
O A:HOH904 2.0 52.1 1.0
OD1 A:ASP393 2.2 41.6 1.0
CG A:ASP393 2.4 41.8 1.0
O A:HOH903 2.4 46.4 1.0
O A:HOH902 2.6 37.3 1.0
PG A:GNP500 2.9 51.7 1.0
O2B A:GNP500 3.0 51.0 1.0
O2G A:GNP500 3.1 52.6 1.0
O A:HOH901 3.4 44.6 1.0
MG A:MG700 3.5 46.0 1.0
N3B A:GNP500 3.6 48.9 1.0
PB A:GNP500 3.6 48.3 1.0
CB A:ASP393 3.9 40.3 1.0
O3A A:GNP500 4.0 44.7 1.0
NZ A:LYS226 4.1 51.7 1.0
O1G A:GNP500 4.3 51.6 1.0
OD2 A:ASP374 4.4 49.6 1.0
O2A A:GNP500 4.4 42.1 1.0
PA A:GNP500 4.6 42.5 1.0
O A:HOH1029 4.6 62.6 1.0
O1A A:GNP500 4.6 39.9 1.0
CA A:GLY395 4.8 47.9 1.0
O A:HOH991 4.8 50.5 1.0
CA A:ASP393 4.8 40.4 1.0
O A:HOH921 4.8 48.5 1.0
N A:GLY395 4.9 45.5 1.0
NE2 A:HIS379 4.9 45.6 1.0
CE1 A:HIS379 4.9 43.5 1.0
O A:ASP393 4.9 39.2 1.0

Magnesium binding site 3 out of 8 in 6cgg

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


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

b:45.6
occ:1.00
 O B:HOH901 1.8 41.2 0.7
O1A B:GNP500 1.9 38.0 1.0
O B:HOH900 2.0 44.8 1.0
O1G B:GNP500 2.0 44.4 0.3
OD2 B:ASP393 2.1 45.2 1.0
NE2 B:HIS379 2.3 44.7 1.0
O2B B:GNP500 2.5 44.5 0.7
O B:HOH904 3.0 52.9 0.7
CG B:ASP393 3.1 43.9 1.0
PA B:GNP500 3.1 39.1 1.0
CD2 B:HIS379 3.2 44.3 1.0
CE1 B:HIS379 3.3 42.7 1.0
PG B:GNP500 3.4 46.3 0.3
PB B:GNP500 3.5 42.3 0.7
CB B:ASP393 3.5 43.0 1.0
O3A B:GNP500 3.5 39.6 0.3
N3B B:GNP500 3.5 43.4 0.3
O3A B:GNP500 3.6 40.5 0.7
O1B B:GNP500 3.6 41.2 0.3
PB B:GNP500 3.7 40.9 0.3
O B:84G600 4.0 59.1 0.5
MG B:MG702 4.0 65.8 1.0
O2A B:GNP500 4.1 38.0 1.0
OD1 B:ASP393 4.1 44.8 1.0
O3G B:GNP500 4.1 47.7 0.3
O1B B:GNP500 4.2 46.7 0.7
O5' B:GNP500 4.3 40.2 1.0
ND1 B:HIS379 4.3 41.3 1.0
CG B:HIS379 4.4 43.2 1.0
O B:HOH1035 4.5 64.2 1.0
O2G B:GNP500 4.5 48.9 0.3
C5' B:GNP500 4.5 42.2 1.0
O3' B:GNP500 4.6 42.5 1.0
N3B B:GNP500 4.8 44.4 0.7
OD1 B:ASN378 4.8 66.0 1.0
C3' B:GNP500 4.9 41.2 1.0

Magnesium binding site 4 out of 8 in 6cgg

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


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

b:65.8
occ:1.00
 O B:HOH904 2.0 52.9 0.7
O1B B:GNP500 2.1 41.2 0.3
O B:HOH903 2.2 78.2 1.0
OD2 B:ASP393 2.3 45.2 1.0
OD1 B:ASP393 2.3 44.8 1.0
O3G B:GNP500 2.4 46.6 0.7
CG B:ASP393 2.6 43.9 1.0
O3G B:GNP500 3.0 47.7 0.3
O2G B:GNP500 3.3 49.7 0.7
PG B:GNP500 3.3 47.5 0.7
O2B B:GNP500 3.5 44.5 0.7
O B:HOH924 3.6 21.6 0.3
PB B:GNP500 3.7 40.9 0.3
PG B:GNP500 3.9 46.3 0.3
O1G B:GNP500 3.9 44.4 0.3
MG B:MG700 4.0 45.6 1.0
N3B B:GNP500 4.0 44.4 0.7
O B:HOH901 4.0 41.2 0.7
N3B B:GNP500 4.1 43.4 0.3
PB B:GNP500 4.2 42.3 0.7
CB B:ASP393 4.2 43.0 1.0
OD2 B:ASP374 4.2 46.5 1.0
O2B B:GNP500 4.3 41.7 0.3
CA B:GLY395 4.4 44.0 1.0
NZ B:LYS226 4.4 51.3 1.0
OD2 B:ASP396 4.5 54.3 1.0
N B:GLY395 4.6 41.9 1.0
O3A B:GNP500 4.7 39.6 0.3
O3A B:GNP500 4.8 40.5 0.7
C B:GLY395 4.8 46.2 1.0
CG B:ASP396 4.8 50.5 1.0
O1G B:GNP500 4.8 46.8 0.7
OD1 B:ASP396 4.8 56.9 1.0
O B:HOH909 4.8 32.1 0.3
O B:ASP393 4.8 40.7 1.0
N B:ASP396 4.9 45.8 1.0
O1A B:GNP500 5.0 38.0 1.0
CA B:ASP393 5.0 42.6 1.0
CE1 B:HIS379 5.0 42.7 1.0

Magnesium binding site 5 out of 8 in 6cgg

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Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:49.4
occ:1.00
 O2A C:GNP500 1.8 46.6 1.0
O C:HOH901 1.8 48.0 1.0
O C:HOH900 1.9 50.3 1.0
OD2 C:ASP393 2.3 45.5 1.0
O2B C:GNP500 2.3 50.5 1.0
NE2 C:HIS379 2.5 45.4 1.0
PA C:GNP500 3.0 45.9 1.0
PB C:GNP500 3.3 48.7 1.0
CD2 C:HIS379 3.4 45.2 1.0
CG C:ASP393 3.4 45.2 1.0
CE1 C:HIS379 3.4 45.2 1.0
O3A C:GNP500 3.4 46.8 1.0
CB C:ASP393 3.8 44.4 1.0
O1B C:GNP500 3.8 51.2 1.0
MG C:MG702 4.0 53.8 1.0
O1A C:GNP500 4.0 43.8 1.0
O C:HOH921 4.1 46.7 1.0
O5' C:GNP500 4.2 46.2 1.0
O C:HOH904 4.2 55.7 1.0
C5' C:GNP500 4.5 46.0 1.0
OD1 C:ASP393 4.5 45.5 1.0
CG C:HIS379 4.5 44.8 1.0
ND1 C:HIS379 4.5 45.0 1.0
O3' C:GNP500 4.6 47.3 1.0
O3G C:GNP500 4.6 52.6 1.0
N3B C:GNP500 4.7 50.5 1.0
C3' C:GNP500 4.9 46.4 1.0

Magnesium binding site 6 out of 8 in 6cgg

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


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

b:53.8
occ:1.00
 O C:HOH904 1.8 55.7 1.0
O3G C:GNP500 2.0 52.6 1.0
O C:HOH903 2.2 55.5 1.0
OD2 C:ASP393 2.2 45.5 1.0
O C:HOH902 2.4 48.7 1.0
OD1 C:ASP393 2.5 45.5 1.0
CG C:ASP393 2.7 45.2 1.0
PG C:GNP500 3.1 55.1 1.0
O2B C:GNP500 3.1 50.5 1.0
O2G C:GNP500 3.2 55.6 1.0
O C:HOH901 3.3 48.0 1.0
N3B C:GNP500 3.9 50.5 1.0
PB C:GNP500 3.9 48.7 1.0
MG C:MG700 4.0 49.4 1.0
CB C:ASP393 4.2 44.4 1.0
OD2 C:ASP374 4.2 51.7 1.0
O C:HOH1083 4.3 61.3 1.0
O1G C:GNP500 4.3 55.2 1.0
NZ C:LYS226 4.5 53.9 1.0
O3A C:GNP500 4.5 46.8 1.0
O C:HOH991 4.5 60.2 1.0
OD2 C:ASP396 4.7 54.0 1.0
O2A C:GNP500 4.8 46.6 1.0
CA C:GLY395 4.8 50.0 1.0
O C:HOH921 4.8 46.7 1.0
OD1 C:ASP396 4.9 54.4 1.0
PA C:GNP500 4.9 45.9 1.0
N C:GLY395 4.9 47.8 1.0
CE1 C:HIS379 4.9 45.2 1.0
O C:HOH1571 5.0 65.2 1.0
CG C:ASP396 5.0 52.9 1.0

Magnesium binding site 7 out of 8 in 6cgg

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


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

b:52.7
occ:1.00
 O1A D:GNP500 1.8 49.8 1.0
O D:HOH900 1.8 58.9 1.0
O2G D:GNP500 1.9 51.8 0.5
OD2 D:ASP393 2.0 57.0 1.0
O D:HOH901 2.1 67.1 0.5
O2B D:GNP500 2.4 55.9 0.5
NE2 D:HIS379 2.6 57.0 1.0
PG D:GNP500 3.0 52.9 0.5
PA D:GNP500 3.0 50.7 1.0
N3B D:GNP500 3.1 52.0 0.5
CG D:ASP393 3.1 57.1 1.0
PB D:GNP500 3.3 55.5 0.5
O3A D:GNP500 3.4 50.7 0.5
O3A D:GNP500 3.4 52.6 0.5
PB D:GNP500 3.4 51.8 0.5
CD2 D:HIS379 3.5 56.4 1.0
CE1 D:HIS379 3.5 57.2 1.0
O1B D:GNP500 3.5 52.6 0.5
CB D:ASP393 3.6 55.9 1.0
MG D:MG702 3.6 72.0 1.0
O1G D:GNP500 3.7 53.2 0.5
O2A D:GNP500 4.0 50.1 1.0
O1B D:GNP500 4.2 58.9 0.5
OD1 D:ASP393 4.2 59.1 1.0
O D:84G600 4.2 87.3 1.0
O3G D:GNP500 4.2 53.9 0.5
O3' D:GNP500 4.3 52.1 1.0
O5' D:GNP500 4.3 52.7 1.0
C5' D:GNP500 4.4 53.4 1.0
O D:HOH902 4.5 69.5 1.0
ND1 D:HIS379 4.6 55.6 1.0
CG D:HIS379 4.6 56.3 1.0
N3B D:GNP500 4.7 57.5 0.5
C3' D:GNP500 4.7 52.7 1.0
OD1 D:ASN378 4.9 77.5 1.0
O2B D:GNP500 4.9 52.7 0.5
C1 D:84G600 4.9 90.5 1.0
C2 D:84G600 4.9 88.0 1.0

Magnesium binding site 8 out of 8 in 6cgg

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


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 Arbekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:72.0
occ:1.00
 O1B D:GNP500 1.9 52.6 0.5
O D:HOH902 2.1 69.5 1.0
OD2 D:ASP393 2.1 57.0 1.0
O1G D:GNP500 2.3 53.2 0.5
O D:HOH903 2.3 60.3 1.0
OD1 D:ASP393 2.4 59.1 1.0
CG D:ASP393 2.6 57.1 1.0
O3G D:GNP500 2.8 61.1 0.5
O2B D:GNP500 3.0 55.9 0.5
O1G D:GNP500 3.1 60.7 0.5
PG D:GNP500 3.2 60.3 0.5
PB D:GNP500 3.3 51.8 0.5
O D:HOH901 3.3 67.1 0.5
PG D:GNP500 3.3 52.9 0.5
N3B D:GNP500 3.6 52.0 0.5
MG D:MG700 3.6 52.7 1.0
N3B D:GNP500 3.7 57.5 0.5
O2G D:GNP500 3.7 51.8 0.5
PB D:GNP500 3.7 55.5 0.5
CB D:ASP393 4.1 55.9 1.0
O2B D:GNP500 4.1 52.7 0.5
O D:HOH1083 4.2 69.3 1.0
O3A D:GNP500 4.3 52.6 0.5
OD2 D:ASP374 4.3 57.4 1.0
O3A D:GNP500 4.3 50.7 0.5
NZ D:LYS226 4.5 68.2 1.0
O1A D:GNP500 4.6 49.8 1.0
O3G D:GNP500 4.6 53.9 0.5
O D:HOH909 4.7 35.3 0.5
CA D:GLY395 4.7 56.0 1.0
O2G D:GNP500 4.7 59.8 0.5
PA D:GNP500 4.8 50.7 1.0
CE1 D:HIS379 4.9 57.2 1.0
OD2 D:ASP396 4.9 55.6 1.0
NE2 D:HIS379 4.9 57.0 1.0
N D:GLY395 4.9 56.3 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 04:29:05 2025

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