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Magnesium in PDB 6ch4: Aminoglycoside Phosphotransferase (2'')-Ia S376N Mutant in Complex with Gmppnp and Magnesium

Enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia S376N Mutant in Complex with Gmppnp and Magnesium

All present enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia S376N Mutant in Complex with Gmppnp and Magnesium:
2.7.1.190;

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia S376N Mutant in Complex with Gmppnp and Magnesium, PDB code: 6ch4 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) 58.89 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.430, 99.910, 93.200, 90.00, 105.17, 90.00
R / Rfree (%) 17 / 21

Other elements in 6ch4:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium (pdb code 6ch4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Aminoglycoside Phosphotransferase (2'')-Ia S376N Mutant in Complex with Gmppnp and Magnesium, PDB code: 6ch4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6ch4

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Magnesium binding site 1 out of 7 in the Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:46.7
occ:1.00
 O A:HOH900 1.9 53.8 1.0
O2A A:GNP500 2.1 51.1 1.0
O A:HOH901 2.2 54.5 1.0
OD2 A:ASP393 2.2 35.3 1.0
NE2 A:HIS379 2.3 42.5 1.0
O2B A:GNP500 2.4 65.5 1.0
CE1 A:HIS379 3.2 39.6 1.0
CD2 A:HIS379 3.2 43.0 1.0
CG A:ASP393 3.2 35.4 1.0
PA A:GNP500 3.3 49.0 1.0
PB A:GNP500 3.5 60.8 1.0
CB A:ASP393 3.6 34.7 1.0
O3A A:GNP500 3.7 54.9 1.0
O A:HOH1221 4.0 56.6 1.0
MG A:MG702 4.0 66.2 1.0
O3' A:GNP500 4.2 49.4 1.0
O1A A:GNP500 4.2 48.9 1.0
ND1 A:HIS379 4.3 37.4 1.0
O1B A:GNP500 4.3 65.6 1.0
CG A:HIS379 4.3 38.0 1.0
OD1 A:ASP393 4.4 37.8 1.0
O A:HOH904 4.4 67.2 1.0
O5' A:GNP500 4.4 48.5 1.0
C5' A:GNP500 4.6 48.2 1.0
C3' A:GNP500 4.7 47.7 1.0
O A:HOH902 4.8 52.7 1.0
O A:HOH921 4.8 71.9 1.0
N3B A:GNP500 4.8 59.3 1.0
OD2 A:ASP374 4.9 45.5 1.0

Magnesium binding site 2 out of 7 in 6ch4

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Magnesium binding site 2 out of 7 in the Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:66.2
occ:1.00
 O A:HOH903 1.8 67.1 1.0
O3G A:GNP500 1.8 60.0 0.5
O A:HOH904 2.2 67.2 1.0
OD2 A:ASP393 2.2 35.3 1.0
OD1 A:ASP393 2.3 37.8 1.0
O A:HOH902 2.5 52.7 1.0
CG A:ASP393 2.6 35.4 1.0
PG A:GNP500 2.8 60.8 0.5
O2G A:GNP500 3.0 60.4 0.5
O2B A:GNP500 3.2 65.5 1.0
N3B A:GNP500 3.4 59.3 1.0
O A:HOH901 3.6 54.5 1.0
PB A:GNP500 3.6 60.8 1.0
MG A:MG700 4.0 46.7 1.0
CB A:ASP393 4.1 34.7 1.0
O3A A:GNP500 4.1 54.9 1.0
NZ A:LYS226 4.2 53.5 1.0
O1G A:GNP500 4.2 56.7 0.5
CA A:GLY395 4.4 40.7 1.0
O A:HOH1029 4.5 59.0 1.0
N A:GLY395 4.5 38.8 1.0
O2A A:GNP500 4.6 51.1 1.0
OD2 A:ASP374 4.7 45.5 1.0
O1A A:GNP500 4.7 48.9 1.0
PA A:GNP500 4.8 49.0 1.0
C A:GLY395 4.9 45.0 1.0
CA A:ASP393 4.9 35.8 1.0
OD2 A:ASP396 5.0 60.7 1.0
O A:ASP393 5.0 37.2 1.0

Magnesium binding site 3 out of 7 in 6ch4

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Magnesium binding site 3 out of 7 in the Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:62.5
occ:1.00
 O B:HOH900 1.5 66.8 1.0
O1A B:GNP500 1.9 65.1 1.0
NE2 B:HIS379 2.2 40.6 1.0
N3B B:GNP500 2.4 73.1 1.0
OD2 B:ASP393 2.4 52.0 1.0
O B:HOH901 2.9 54.6 0.7
CD2 B:HIS379 3.0 41.8 1.0
CE1 B:HIS379 3.2 35.5 1.0
PA B:GNP500 3.3 64.4 1.0
CG B:ASP393 3.4 45.2 1.0
CB B:ASP393 3.6 42.4 1.0
PB B:GNP500 3.6 70.7 1.0
O3A B:GNP500 3.7 67.9 1.0
O B:HOH904 3.9 69.5 0.7
O3' B:GNP500 4.2 58.4 1.0
O2A B:GNP500 4.2 63.0 1.0
CG B:HIS379 4.2 36.3 1.0
ND1 B:HIS379 4.2 35.3 1.0
O5' B:GNP500 4.3 61.8 1.0
C5' B:GNP500 4.4 60.0 1.0
MG B:MG702 4.4 66.3 1.0
C3' B:GNP500 4.5 56.9 1.0
OD1 B:ASP393 4.5 44.2 1.0
O B:HOH1260 4.5 57.9 1.0
O2B B:GNP500 4.6 75.9 1.0
O1B B:GNP500 4.7 70.5 1.0

Magnesium binding site 4 out of 7 in 6ch4

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Magnesium binding site 4 out of 7 in the Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:66.3
occ:1.00
 O B:HOH904 2.0 69.5 0.7
O B:HOH903 2.2 60.0 1.0
OD2 B:ASP393 2.4 52.0 1.0
O B:HOH902 2.4 57.0 1.0
OD1 B:ASP393 2.7 44.2 1.0
O1B B:GNP500 2.9 70.5 1.0
CG B:ASP393 2.9 45.2 1.0
N3B B:GNP500 3.3 73.1 1.0
PB B:GNP500 3.7 70.7 1.0
O B:HOH901 4.0 54.6 0.7
CA B:GLY395 4.4 37.0 1.0
MG B:MG700 4.4 62.5 1.0
CB B:ASP393 4.5 42.4 1.0
OD2 B:ASP374 4.5 42.5 1.0
OD2 B:ASP396 4.5 61.2 1.0
O3A B:GNP500 4.6 67.9 1.0
OD1 B:ASP396 4.6 52.4 1.0
N B:GLY395 4.7 36.8 1.0
CG B:ASP396 4.7 46.7 1.0
C B:GLY395 4.7 37.1 1.0
NZ B:LYS226 4.8 56.8 1.0
O2B B:GNP500 4.9 75.9 1.0
N B:ASP396 4.9 38.4 1.0

Magnesium binding site 5 out of 7 in 6ch4

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Magnesium binding site 5 out of 7 in the Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:59.4
occ:1.00
 O C:HOH900 2.0 54.6 1.0
O C:HOH901 2.1 60.9 1.0
O2A C:GNP500 2.2 62.0 1.0
OD2 C:ASP393 2.3 44.4 1.0
NE2 C:HIS379 2.3 41.8 1.0
O2B C:GNP500 2.5 67.1 1.0
CD2 C:HIS379 3.2 45.1 1.0
CE1 C:HIS379 3.2 39.4 1.0
CG C:ASP393 3.3 43.0 1.0
PA C:GNP500 3.4 60.9 1.0
PB C:GNP500 3.5 66.4 1.0
CB C:ASP393 3.6 38.3 1.0
O3A C:GNP500 3.8 62.2 1.0
O C:HOH921 4.0 66.5 1.0
O C:HOH904 4.1 62.5 1.0
O1A C:GNP500 4.1 58.4 1.0
MG C:MG702 4.2 71.9 1.0
O1B C:GNP500 4.3 67.1 1.0
ND1 C:HIS379 4.3 41.2 1.0
CG C:HIS379 4.3 40.8 1.0
O C:HOH1260 4.4 60.6 1.0
O3' C:GNP500 4.4 58.0 1.0
OD1 C:ASP393 4.4 46.4 1.0
O5' C:GNP500 4.5 58.2 1.0
C5' C:GNP500 4.7 57.1 1.0
C3' C:GNP500 4.8 56.6 1.0
O C:HOH902 4.9 54.9 1.0
N3B C:GNP500 4.9 67.3 1.0
OD2 C:ASP374 4.9 44.6 1.0
O C:HOH1221 5.0 71.3 1.0

Magnesium binding site 6 out of 7 in 6ch4

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Magnesium binding site 6 out of 7 in the Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:71.9
occ:1.00
 O C:HOH904 2.2 62.5 1.0
OD2 C:ASP393 2.3 44.4 1.0
O3G C:GNP500 2.3 66.4 0.2
OD1 C:ASP393 2.4 46.4 1.0
CG C:ASP393 2.7 43.0 1.0
O C:HOH902 2.7 54.9 1.0
O2G C:GNP500 2.9 67.3 0.2
PG C:GNP500 2.9 67.1 0.2
O2B C:GNP500 3.2 67.1 1.0
N3B C:GNP500 3.5 67.3 1.0
PB C:GNP500 3.6 66.4 1.0
O C:HOH901 3.9 60.9 1.0
MG C:MG700 4.2 59.4 1.0
CB C:ASP393 4.2 38.3 1.0
NZ C:LYS226 4.2 51.1 1.0
CA C:GLY395 4.2 46.2 1.0
O1G C:GNP500 4.4 65.7 0.2
O3A C:GNP500 4.4 62.2 1.0
N C:GLY395 4.5 43.0 1.0
O C:HOH921 4.7 66.5 1.0
C C:GLY395 4.8 46.5 1.0
OD2 C:ASP374 4.8 44.6 1.0
O1A C:GNP500 4.8 58.4 1.0
OD1 C:ASP396 4.9 59.0 1.0
OD2 C:ASP396 4.9 62.0 1.0
PA C:GNP500 5.0 60.9 1.0
O C:ASP393 5.0 42.6 1.0
CA C:ASP393 5.0 40.1 1.0

Magnesium binding site 7 out of 7 in 6ch4

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Magnesium binding site 7 out of 7 in the Aminoglycoside Phosphotransferase (2'')-Ia S376N 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 S376N Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:56.9
occ:1.00
 O1G D:GNP500 2.0 63.7 0.5
O1A D:GNP500 2.3 60.5 1.0
O D:HOH900 2.3 59.7 1.0
NE2 D:HIS379 2.3 54.2 1.0
OD2 D:ASP393 2.4 61.1 1.0
N3B D:GNP500 2.5 71.9 1.0
PG D:GNP500 2.7 72.8 0.5
CE1 D:HIS379 3.2 52.0 1.0
CD2 D:HIS379 3.3 50.4 1.0
PB D:GNP500 3.4 73.8 1.0
CG D:ASP393 3.4 56.1 1.0
PA D:GNP500 3.6 66.5 1.0
O3G D:GNP500 3.6 68.6 0.5
O3A D:GNP500 3.7 68.5 1.0
CB D:ASP393 3.9 53.2 1.0
O2G D:GNP500 3.9 71.3 0.5
O1B D:GNP500 4.0 78.0 1.0
ND1 D:HIS379 4.3 48.4 1.0
CG D:HIS379 4.4 48.3 1.0
O D:HOH902 4.5 56.8 1.0
OD1 D:ASP393 4.5 58.2 1.0
O3' D:GNP500 4.6 53.5 1.0
O2A D:GNP500 4.6 61.2 1.0
OD2 D:ASP374 4.7 47.4 1.0
O2B D:GNP500 4.7 81.4 1.0
C5' D:GNP500 4.7 59.2 1.0
O5' D:GNP500 4.8 59.0 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 04:29:21 2025

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