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Magnesium in PDB 5iqh: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium, PDB code: 5iqh 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) 89.99 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.220, 99.710, 93.280, 90.00, 105.26, 90.00
R / Rfree (%) 15.9 / 19.9

Other elements in 5iqh:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium (pdb code 5iqh). 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 (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A Mutant in Complex with Gmppnp and Magnesium, PDB code: 5iqh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5iqh

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Magnesium binding site 1 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:35.8
occ:1.00
 O2G A:GNP500 1.6 44.8 1.0
O2A A:GNP500 1.9 37.3 1.0
OD2 A:ASP393 2.1 33.5 1.0
O A:HOH900 2.1 40.7 1.0
NE2 A:HIS379 2.2 36.1 1.0
PG A:GNP500 2.8 49.0 1.0
N3B A:GNP500 3.1 43.1 1.0
CE1 A:HIS379 3.2 33.7 1.0
CG A:ASP393 3.2 34.5 1.0
CD2 A:HIS379 3.2 33.0 1.0
PA A:GNP500 3.2 36.4 1.0
CB A:ASP393 3.6 33.0 1.0
O3G A:GNP500 3.7 49.6 1.0
MG A:MG702 3.7 47.0 1.0
PB A:GNP500 3.8 38.3 1.0
O3A A:GNP500 3.8 39.2 1.0
O2B A:GNP500 3.8 42.3 1.0
O1G A:GNP500 4.1 46.7 1.0
O1A A:GNP500 4.1 35.6 1.0
ND1 A:HIS379 4.2 32.0 1.0
OD1 A:ASP393 4.3 31.7 1.0
CG A:HIS379 4.3 30.7 1.0
O5' A:GNP500 4.4 36.9 1.0
O3' A:GNP500 4.4 35.3 1.0
ND2 A:ASN378 4.5 60.1 1.0
C5' A:GNP500 4.7 36.5 1.0
C3' A:GNP500 4.8 35.8 1.0
O A:HOH903 4.8 38.2 1.0
OD2 A:ASP374 4.9 38.6 1.0

Magnesium binding site 2 out of 9 in 5iqh

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Magnesium binding site 2 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:47.0
occ:1.00
 O A:HOH902 1.9 43.0 1.0
O2B A:GNP500 1.9 42.3 1.0
OD2 A:ASP393 2.0 33.5 1.0
O3G A:GNP500 2.0 49.6 1.0
OD1 A:ASP393 2.1 31.7 1.0
O A:HOH903 2.3 38.2 1.0
CG A:ASP393 2.3 34.5 1.0
PG A:GNP500 3.2 49.0 1.0
PB A:GNP500 3.3 38.3 1.0
O2G A:GNP500 3.6 44.8 1.0
MG A:MG700 3.7 35.8 1.0
O A:HOH911 3.7 43.1 1.0
N3B A:GNP500 3.8 43.1 1.0
CB A:ASP393 3.8 33.0 1.0
O A:HOH1286 3.9 58.5 1.0
O1B A:GNP500 4.1 42.0 1.0
NZ A:LYS226 4.2 42.0 1.0
O3A A:GNP500 4.3 39.2 1.0
OD2 A:ASP374 4.4 38.6 1.0
O2A A:GNP500 4.4 37.3 1.0
CA A:GLY395 4.4 35.2 1.0
O1G A:GNP500 4.5 46.7 1.0
O1A A:GNP500 4.5 35.6 1.0
PA A:GNP500 4.5 36.4 1.0
N A:GLY395 4.5 33.3 1.0
CA A:ASP393 4.6 32.9 1.0
O A:ASP393 4.7 28.9 1.0
O A:HOH909 4.7 43.5 1.0
OD2 A:ASP396 4.7 50.6 1.0
C A:ASP393 4.8 31.5 1.0
CE1 A:HIS379 4.8 33.7 1.0
NE2 A:HIS379 4.9 36.1 1.0
C A:GLY395 5.0 36.4 1.0

Magnesium binding site 3 out of 9 in 5iqh

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Magnesium binding site 3 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:29.3
occ:1.00
 O2G B:GNP500 1.8 40.3 1.0
O2A B:GNP500 1.9 36.3 1.0
O B:HOH900 2.0 35.7 1.0
OD2 B:ASP393 2.1 35.8 1.0
NE2 B:HIS379 2.2 32.6 1.0
PG B:GNP500 3.0 41.7 1.0
CG B:ASP393 3.1 36.0 1.0
CE1 B:HIS379 3.1 30.6 1.0
CD2 B:HIS379 3.2 33.1 1.0
PA B:GNP500 3.2 37.4 1.0
N3B B:GNP500 3.2 40.2 1.0
CB B:ASP393 3.5 36.4 1.0
O3A B:GNP500 3.7 39.4 1.0
O3G B:GNP500 3.8 40.4 1.0
MG B:MG702 3.8 44.4 1.0
PB B:GNP500 3.8 40.6 1.0
O2B B:GNP500 3.9 41.0 1.0
O1A B:GNP500 4.1 37.0 1.0
O B:HOH1260 4.1 54.5 1.0
OD1 B:ASP393 4.2 37.5 1.0
ND1 B:HIS379 4.2 29.7 1.0
CG B:HIS379 4.3 29.9 1.0
O1G B:GNP500 4.3 41.5 1.0
O3' B:GNP500 4.3 36.0 1.0
O5' B:GNP500 4.3 37.8 1.0
O B:HOH1035 4.4 56.5 1.0
C5' B:GNP500 4.5 37.0 1.0
ND2 B:ASN378 4.6 52.2 1.0
O B:HOH903 4.7 36.4 1.0
C3' B:GNP500 4.8 36.1 1.0
OD2 B:ASP374 4.9 33.8 1.0
CA B:ASP393 5.0 33.5 1.0

Magnesium binding site 4 out of 9 in 5iqh

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Magnesium binding site 4 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:44.4
occ:1.00
 O3G B:GNP500 2.0 40.4 1.0
O2B B:GNP500 2.1 41.0 1.0
O B:HOH902 2.1 42.8 1.0
OD2 B:ASP393 2.1 35.8 1.0
O B:HOH903 2.1 36.4 1.0
OD1 B:ASP393 2.3 37.5 1.0
CG B:ASP393 2.5 36.0 1.0
PG B:GNP500 3.1 41.7 1.0
PB B:GNP500 3.5 40.6 1.0
O2G B:GNP500 3.6 40.3 1.0
N3B B:GNP500 3.8 40.2 1.0
MG B:MG700 3.8 29.3 1.0
O B:HOH911 3.8 36.9 1.0
CB B:ASP393 4.0 36.4 1.0
O B:HOH1299 4.1 54.9 1.0
OD2 B:ASP374 4.2 33.8 1.0
O B:HOH1083 4.3 51.2 1.0
O1B B:GNP500 4.4 41.6 1.0
OD2 B:ASP396 4.4 49.0 1.0
O3A B:GNP500 4.4 39.4 1.0
CA B:GLY395 4.4 32.8 1.0
O1G B:GNP500 4.5 41.5 1.0
NZ B:LYS226 4.5 41.1 1.0
N B:GLY395 4.6 32.0 1.0
O2A B:GNP500 4.6 36.3 1.0
PA B:GNP500 4.8 37.4 1.0
O B:ASP393 4.8 31.4 1.0
CE1 B:HIS379 4.8 30.6 1.0
O1A B:GNP500 4.8 37.0 1.0
CA B:ASP393 4.9 33.5 1.0
C B:GLY395 4.9 32.4 1.0
O B:HOH909 4.9 34.3 1.0
NE2 B:HIS379 5.0 32.6 1.0
CG B:ASP396 5.0 41.7 1.0
O B:HOH951 5.0 27.1 1.0

Magnesium binding site 5 out of 9 in 5iqh

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Magnesium binding site 5 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:33.1
occ:1.00
 O2G C:GNP500 1.7 45.3 1.0
O C:HOH900 1.9 36.7 1.0
O2A C:GNP500 1.9 35.8 1.0
OD2 C:ASP393 2.1 38.4 1.0
NE2 C:HIS379 2.2 34.1 1.0
PG C:GNP500 3.0 51.8 1.0
CG C:ASP393 3.1 36.7 1.0
N3B C:GNP500 3.1 48.0 1.0
CD2 C:HIS379 3.2 34.4 1.0
CE1 C:HIS379 3.2 33.5 1.0
PA C:GNP500 3.2 38.2 1.0
CB C:ASP393 3.6 33.3 1.0
O2B C:GNP500 3.6 49.0 1.0
MG C:MG702 3.7 46.5 1.0
PB C:GNP500 3.7 44.1 1.0
O3G C:GNP500 3.7 49.9 1.0
O3A C:GNP500 3.8 40.5 1.0
O1A C:GNP500 4.0 37.8 1.0
O C:HOH1260 4.1 55.9 1.0
OD1 C:ASP393 4.2 36.7 1.0
ND1 C:HIS379 4.3 32.5 1.0
O1G C:GNP500 4.3 50.4 1.0
CG C:HIS379 4.3 33.2 1.0
O3' C:GNP500 4.4 38.3 1.0
O5' C:GNP500 4.4 40.0 1.0
ND2 C:ASN378 4.4 54.4 1.0
C5' C:GNP500 4.7 41.3 1.0
C3' C:GNP500 4.8 39.5 1.0
OD2 C:ASP374 4.9 42.9 1.0
O C:HOH903 4.9 39.0 1.0

Magnesium binding site 6 out of 9 in 5iqh

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Magnesium binding site 6 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:46.5
occ:1.00
 O3G C:GNP500 1.7 49.9 1.0
O C:HOH902 1.9 41.4 1.0
OD2 C:ASP393 2.1 38.4 1.0
O2B C:GNP500 2.2 49.0 1.0
O C:HOH903 2.3 39.0 1.0
OD1 C:ASP393 2.4 36.7 1.0
CG C:ASP393 2.6 36.7 1.0
PG C:GNP500 3.0 51.8 1.0
O2G C:GNP500 3.4 45.3 1.0
PB C:GNP500 3.6 44.1 1.0
MG C:MG700 3.7 33.1 1.0
N3B C:GNP500 3.7 48.0 1.0
O C:HOH1083 3.8 63.2 1.0
CB C:ASP393 4.1 33.3 1.0
OD2 C:ASP374 4.1 42.9 1.0
O C:HOH911 4.1 42.2 1.0
O1B C:GNP500 4.3 50.0 1.0
O1G C:GNP500 4.3 50.4 1.0
OD2 C:ASP396 4.4 45.3 1.0
O3A C:GNP500 4.6 40.5 1.0
CA C:GLY395 4.6 36.6 1.0
O2A C:GNP500 4.6 35.8 1.0
NZ C:LYS226 4.6 43.0 1.0
N C:GLY395 4.7 35.1 1.0
CE1 C:HIS379 4.7 33.5 1.0
O1A C:GNP500 4.8 37.8 1.0
PA C:GNP500 4.8 38.2 1.0
O C:HOH909 4.8 40.6 1.0
NE2 C:HIS379 4.8 34.1 1.0
O C:ASP393 4.8 33.4 1.0
CA C:ASP393 5.0 33.4 1.0
CG C:ASP396 5.0 41.0 1.0

Magnesium binding site 7 out of 9 in 5iqh

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Magnesium binding site 7 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg800

b:66.8
occ:1.00
 O C:HOH1636 2.1 65.2 1.0
O C:HOH1638 2.3 57.4 1.0
O C:HOH1637 2.5 52.2 1.0
OD1 C:ASN385 2.6 54.1 1.0
CG C:ASN385 3.7 53.5 1.0
ND2 C:ASN385 4.2 54.4 1.0
O C:GLY384 4.7 52.5 1.0
CB C:ASN385 5.0 51.7 1.0

Magnesium binding site 8 out of 9 in 5iqh

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Magnesium binding site 8 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:34.7
occ:1.00
 O2G D:GNP500 1.8 44.5 1.0
O2A D:GNP500 1.9 40.6 1.0
OD2 D:ASP393 2.1 38.1 1.0
O D:HOH900 2.2 44.7 1.0
NE2 D:HIS379 2.2 41.8 1.0
PG D:GNP500 3.0 47.0 1.0
CE1 D:HIS379 3.1 39.0 1.0
CG D:ASP393 3.2 37.1 1.0
CD2 D:HIS379 3.2 41.8 1.0
PA D:GNP500 3.2 40.0 1.0
N3B D:GNP500 3.3 47.5 1.0
CB D:ASP393 3.6 37.1 1.0
O3A D:GNP500 3.7 43.9 1.0
O3G D:GNP500 3.8 48.1 1.0
O2B D:GNP500 3.8 47.8 1.0
PB D:GNP500 3.8 46.9 1.0
MG D:MG702 3.9 42.4 1.0
O1A D:GNP500 4.0 37.6 1.0
ND1 D:HIS379 4.2 38.8 1.0
OD1 D:ASP393 4.3 38.8 1.0
O1G D:GNP500 4.3 47.1 1.0
CG D:HIS379 4.3 40.0 1.0
O3' D:GNP500 4.3 38.1 1.0
O5' D:GNP500 4.4 38.8 1.0
ND2 D:ASN378 4.5 56.9 1.0
C5' D:GNP500 4.6 39.8 1.0
C3' D:GNP500 4.8 39.4 1.0
O D:HOH903 4.8 37.8 1.0
OD2 D:ASP374 4.9 43.6 1.0

Magnesium binding site 9 out of 9 in 5iqh

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Magnesium binding site 9 out of 9 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A 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 9 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) S214A Mutant in Complex with Gmppnp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:42.4
occ:1.00
 O3G D:GNP500 2.0 48.1 1.0
O2B D:GNP500 2.0 47.8 1.0
O D:HOH902 2.0 39.4 1.0
O D:HOH903 2.1 37.8 1.0
OD2 D:ASP393 2.2 38.1 1.0
OD1 D:ASP393 2.3 38.8 1.0
CG D:ASP393 2.6 37.1 1.0
PG D:GNP500 3.1 47.0 1.0
PB D:GNP500 3.4 46.9 1.0
O2G D:GNP500 3.6 44.5 1.0
N3B D:GNP500 3.7 47.5 1.0
O D:HOH1299 3.8 60.1 1.0
MG D:MG700 3.9 34.7 1.0
O D:HOH911 3.9 44.5 1.0
CB D:ASP393 4.1 37.1 1.0
OD2 D:ASP374 4.2 43.6 1.0
O D:HOH1501 4.2 56.1 1.0
O1B D:GNP500 4.2 49.1 1.0
OD2 D:ASP396 4.4 51.7 1.0
O1G D:GNP500 4.4 47.1 1.0
NZ D:LYS226 4.5 42.5 1.0
CA D:GLY395 4.5 39.1 1.0
O3A D:GNP500 4.5 43.9 1.0
N D:GLY395 4.6 37.2 1.0
O2A D:GNP500 4.7 40.6 1.0
O1A D:GNP500 4.8 37.6 1.0
PA D:GNP500 4.8 40.0 1.0
O D:ASP393 4.8 36.0 1.0
CE1 D:HIS379 4.9 39.0 1.0
C D:GLY395 4.9 39.0 1.0
CA D:ASP393 4.9 36.9 1.0
O D:HOH909 4.9 44.8 1.0
CG D:ASP396 4.9 45.2 1.0
O D:HOH951 5.0 33.5 1.0
N D:ASP396 5.0 38.9 1.0
NE2 D:HIS379 5.0 41.8 1.0

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 16:53:28 2024

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