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Magnesium in PDB 5iqg: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1, PDB code: 5iqg 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) 89.74 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.260, 98.480, 93.020, 90.00, 105.26, 90.00
R / Rfree (%) 18.9 / 23

Other elements in 5iqg:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1 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) in Complex with Gdp, Magnesium, and Gentamicin C1 (pdb code 5iqg). 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 (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1, PDB code: 5iqg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5iqg

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Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:64.3
occ:1.00
 O2B A:GDP500 1.7 59.5 1.0
O A:HOH900 1.9 46.7 1.0
OD2 A:ASP393 2.1 43.9 1.0
O2A A:GDP500 2.3 57.2 1.0
O A:HOH901 2.4 54.0 1.0
NE2 A:HIS379 2.5 47.4 1.0
PB A:GDP500 3.1 61.2 1.0
CE1 A:HIS379 3.2 46.0 1.0
CG A:ASP393 3.2 44.6 1.0
PA A:GDP500 3.4 59.9 1.0
O3A A:GDP500 3.5 61.1 1.0
CD2 A:HIS379 3.6 48.6 1.0
O3B A:GDP500 3.7 62.8 1.0
O A:HOH904 3.8 50.9 1.0
CB A:ASP393 3.8 44.2 1.0
MG A:MG702 3.8 58.2 1.0
O1B A:GDP500 4.0 62.9 1.0
O5' A:GDP500 4.1 59.9 1.0
OD1 A:ASP393 4.3 43.7 1.0
ND1 A:HIS379 4.4 46.3 1.0
OD2 A:ASP374 4.4 52.1 1.0
O1A A:GDP500 4.5 54.2 1.0
O A:HOH1260 4.5 53.7 1.0
O3' A:GDP500 4.6 61.0 1.0
CG A:HIS379 4.6 46.9 1.0
O A:HOH902 4.7 50.7 1.0
ND2 A:ASN378 4.7 63.6 1.0

Magnesium binding site 2 out of 8 in 5iqg

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Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:58.2
occ:1.00
 O3B A:GDP500 1.7 62.8 1.0
O A:HOH903 1.8 55.6 1.0
OD1 A:ASP393 2.0 43.7 1.0
O A:HOH904 2.2 50.9 1.0
OD2 A:ASP393 2.3 43.9 1.0
O A:HOH902 2.3 50.7 1.0
CG A:ASP393 2.5 44.6 1.0
PB A:GDP500 2.9 61.2 1.0
O2B A:GDP500 3.3 59.5 1.0
O3A A:GDP500 3.6 61.1 1.0
MG A:MG700 3.8 64.3 1.0
O1B A:GDP500 4.0 62.9 1.0
NZ A:LYS226 4.0 58.4 1.0
CB A:ASP393 4.0 44.2 1.0
CA A:GLY395 4.1 54.1 1.0
N A:GLY395 4.2 52.7 1.0
OD2 A:ASP396 4.2 61.8 1.0
OD2 A:ASP374 4.4 52.1 1.0
O A:HOH901 4.5 54.0 1.0
C A:GLY395 4.6 56.6 1.0
O2A A:GDP500 4.6 57.2 1.0
PA A:GDP500 4.6 59.9 1.0
O A:ASP393 4.7 45.8 1.0
CA A:ASP393 4.7 45.7 1.0
O A:HOH951 4.7 51.0 1.0
C A:ASP393 4.8 45.8 1.0
N A:ASP396 4.8 56.0 1.0
CG A:ASP396 5.0 60.2 1.0
O1A A:GDP500 5.0 54.2 1.0

Magnesium binding site 3 out of 8 in 5iqg

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Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:71.0
occ:1.00
 O1B B:GDP500 1.9 71.4 1.0
O B:HOH900 2.0 63.0 1.0
O1A B:GDP500 2.0 66.3 1.0
O B:HOH901 2.1 68.0 1.0
OD2 B:ASP393 2.1 40.1 1.0
NE2 B:HIS379 2.3 43.2 1.0
CG B:ASP393 3.1 41.5 1.0
PB B:GDP500 3.2 71.2 1.0
PA B:GDP500 3.2 67.6 1.0
CE1 B:HIS379 3.2 40.4 1.0
CD2 B:HIS379 3.4 43.1 1.0
O3A B:GDP500 3.4 69.3 1.0
CB B:ASP393 3.6 40.1 1.0
MG B:MG702 3.8 65.1 1.0
O B:HOH904 3.8 75.3 1.0
O3B B:GDP500 4.1 69.0 1.0
O5' B:GDP500 4.1 67.8 1.0
O2B B:GDP500 4.1 73.9 1.0
OD1 B:ASP393 4.2 42.3 1.0
O2A B:GDP500 4.2 65.0 1.0
O3' B:GDP500 4.2 68.0 1.0
ND1 B:HIS379 4.3 39.2 1.0
C5' B:GDP500 4.4 68.6 1.0
CG B:HIS379 4.4 40.0 1.0
C3' B:GDP500 4.6 67.1 1.0
ND2 B:ASN378 4.7 58.5 1.0
OD2 B:ASP374 4.7 49.6 1.0
O B:HOH902 4.8 61.3 1.0
O B:HOH1260 4.9 55.5 1.0

Magnesium binding site 4 out of 8 in 5iqg

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Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:65.1
occ:1.00
 O B:HOH904 1.8 75.3 1.0
O B:HOH903 1.8 64.8 1.0
O B:HOH902 2.1 61.3 1.0
OD2 B:ASP393 2.2 40.1 1.0
O3B B:GDP500 2.2 69.0 1.0
OD1 B:ASP393 2.4 42.3 1.0
CG B:ASP393 2.6 41.5 1.0
PB B:GDP500 3.1 71.2 1.0
O1B B:GDP500 3.3 71.4 1.0
MG B:MG700 3.8 71.0 1.0
OD2 B:ASP374 4.0 49.6 1.0
CB B:ASP393 4.1 40.1 1.0
O3A B:GDP500 4.2 69.3 1.0
O2B B:GDP500 4.2 73.9 1.0
O B:HOH901 4.2 68.0 1.0
OD2 B:ASP396 4.3 65.1 1.0
CA B:GLY395 4.4 50.8 1.0
NZ B:LYS226 4.4 56.8 1.0
N B:GLY395 4.6 52.0 1.0
O1A B:GDP500 4.6 66.3 1.0
PA B:GDP500 4.7 67.6 1.0
C B:GLY395 4.8 54.0 1.0
CG B:ASP396 4.8 59.8 1.0
O B:ASP393 4.8 42.3 1.0
O2A B:GDP500 4.9 65.0 1.0
O B:HOH951 4.9 44.0 1.0
N B:ASP396 4.9 53.1 1.0
CA B:ASP393 4.9 41.3 1.0

Magnesium binding site 5 out of 8 in 5iqg

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Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:77.5
occ:1.00
 O3B C:GDP500 1.7 54.7 1.0
O C:HOH901 1.8 47.0 1.0
O C:HOH900 2.0 50.0 1.0
OD2 C:ASP393 2.1 42.6 1.0
O2A C:GDP500 2.1 55.0 1.0
NE2 C:HIS379 2.5 47.4 1.0
PB C:GDP500 3.0 55.0 1.0
CG C:ASP393 3.1 45.5 1.0
PA C:GDP500 3.2 53.0 1.0
CE1 C:HIS379 3.3 47.6 1.0
O3A C:GDP500 3.4 53.6 1.0
O C:HOH904 3.5 42.3 1.0
CD2 C:HIS379 3.5 48.9 1.0
MG C:MG702 3.7 52.0 1.0
CB C:ASP393 3.7 43.7 1.0
O2B C:GDP500 3.8 56.4 1.0
O5' C:GDP500 4.0 51.9 1.0
O C:HOH1575 4.1 53.5 1.0
O1B C:GDP500 4.1 54.6 1.0
OD1 C:ASP393 4.2 48.4 1.0
O1A C:GDP500 4.2 49.6 1.0
O3' C:GDP500 4.4 56.5 1.0
ND1 C:HIS379 4.4 45.9 1.0
O C:HOH902 4.6 38.3 1.0
CG C:HIS379 4.6 46.8 1.0
OD2 C:ASP374 4.7 53.3 1.0
ND2 C:ASN378 4.8 58.9 1.0
O C:HOH1260 4.8 50.4 1.0

Magnesium binding site 6 out of 8 in 5iqg

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Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:52.0
occ:1.00
 O C:HOH903 1.9 56.8 1.0
O C:HOH904 1.9 42.3 1.0
OD2 C:ASP393 2.2 42.6 1.0
O2B C:GDP500 2.2 56.4 1.0
O C:HOH902 2.3 38.3 1.0
OD1 C:ASP393 2.3 48.4 1.0
CG C:ASP393 2.5 45.5 1.0
PB C:GDP500 3.2 55.0 1.0
O3B C:GDP500 3.4 54.7 1.0
MG C:MG700 3.7 77.5 1.0
O C:HOH901 3.7 47.0 1.0
O C:HOH991 3.8 59.2 1.0
O3A C:GDP500 3.8 53.6 1.0
CB C:ASP393 4.0 43.7 1.0
OD2 C:ASP396 4.2 61.2 1.0
OD2 C:ASP374 4.2 53.3 1.0
CA C:GLY395 4.4 55.1 1.0
NZ C:LYS226 4.4 59.4 1.0
O1B C:GDP500 4.4 54.6 1.0
O C:HOH1083 4.5 55.1 1.0
N C:GLY395 4.5 51.7 1.0
O C:HOH909 4.7 45.8 1.0
O2A C:GDP500 4.7 55.0 1.0
O C:ASP393 4.8 43.2 1.0
CA C:ASP393 4.8 45.2 1.0
PA C:GDP500 4.8 53.0 1.0
C C:GLY395 4.9 56.0 1.0
O C:HOH1575 4.9 53.5 1.0
C C:ASP393 5.0 44.2 1.0

Magnesium binding site 7 out of 8 in 5iqg

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Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:50.5
occ:1.00
 O3B D:GDP500 1.8 57.7 1.0
O D:HOH900 1.9 48.9 1.0
OD2 D:ASP393 2.0 44.6 1.0
O1A D:GDP500 2.1 44.9 1.0
NE2 D:HIS379 2.2 54.7 1.0
O D:HOH901 2.3 50.5 1.0
CE1 D:HIS379 2.9 53.1 1.0
CG D:ASP393 3.1 45.7 1.0
PB D:GDP500 3.2 56.5 1.0
CD2 D:HIS379 3.4 51.9 1.0
PA D:GDP500 3.4 51.8 1.0
O D:HOH924 3.6 52.0 1.0
MG D:MG702 3.6 54.0 1.0
O3A D:GDP500 3.7 50.8 1.0
CB D:ASP393 3.7 46.6 1.0
O1B D:GDP500 3.8 54.7 1.0
O D:HOH904 3.8 39.0 1.0
O3' D:GDP500 4.1 52.4 1.0
ND1 D:HIS379 4.1 51.3 1.0
O2B D:GDP500 4.1 55.2 1.0
OD1 D:ASP393 4.2 45.1 1.0
O2A D:GDP500 4.3 49.0 1.0
OD2 D:ASP374 4.3 59.5 1.0
CG D:HIS379 4.4 52.6 1.0
O5' D:GDP500 4.4 51.0 1.0
O D:HOH902 4.5 57.0 1.0
ND2 D:ASN378 4.5 61.4 1.0
C5' D:GDP500 4.6 52.6 1.0
C3' D:GDP500 4.6 53.6 1.0
O D:HOH1260 4.6 50.0 1.0
CA D:GLY211 5.0 59.9 1.0

Magnesium binding site 8 out of 8 in 5iqg

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Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1


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) in Complex with Gdp, Magnesium, and Gentamicin C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:54.0
occ:1.00
 O D:HOH903 1.9 48.2 1.0
O D:HOH904 1.9 39.0 1.0
O1B D:GDP500 1.9 54.7 1.0
OD2 D:ASP393 2.1 44.6 1.0
OD1 D:ASP393 2.2 45.1 1.0
O D:HOH902 2.3 57.0 1.0
CG D:ASP393 2.4 45.7 1.0
PB D:GDP500 3.0 56.5 1.0
O3B D:GDP500 3.3 57.7 1.0
MG D:MG700 3.6 50.5 1.0
O3A D:GDP500 3.8 50.8 1.0
CB D:ASP393 3.9 46.6 1.0
O D:HOH909 4.0 52.8 1.0
OD2 D:ASP396 4.0 66.8 1.0
OD2 D:ASP374 4.1 59.5 1.0
O D:HOH901 4.2 50.5 1.0
O2B D:GDP500 4.2 55.2 1.0
NZ D:LYS226 4.3 61.9 1.0
O1A D:GDP500 4.3 44.9 1.0
OD2 D:ASP213 4.3 74.4 1.0
CA D:GLY395 4.4 50.8 1.0
PA D:GDP500 4.5 51.8 1.0
N D:GLY395 4.5 54.4 1.0
O2A D:GDP500 4.6 49.0 1.0
O D:HOH924 4.6 52.0 1.0
O D:ASP393 4.7 43.0 1.0
CA D:ASP393 4.8 47.3 1.0
C D:GLY395 4.8 51.0 1.0
C D:ASP393 4.9 46.9 1.0
CG D:ASP396 4.9 58.6 1.0
CB D:ASP213 4.9 61.1 1.0
O D:HOH951 4.9 48.2 1.0
N D:ASP396 4.9 49.9 1.0
CG D:ASP213 5.0 65.4 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 16:51:22 2024

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