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Magnesium in PDB 5iqf: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium, PDB code: 5iqf 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) 89.13 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.454, 99.075, 92.350, 90.00, 105.18, 90.00
R / Rfree (%) 18 / 22.8

Other elements in 5iqf:

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

Magnesium binding site 1 out of 8 in 5iqf

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Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:44.7
occ:1.00
 O2B A:GDP500 1.9 40.6 1.0
O2A A:GDP500 1.9 41.2 1.0
OD2 A:ASP393 1.9 36.0 1.0
O A:HOH900 2.1 34.4 1.0
O A:HOH901 2.3 39.1 1.0
NE2 A:HIS379 2.5 35.3 1.0
CG A:ASP393 3.0 35.6 1.0
PB A:GDP500 3.0 40.8 1.0
PA A:GDP500 3.0 40.6 1.0
O3A A:GDP500 3.3 40.8 1.0
CE1 A:HIS379 3.3 34.5 1.0
CD2 A:HIS379 3.6 36.4 1.0
CB A:ASP393 3.6 34.3 1.0
O3B A:GDP500 3.6 38.9 1.0
O A:HOH904 3.7 41.8 1.0
MG A:MG702 3.7 37.8 1.0
O A:HOH1287 3.8 49.0 1.0
O1A A:GDP500 4.0 39.7 1.0
OD1 A:ASP393 4.0 35.7 1.0
O3' A:GDP500 4.1 45.2 1.0
O5' A:GDP500 4.1 41.0 1.0
C5' A:GDP500 4.3 41.4 1.0
O1B A:GDP500 4.3 41.0 1.0
O A:HOH1221 4.4 59.7 1.0
ND1 A:HIS379 4.5 35.0 1.0
C3' A:GDP500 4.6 42.9 1.0
CG A:HIS379 4.6 35.4 1.0
OD2 A:ASP374 4.6 37.7 1.0
O A:HOH902 4.8 33.0 1.0
C4' A:GDP500 5.0 42.5 1.0

Magnesium binding site 2 out of 8 in 5iqf

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Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:37.8
occ:1.00
 O A:HOH904 1.9 41.8 1.0
O A:HOH903 1.9 33.6 1.0
O3B A:GDP500 2.0 38.9 1.0
O A:HOH902 2.2 33.0 1.0
OD1 A:ASP393 2.2 35.7 1.0
OD2 A:ASP393 2.3 36.0 1.0
CG A:ASP393 2.6 35.6 1.0
PB A:GDP500 3.0 40.8 1.0
O2B A:GDP500 3.1 40.6 1.0
MG A:MG700 3.7 44.7 1.0
OD2 A:ASP374 4.0 37.7 1.0
O1B A:GDP500 4.0 41.0 1.0
O A:HOH901 4.1 39.1 1.0
CB A:ASP393 4.1 34.3 1.0
OD1 A:ASP396 4.3 39.1 1.0
O3A A:GDP500 4.3 40.8 1.0
CA A:GLY395 4.3 39.7 1.0
O A:HOH991 4.3 45.6 1.0
N A:GLY395 4.5 37.7 1.0
CG A:ASP396 4.6 42.0 1.0
NZ A:LYS226 4.6 50.7 1.0
O A:HOH1287 4.6 49.0 1.0
OD2 A:ASP396 4.7 46.5 1.0
O1A A:GDP500 4.7 39.7 1.0
O2A A:GDP500 4.7 41.2 1.0
PA A:GDP500 4.7 40.6 1.0
C A:GLY395 4.7 40.5 1.0
O A:ASP393 4.8 31.6 1.0
N A:ASP396 4.8 38.5 1.0
O A:HOH951 4.9 29.6 1.0
CA A:ASP393 4.9 35.0 1.0

Magnesium binding site 3 out of 8 in 5iqf

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Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:43.0
occ:1.00
 O2A B:GDP500 1.9 46.2 1.0
O B:HOH901 1.9 40.5 1.0
O1B B:GDP500 2.1 46.3 1.0
O B:HOH900 2.1 36.6 1.0
OD2 B:ASP393 2.1 39.6 1.0
NE2 B:HIS379 2.3 36.4 1.0
PA B:GDP500 3.0 47.4 1.0
PB B:GDP500 3.1 49.3 1.0
CG B:ASP393 3.2 38.5 1.0
CE1 B:HIS379 3.2 34.6 1.0
O3A B:GDP500 3.3 45.7 1.0
CD2 B:HIS379 3.4 36.1 1.0
CB B:ASP393 3.6 37.3 1.0
MG B:MG702 3.7 42.1 1.0
O3' B:GDP500 3.8 43.4 1.0
O2B B:GDP500 3.9 45.7 1.0
O B:HOH1260 4.1 46.0 1.0
O1A B:GDP500 4.1 45.1 1.0
O5' B:GDP500 4.2 46.3 1.0
O B:HOH904 4.2 47.7 1.0
OD1 B:ASP393 4.2 39.8 1.0
ND1 B:HIS379 4.3 34.9 1.0
O3B B:GDP500 4.3 48.5 1.0
C5' B:GDP500 4.4 46.3 1.0
CG B:HIS379 4.5 35.4 1.0
C3' B:GDP500 4.5 43.9 1.0
OD2 B:ASP374 4.7 39.6 1.0
ND2 B:ASN378 4.7 56.5 1.0
O B:HOH902 4.9 34.1 1.0
CA B:GLY211 4.9 57.6 1.0

Magnesium binding site 4 out of 8 in 5iqf

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Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:42.1
occ:1.00
 O B:HOH904 2.0 47.7 1.0
O B:HOH903 2.0 43.7 1.0
O2B B:GDP500 2.1 45.7 1.0
OD2 B:ASP393 2.1 39.6 1.0
O B:HOH902 2.2 34.1 1.0
OD1 B:ASP393 2.2 39.8 1.0
CG B:ASP393 2.5 38.5 1.0
O1B B:GDP500 3.0 46.3 1.0
PB B:GDP500 3.0 49.3 1.0
MG B:MG700 3.7 43.0 1.0
O B:HOH901 3.7 40.5 1.0
O B:HOH909 3.9 41.2 1.0
OD2 B:ASP374 3.9 39.6 1.0
OD2 B:ASP213 4.0 65.9 1.0
CB B:ASP393 4.0 37.3 1.0
O3A B:GDP500 4.1 45.7 1.0
O3B B:GDP500 4.3 48.5 1.0
OD1 B:ASP396 4.3 60.0 1.0
CA B:GLY395 4.5 44.5 1.0
PA B:GDP500 4.5 47.4 1.0
O2A B:GDP500 4.6 46.2 1.0
N B:GLY395 4.7 44.1 1.0
NZ B:LYS226 4.7 46.3 1.0
CG B:ASP396 4.8 51.5 1.0
O B:ASP393 4.8 36.1 1.0
O1A B:GDP500 4.8 45.1 1.0
CE1 B:HIS379 4.8 34.6 1.0
C B:GLY395 4.9 44.3 1.0
CA B:ASP393 4.9 37.2 1.0
CB B:ASP213 4.9 61.8 1.0
CG B:ASP213 4.9 64.8 1.0
N B:ASP396 4.9 44.5 1.0
NE2 B:HIS379 4.9 36.4 1.0
C B:ASP393 5.0 36.5 1.0

Magnesium binding site 5 out of 8 in 5iqf

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Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:37.9
occ:1.00
 O1B C:GDP500 1.8 31.6 1.0
O C:HOH900 2.0 31.8 1.0
OD2 C:ASP393 2.1 32.0 1.0
O2A C:GDP500 2.1 32.6 1.0
O C:HOH901 2.2 30.9 1.0
NE2 C:HIS379 2.4 35.6 1.0
PB C:GDP500 3.0 33.4 1.0
CG C:ASP393 3.1 32.3 1.0
PA C:GDP500 3.2 31.4 1.0
CE1 C:HIS379 3.2 34.2 1.0
O3A C:GDP500 3.4 32.4 1.0
CD2 C:HIS379 3.4 34.4 1.0
CB C:ASP393 3.6 31.4 1.0
O C:HOH904 3.7 30.9 1.0
O2B C:GDP500 3.7 32.0 1.0
MG C:MG702 3.8 37.7 1.0
O C:HOH1571 3.9 53.9 1.0
O C:HOH924 4.1 41.3 1.0
O1A C:GDP500 4.1 31.1 1.0
OD1 C:ASP393 4.2 33.4 1.0
O3' C:GDP500 4.2 38.1 1.0
O5' C:GDP500 4.2 33.1 1.0
O3B C:GDP500 4.3 33.6 1.0
O C:HOH1260 4.3 39.2 1.0
C5' C:GDP500 4.3 34.5 1.0
ND1 C:HIS379 4.4 33.0 1.0
CG C:HIS379 4.5 32.9 1.0
C3' C:GDP500 4.7 35.5 1.0
ND2 C:ASN378 4.7 47.4 1.0
OD2 C:ASP374 4.8 43.1 1.0
O C:HOH902 4.9 28.9 1.0

Magnesium binding site 6 out of 8 in 5iqf

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Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:37.7
occ:1.00
 O C:HOH903 2.0 32.0 1.0
O C:HOH904 2.1 30.9 1.0
O2B C:GDP500 2.1 32.0 1.0
O C:HOH902 2.2 28.9 1.0
OD1 C:ASP393 2.2 33.4 1.0
OD2 C:ASP393 2.2 32.0 1.0
CG C:ASP393 2.5 32.3 1.0
PB C:GDP500 3.2 33.4 1.0
O1B C:GDP500 3.5 31.6 1.0
MG C:MG700 3.8 37.9 1.0
O C:HOH1301 3.8 51.2 1.0
O C:HOH901 3.9 30.9 1.0
OD2 C:ASP374 4.1 43.1 1.0
CB C:ASP393 4.1 31.4 1.0
O C:HOH1083 4.1 47.7 1.0
O3B C:GDP500 4.1 33.6 1.0
O3A C:GDP500 4.3 32.4 1.0
CA C:GLY395 4.4 39.2 1.0
OD1 C:ASP396 4.4 47.3 1.0
NZ C:LYS226 4.5 44.0 1.0
O C:HOH909 4.6 47.5 1.0
N C:GLY395 4.6 36.4 1.0
O C:HOH1575 4.7 80.7 1.0
O C:ASP393 4.8 35.5 1.0
CG C:ASP396 4.8 41.1 1.0
C C:GLY395 4.8 39.3 1.0
CA C:ASP393 4.8 33.4 1.0
PA C:GDP500 4.9 31.4 1.0
O2A C:GDP500 4.9 32.6 1.0
O C:HOH924 4.9 41.3 1.0
OD2 C:ASP396 4.9 40.6 1.0
O C:HOH951 4.9 30.6 1.0
N C:ASP396 4.9 37.4 1.0
O1A C:GDP500 5.0 31.1 1.0
C C:ASP393 5.0 33.4 1.0
CE1 C:HIS379 5.0 34.2 1.0

Magnesium binding site 7 out of 8 in 5iqf

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Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:29.2
occ:1.00
 OD2 D:ASP393 1.9 34.9 1.0
O2A D:GDP500 2.0 30.4 1.0
O D:HOH901 2.1 27.4 1.0
O1B D:GDP500 2.1 31.5 1.0
NE2 D:HIS379 2.2 36.1 1.0
O D:HOH900 2.3 28.2 1.0
CE1 D:HIS379 2.9 35.8 1.0
CG D:ASP393 3.0 33.8 1.0
PB D:GDP500 3.1 32.5 1.0
PA D:GDP500 3.3 31.4 1.0
CD2 D:HIS379 3.4 33.7 1.0
O2B D:GDP500 3.5 31.5 1.0
MG D:MG702 3.6 33.4 1.0
O3A D:GDP500 3.6 31.1 1.0
CB D:ASP393 3.6 33.4 1.0
O D:HOH924 3.7 30.9 1.0
O D:HOH904 3.8 26.0 1.0
OD1 D:ASP393 4.0 33.4 1.0
ND1 D:HIS379 4.1 35.1 1.0
OD2 D:ASP374 4.2 36.8 1.0
O1A D:GDP500 4.2 31.7 1.0
O3' D:GDP500 4.2 34.4 1.0
O3B D:GDP500 4.3 31.1 1.0
CG D:HIS379 4.4 34.6 1.0
O D:HOH1119 4.4 44.9 1.0
O5' D:GDP500 4.5 31.8 1.0
O D:HOH902 4.5 25.4 1.0
ND2 D:ASN378 4.8 63.8 1.0
C5' D:GDP500 4.8 33.8 1.0
C3' D:GDP500 4.8 35.3 1.0
CA D:GLY211 5.0 42.6 1.0

Magnesium binding site 8 out of 8 in 5iqf

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Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:33.4
occ:1.00
 O2B D:GDP500 1.9 31.5 1.0
O D:HOH904 2.0 26.0 1.0
O D:HOH903 2.1 30.2 1.0
O D:HOH902 2.2 25.4 1.0
OD2 D:ASP393 2.2 34.9 1.0
OD1 D:ASP393 2.2 33.4 1.0
CG D:ASP393 2.5 33.8 1.0
PB D:GDP500 3.1 32.5 1.0
O1B D:GDP500 3.4 31.5 1.0
MG D:MG700 3.6 29.2 1.0
O D:HOH909 3.8 34.1 1.0
OD2 D:ASP374 3.9 36.8 1.0
OD2 D:ASP213 3.9 51.8 1.0
CB D:ASP393 4.0 33.4 1.0
O D:HOH901 4.0 27.4 1.0
OD1 D:ASP396 4.2 54.0 1.0
O3A D:GDP500 4.2 31.1 1.0
O3B D:GDP500 4.3 31.1 1.0
CA D:GLY395 4.4 37.7 1.0
O2A D:GDP500 4.5 30.4 1.0
O D:HOH924 4.5 30.9 1.0
N D:GLY395 4.6 37.4 1.0
PA D:GDP500 4.6 31.4 1.0
CG D:ASP396 4.6 47.5 1.0
O1A D:GDP500 4.6 31.7 1.0
O D:HOH1501 4.7 48.9 1.0
O D:ASP393 4.7 31.2 1.0
O D:HOH991 4.7 37.1 1.0
NZ D:LYS226 4.7 36.1 1.0
C D:GLY395 4.7 38.0 1.0
N D:ASP396 4.8 35.6 1.0
CA D:ASP393 4.8 33.7 1.0
CG D:ASP213 4.8 45.6 1.0
OD2 D:ASP396 4.9 49.1 1.0
O D:HOH951 4.9 30.1 1.0
CB D:ASP213 4.9 41.7 1.0
CE1 D:HIS379 4.9 35.8 1.0
C D:ASP393 4.9 33.0 1.0
CG D:ASP374 5.0 35.0 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: Mon Dec 14 20:30:46 2020

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