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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium, PDB code: 5byl 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) 58.92 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.290, 99.900, 93.620, 90.00, 105.09, 90.00
R / Rfree (%) 15.6 / 19.8

Other elements in 5byl:

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

Magnesium binding site 1 out of 9 in 5byl

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

b:30.8
occ:1.00
 O2G A:GCP500 1.8 37.8 0.8
O2A A:GCP500 1.9 32.6 1.0
O A:HOH900 2.0 37.6 1.0
OD2 A:ASP393 2.2 37.1 1.0
NE2 A:HIS379 2.2 30.1 1.0
O A:HOH901 2.2 51.1 0.2
O1B A:GCP500 2.4 30.4 0.2
CE1 A:HIS379 3.1 29.0 1.0
CD2 A:HIS379 3.2 28.1 1.0
PA A:GCP500 3.2 35.4 1.0
CG A:ASP393 3.2 38.4 1.0
PG A:GCP500 3.2 39.9 0.8
O3A A:GCP500 3.4 36.7 0.8
PB A:GCP500 3.5 30.1 0.2
CB A:ASP393 3.6 35.0 1.0
O3A A:GCP500 3.6 32.0 0.2
O3G A:GCP500 3.6 41.8 0.8
MG A:MG702 3.9 47.0 1.0
O2B A:GCP500 3.9 34.5 0.8
O A:HOH1221 3.9 57.2 1.0
O1A A:GCP500 4.1 34.2 1.0
PB A:GCP500 4.1 34.2 0.8
C3B A:GCP500 4.2 37.5 0.8
ND1 A:HIS379 4.2 27.1 1.0
O2B A:GCP500 4.2 32.1 0.2
CG A:HIS379 4.3 26.1 1.0
O1G A:GCP500 4.3 38.2 0.8
OD1 A:ASP393 4.3 36.0 1.0
O5' A:GCP500 4.4 35.4 1.0
ND2 A:ASN378 4.5 63.4 1.0
O3' A:GCP500 4.5 39.3 1.0
C5' A:GCP500 4.6 35.2 1.0
OD2 A:ASP374 4.8 36.3 1.0
C3' A:GCP500 4.8 35.1 1.0
O A:HOH902 4.9 36.3 1.0

Magnesium binding site 2 out of 9 in 5byl

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

b:47.0
occ:1.00
 O A:HOH903 1.9 40.9 1.0
O3G A:GCP500 2.0 41.8 0.8
O2B A:GCP500 2.1 34.5 0.8
O3G A:GCP500 2.1 26.6 0.2
OD2 A:ASP393 2.1 37.1 1.0
O A:HOH902 2.2 36.3 1.0
OD1 A:ASP393 2.3 36.0 1.0
CG A:ASP393 2.5 38.4 1.0
O1B A:GCP500 3.0 30.4 0.2
PG A:GCP500 3.2 27.8 0.2
PG A:GCP500 3.2 39.9 0.8
O2G A:GCP500 3.2 28.9 0.2
PB A:GCP500 3.4 34.2 0.8
O2G A:GCP500 3.5 37.8 0.8
C3B A:GCP500 3.7 37.5 0.8
PB A:GCP500 3.8 30.1 0.2
O A:HOH901 3.9 51.1 0.2
MG A:MG700 3.9 30.8 1.0
C3B A:GCP500 4.0 29.1 0.2
O A:HOH911 4.0 39.5 1.0
CB A:ASP393 4.0 35.0 1.0
OD2 A:ASP374 4.1 36.3 1.0
O3A A:GCP500 4.2 32.0 0.2
O3A A:GCP500 4.2 36.7 0.8
NZ A:LYS226 4.3 40.3 1.0
O A:HOH1083 4.4 51.6 1.0
O1G A:GCP500 4.4 28.1 0.2
O1B A:GCP500 4.4 36.4 0.8
O2A A:GCP500 4.5 32.6 1.0
O1G A:GCP500 4.5 38.2 0.8
CA A:GLY395 4.5 35.3 1.0
O1A A:GCP500 4.6 34.2 1.0
N A:GLY395 4.6 33.1 1.0
OD2 A:ASP396 4.6 49.7 1.0
PA A:GCP500 4.7 35.4 1.0
CA A:ASP393 4.9 35.7 1.0
O A:ASP393 4.9 31.4 1.0
C A:GLY395 5.0 38.6 1.0
CE1 A:HIS379 5.0 29.0 1.0

Magnesium binding site 3 out of 9 in 5byl

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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) in Complex with Gmppcp 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) in Complex with Gmppcp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:26.9
occ:1.00
 O2G B:GCP500 1.7 45.4 1.0
O B:HOH900 1.9 34.3 1.0
O2A B:GCP500 2.0 31.3 1.0
OD2 B:ASP393 2.2 32.9 1.0
NE2 B:HIS379 2.2 29.7 1.0
CE1 B:HIS379 3.1 26.4 1.0
CG B:ASP393 3.2 35.7 1.0
CD2 B:HIS379 3.2 31.2 1.0
PG B:GCP500 3.2 46.3 1.0
PA B:GCP500 3.2 35.2 1.0
O3A B:GCP500 3.5 38.5 1.0
CB B:ASP393 3.6 35.0 1.0
O3G B:GCP500 3.8 39.6 1.0
MG B:MG702 3.9 40.8 1.0
O2B B:GCP500 4.0 38.6 1.0
C3B B:GCP500 4.0 42.3 1.0
PB B:GCP500 4.0 39.0 1.0
O1A B:GCP500 4.1 34.8 1.0
ND1 B:HIS379 4.2 27.7 1.0
OD1 B:ASP393 4.3 33.8 1.0
CG B:HIS379 4.3 29.1 1.0
O1G B:GCP500 4.3 44.5 1.0
O B:HOH1260 4.3 60.7 1.0
O3' B:GCP500 4.4 36.5 1.0
O5' B:GCP500 4.4 36.8 1.0
ND2 B:ASN378 4.5 52.9 1.0
C5' B:GCP500 4.6 37.5 1.0
O B:HOH902 4.7 34.9 1.0
OD2 B:ASP374 4.8 30.5 1.0
C3' B:GCP500 4.8 35.6 1.0

Magnesium binding site 4 out of 9 in 5byl

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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) in Complex with Gmppcp 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) in Complex with Gmppcp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:40.8
occ:1.00
 O B:HOH903 1.9 36.0 1.0
O3G B:GCP500 2.0 39.6 1.0
O2B B:GCP500 2.1 38.6 1.0
O B:HOH902 2.2 34.9 1.0
OD2 B:ASP393 2.2 32.9 1.0
OD1 B:ASP393 2.3 33.8 1.0
CG B:ASP393 2.5 35.7 1.0
PG B:GCP500 3.2 46.3 1.0
PB B:GCP500 3.5 39.0 1.0
O2G B:GCP500 3.5 45.4 1.0
O B:HOH1299 3.8 69.0 1.0
C3B B:GCP500 3.8 42.3 1.0
MG B:MG700 3.9 26.9 1.0
O B:HOH911 3.9 38.0 1.0
CB B:ASP393 4.1 35.0 1.0
OD2 B:ASP374 4.2 30.5 1.0
O B:HOH1083 4.3 51.2 1.0
O3A B:GCP500 4.3 38.5 1.0
NZ B:LYS226 4.3 37.2 1.0
O1B B:GCP500 4.4 38.4 1.0
CA B:GLY395 4.4 34.5 1.0
O1G B:GCP500 4.5 44.5 1.0
OD2 B:ASP396 4.6 48.9 1.0
N B:GLY395 4.6 31.6 1.0
O2A B:GCP500 4.6 31.3 1.0
O1A B:GCP500 4.6 34.8 1.0
PA B:GCP500 4.8 35.2 1.0
C B:GLY395 4.9 32.7 1.0
O B:ASP393 4.9 31.8 1.0
CA B:ASP393 4.9 32.1 1.0

Magnesium binding site 5 out of 9 in 5byl

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

b:35.0
occ:1.00
 O2G C:GCP500 1.7 42.4 0.7
O C:HOH900 1.9 37.3 1.0
O2A C:GCP500 2.0 33.7 1.0
OD2 C:ASP393 2.2 34.4 1.0
NE2 C:HIS379 2.2 35.6 1.0
O1B C:GCP500 2.3 33.9 0.3
O C:HOH901 2.5 27.2 0.3
CE1 C:HIS379 3.1 33.4 1.0
PG C:GCP500 3.1 41.9 0.7
CG C:ASP393 3.2 34.8 1.0
CD2 C:HIS379 3.2 34.6 1.0
PA C:GCP500 3.3 37.0 1.0
PB C:GCP500 3.5 37.6 0.3
O3A C:GCP500 3.6 37.8 0.7
O3G C:GCP500 3.6 45.4 0.7
CB C:ASP393 3.7 32.3 1.0
O3A C:GCP500 3.8 36.7 0.3
O2B C:GCP500 3.8 38.2 0.7
O C:HOH1260 3.9 53.0 1.0
MG C:MG702 4.0 43.0 1.0
C3B C:GCP500 4.0 43.4 0.7
PB C:GCP500 4.1 40.9 0.7
O1A C:GCP500 4.2 37.2 1.0
O2B C:GCP500 4.2 38.2 0.3
O1G C:GCP500 4.2 40.8 0.7
O C:HOH904 4.2 29.1 0.3
ND1 C:HIS379 4.2 30.8 1.0
OD1 C:ASP393 4.3 34.8 1.0
CG C:HIS379 4.3 33.7 1.0
O3' C:GCP500 4.4 42.5 1.0
O5' C:GCP500 4.4 38.9 1.0
ND2 C:ASN378 4.4 53.1 1.0
OD2 C:ASP374 4.8 36.8 1.0
C5' C:GCP500 4.8 39.2 1.0
O C:HOH902 4.9 36.6 1.0
C3' C:GCP500 4.9 39.7 1.0

Magnesium binding site 6 out of 9 in 5byl

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

b:43.0
occ:1.00
 O C:HOH904 1.6 29.1 0.3
O C:HOH903 1.8 48.5 1.0
O2B C:GCP500 2.1 38.2 0.7
O C:HOH902 2.2 36.6 1.0
O3G C:GCP500 2.2 45.4 0.7
OD2 C:ASP393 2.3 34.4 1.0
OD1 C:ASP393 2.3 34.8 1.0
O3G C:GCP500 2.4 37.4 0.3
CG C:ASP393 2.6 34.8 1.0
O2G C:GCP500 2.7 39.5 0.3
O1B C:GCP500 3.0 33.9 0.3
PG C:GCP500 3.1 41.2 0.3
PG C:GCP500 3.5 41.9 0.7
O C:HOH901 3.6 27.2 0.3
PB C:GCP500 3.6 40.9 0.7
O2G C:GCP500 3.7 42.4 0.7
PB C:GCP500 3.9 37.6 0.3
MG C:MG700 4.0 35.0 1.0
O C:HOH911 4.0 45.8 1.0
OD2 C:ASP374 4.1 36.8 1.0
C3B C:GCP500 4.1 43.4 0.7
C3B C:GCP500 4.1 39.0 0.3
CB C:ASP393 4.1 32.3 1.0
CA C:GLY395 4.4 40.6 1.0
NZ C:LYS226 4.4 45.5 1.0
O1G C:GCP500 4.4 40.0 0.3
O3A C:GCP500 4.5 36.7 0.3
O3A C:GCP500 4.5 37.8 0.7
N C:GLY395 4.6 36.2 1.0
OD2 C:ASP396 4.6 54.2 1.0
O1B C:GCP500 4.6 41.4 0.7
O2A C:GCP500 4.7 33.7 1.0
O1G C:GCP500 4.8 40.8 0.7
C C:GLY395 4.9 40.9 1.0
PA C:GCP500 4.9 37.0 1.0
O1A C:GCP500 4.9 37.2 1.0
O C:ASP393 4.9 33.6 1.0
CA C:ASP393 4.9 32.9 1.0
CG C:ASP396 5.0 43.9 1.0

Magnesium binding site 7 out of 9 in 5byl

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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) in Complex with Gmppcp 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) in Complex with Gmppcp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg800

b:74.1
occ:1.00
 O C:HOH1638 2.3 59.5 1.0
O C:HOH1637 2.3 46.1 1.0
OD1 C:ASN385 2.3 59.0 1.0
O C:HOH1636 2.4 53.1 1.0
CG C:ASN385 3.4 53.8 1.0
ND2 C:ASN385 3.9 54.0 1.0
O C:GLY384 4.4 54.9 1.0
C C:GLY384 4.7 50.3 1.0
CB C:ASN385 4.7 52.0 1.0
N C:ASN385 4.9 49.1 1.0
CA C:ASN385 5.0 50.4 1.0

Magnesium binding site 8 out of 9 in 5byl

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

b:36.9
occ:1.00
 O2G D:GCP500 1.8 47.2 1.0
O2A D:GCP500 1.9 37.0 1.0
O D:HOH900 2.0 42.4 1.0
NE2 D:HIS379 2.1 37.9 1.0
OD2 D:ASP393 2.1 38.4 1.0
CE1 D:HIS379 3.1 34.5 1.0
CD2 D:HIS379 3.1 36.9 1.0
CG D:ASP393 3.1 38.2 1.0
PA D:GCP500 3.2 39.5 1.0
PG D:GCP500 3.2 50.0 1.0
CB D:ASP393 3.5 39.8 1.0
O3A D:GCP500 3.6 44.5 1.0
O3G D:GCP500 3.8 45.2 1.0
MG D:MG702 3.8 41.1 1.0
O2B D:GCP500 3.9 45.5 1.0
C3B D:GCP500 4.0 50.0 1.0
O1A D:GCP500 4.0 36.4 1.0
PB D:GCP500 4.1 49.1 1.0
ND1 D:HIS379 4.1 33.7 1.0
CG D:HIS379 4.2 36.2 1.0
OD1 D:ASP393 4.2 39.8 1.0
O3' D:GCP500 4.3 38.8 1.0
O1G D:GCP500 4.3 49.8 1.0
O5' D:GCP500 4.4 40.8 1.0
ND2 D:ASN378 4.5 61.3 1.0
O D:HOH1119 4.6 65.5 1.0
C5' D:GCP500 4.6 42.2 1.0
C3' D:GCP500 4.7 39.9 1.0
OD2 D:ASP374 4.8 42.9 1.0
O D:HOH902 4.8 38.0 1.0

Magnesium binding site 9 out of 9 in 5byl

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

b:41.1
occ:1.00
 O D:HOH903 1.9 41.7 1.0
O2B D:GCP500 1.9 45.5 1.0
O3G D:GCP500 2.0 45.2 1.0
OD2 D:ASP393 2.1 38.4 1.0
O D:HOH902 2.2 38.0 1.0
OD1 D:ASP393 2.3 39.8 1.0
CG D:ASP393 2.5 38.2 1.0
PG D:GCP500 3.0 50.0 1.0
PB D:GCP500 3.3 49.1 1.0
O2G D:GCP500 3.4 47.2 1.0
C3B D:GCP500 3.6 50.0 1.0
O D:HOH1299 3.6 65.8 1.0
MG D:MG700 3.8 36.9 1.0
O D:HOH911 3.9 44.1 1.0
CB D:ASP393 4.0 39.8 1.0
OD2 D:ASP374 4.2 42.9 1.0
O3A D:GCP500 4.2 44.5 1.0
NZ D:LYS226 4.3 46.7 1.0
O1G D:GCP500 4.3 49.8 1.0
O1B D:GCP500 4.4 47.6 1.0
O2A D:GCP500 4.5 37.0 1.0
CA D:GLY395 4.5 39.6 1.0
O1A D:GCP500 4.6 36.4 1.0
PA D:GCP500 4.6 39.5 1.0
OD2 D:ASP396 4.6 50.0 1.0
N D:GLY395 4.6 38.8 1.0
O D:HOH1029 4.8 58.1 1.0
CA D:ASP393 4.9 39.5 1.0
C D:GLY395 4.9 39.5 1.0
O D:ASP393 4.9 36.7 1.0
CE1 D:HIS379 5.0 34.5 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 01:47:13 2024

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