Atomistry » Magnesium » PDB 5btc-5c1b » 5byl
Atomistry »
  Magnesium »
    PDB 5btc-5c1b »
      5byl »

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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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

Go back to Magnesium Binding Sites List in 5byl
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: Mon Dec 14 20:04:37 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy