Atomistry » Magnesium » PDB 5btm-5c25 » 5byl
Atomistry »
  Magnesium »
    PDB 5btm-5c25 »
      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: Sun Sep 29 01:47:13 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy