Atomistry » Magnesium » PDB 6cfv-6cpt » 6cgg
Atomistry »
  Magnesium »
    PDB 6cfv-6cpt »
      6cgg »

Magnesium in PDB 6cgg: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin

Enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin

All present enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin:
2.7.1.190;

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin, PDB code: 6cgg 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) 90.14 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.330, 99.780, 93.510, 90.00, 105.43, 90.00
R / Rfree (%) 17.8 / 22.3

Other elements in 6cgg:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin 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 in Complex with Gmppnp, Magnesium, and Arbekacin (pdb code 6cgg). 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 in Complex with Gmppnp, Magnesium, and Arbekacin, PDB code: 6cgg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:46.0
occ:1.00
 O A:HOH901 1.8 44.6 1.0
O2A A:GNP500 2.0 42.1 1.0
O A:HOH900 2.0 45.3 1.0
OD2 A:ASP393 2.1 43.4 1.0
NE2 A:HIS379 2.4 45.6 1.0
O2B A:GNP500 2.6 51.0 1.0
PA A:GNP500 3.1 42.5 1.0
CG A:ASP393 3.2 41.8 1.0
PB A:GNP500 3.3 48.3 1.0
CE1 A:HIS379 3.3 43.5 1.0
O3A A:GNP500 3.4 44.7 1.0
CD2 A:HIS379 3.4 45.0 1.0
MG A:MG702 3.5 47.9 1.0
CB A:ASP393 3.7 40.3 1.0
O A:HOH1221 3.8 45.4 1.0
O1B A:GNP500 3.8 49.6 1.0
O A:HOH904 4.1 52.1 1.0
O1A A:GNP500 4.1 39.9 1.0
O A:HOH921 4.2 48.5 1.0
OD1 A:ASP393 4.3 41.6 1.0
O5' A:GNP500 4.4 43.2 1.0
ND1 A:HIS379 4.5 43.2 1.0
CG A:HIS379 4.5 42.0 1.0
C5' A:GNP500 4.5 44.7 1.0
N3B A:GNP500 4.6 48.9 1.0
O3G A:GNP500 4.7 49.5 1.0
O A:HOH902 4.8 37.3 1.0
O3' A:GNP500 4.9 42.1 1.0

Magnesium binding site 2 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:47.9
occ:1.00
 O3G A:GNP500 1.9 49.5 1.0
OD2 A:ASP393 1.9 43.4 1.0
O A:HOH904 2.0 52.1 1.0
OD1 A:ASP393 2.2 41.6 1.0
CG A:ASP393 2.4 41.8 1.0
O A:HOH903 2.4 46.4 1.0
O A:HOH902 2.6 37.3 1.0
PG A:GNP500 2.9 51.7 1.0
O2B A:GNP500 3.0 51.0 1.0
O2G A:GNP500 3.1 52.6 1.0
O A:HOH901 3.4 44.6 1.0
MG A:MG700 3.5 46.0 1.0
N3B A:GNP500 3.6 48.9 1.0
PB A:GNP500 3.6 48.3 1.0
CB A:ASP393 3.9 40.3 1.0
O3A A:GNP500 4.0 44.7 1.0
NZ A:LYS226 4.1 51.7 1.0
O1G A:GNP500 4.3 51.6 1.0
OD2 A:ASP374 4.4 49.6 1.0
O2A A:GNP500 4.4 42.1 1.0
PA A:GNP500 4.6 42.5 1.0
O A:HOH1029 4.6 62.6 1.0
O1A A:GNP500 4.6 39.9 1.0
CA A:GLY395 4.8 47.9 1.0
O A:HOH991 4.8 50.5 1.0
CA A:ASP393 4.8 40.4 1.0
O A:HOH921 4.8 48.5 1.0
N A:GLY395 4.9 45.5 1.0
NE2 A:HIS379 4.9 45.6 1.0
CE1 A:HIS379 4.9 43.5 1.0
O A:ASP393 4.9 39.2 1.0

Magnesium binding site 3 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:45.6
occ:1.00
 O B:HOH901 1.8 41.2 0.7
O1A B:GNP500 1.9 38.0 1.0
O B:HOH900 2.0 44.8 1.0
O1G B:GNP500 2.0 44.4 0.3
OD2 B:ASP393 2.1 45.2 1.0
NE2 B:HIS379 2.3 44.7 1.0
O2B B:GNP500 2.5 44.5 0.7
O B:HOH904 3.0 52.9 0.7
CG B:ASP393 3.1 43.9 1.0
PA B:GNP500 3.1 39.1 1.0
CD2 B:HIS379 3.2 44.3 1.0
CE1 B:HIS379 3.3 42.7 1.0
PG B:GNP500 3.4 46.3 0.3
PB B:GNP500 3.5 42.3 0.7
CB B:ASP393 3.5 43.0 1.0
O3A B:GNP500 3.5 39.6 0.3
N3B B:GNP500 3.5 43.4 0.3
O3A B:GNP500 3.6 40.5 0.7
O1B B:GNP500 3.6 41.2 0.3
PB B:GNP500 3.7 40.9 0.3
O B:84G600 4.0 59.1 0.5
MG B:MG702 4.0 65.8 1.0
O2A B:GNP500 4.1 38.0 1.0
OD1 B:ASP393 4.1 44.8 1.0
O3G B:GNP500 4.1 47.7 0.3
O1B B:GNP500 4.2 46.7 0.7
O5' B:GNP500 4.3 40.2 1.0
ND1 B:HIS379 4.3 41.3 1.0
CG B:HIS379 4.4 43.2 1.0
O B:HOH1035 4.5 64.2 1.0
O2G B:GNP500 4.5 48.9 0.3
C5' B:GNP500 4.5 42.2 1.0
O3' B:GNP500 4.6 42.5 1.0
N3B B:GNP500 4.8 44.4 0.7
OD1 B:ASN378 4.8 66.0 1.0
C3' B:GNP500 4.9 41.2 1.0

Magnesium binding site 4 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:65.8
occ:1.00
 O B:HOH904 2.0 52.9 0.7
O1B B:GNP500 2.1 41.2 0.3
O B:HOH903 2.2 78.2 1.0
OD2 B:ASP393 2.3 45.2 1.0
OD1 B:ASP393 2.3 44.8 1.0
O3G B:GNP500 2.4 46.6 0.7
CG B:ASP393 2.6 43.9 1.0
O3G B:GNP500 3.0 47.7 0.3
O2G B:GNP500 3.3 49.7 0.7
PG B:GNP500 3.3 47.5 0.7
O2B B:GNP500 3.5 44.5 0.7
O B:HOH924 3.6 21.6 0.3
PB B:GNP500 3.7 40.9 0.3
PG B:GNP500 3.9 46.3 0.3
O1G B:GNP500 3.9 44.4 0.3
MG B:MG700 4.0 45.6 1.0
N3B B:GNP500 4.0 44.4 0.7
O B:HOH901 4.0 41.2 0.7
N3B B:GNP500 4.1 43.4 0.3
PB B:GNP500 4.2 42.3 0.7
CB B:ASP393 4.2 43.0 1.0
OD2 B:ASP374 4.2 46.5 1.0
O2B B:GNP500 4.3 41.7 0.3
CA B:GLY395 4.4 44.0 1.0
NZ B:LYS226 4.4 51.3 1.0
OD2 B:ASP396 4.5 54.3 1.0
N B:GLY395 4.6 41.9 1.0
O3A B:GNP500 4.7 39.6 0.3
O3A B:GNP500 4.8 40.5 0.7
C B:GLY395 4.8 46.2 1.0
CG B:ASP396 4.8 50.5 1.0
O1G B:GNP500 4.8 46.8 0.7
OD1 B:ASP396 4.8 56.9 1.0
O B:HOH909 4.8 32.1 0.3
O B:ASP393 4.8 40.7 1.0
N B:ASP396 4.9 45.8 1.0
O1A B:GNP500 5.0 38.0 1.0
CA B:ASP393 5.0 42.6 1.0
CE1 B:HIS379 5.0 42.7 1.0

Magnesium binding site 5 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:49.4
occ:1.00
 O2A C:GNP500 1.8 46.6 1.0
O C:HOH901 1.8 48.0 1.0
O C:HOH900 1.9 50.3 1.0
OD2 C:ASP393 2.3 45.5 1.0
O2B C:GNP500 2.3 50.5 1.0
NE2 C:HIS379 2.5 45.4 1.0
PA C:GNP500 3.0 45.9 1.0
PB C:GNP500 3.3 48.7 1.0
CD2 C:HIS379 3.4 45.2 1.0
CG C:ASP393 3.4 45.2 1.0
CE1 C:HIS379 3.4 45.2 1.0
O3A C:GNP500 3.4 46.8 1.0
CB C:ASP393 3.8 44.4 1.0
O1B C:GNP500 3.8 51.2 1.0
MG C:MG702 4.0 53.8 1.0
O1A C:GNP500 4.0 43.8 1.0
O C:HOH921 4.1 46.7 1.0
O5' C:GNP500 4.2 46.2 1.0
O C:HOH904 4.2 55.7 1.0
C5' C:GNP500 4.5 46.0 1.0
OD1 C:ASP393 4.5 45.5 1.0
CG C:HIS379 4.5 44.8 1.0
ND1 C:HIS379 4.5 45.0 1.0
O3' C:GNP500 4.6 47.3 1.0
O3G C:GNP500 4.6 52.6 1.0
N3B C:GNP500 4.7 50.5 1.0
C3' C:GNP500 4.9 46.4 1.0

Magnesium binding site 6 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:53.8
occ:1.00
 O C:HOH904 1.8 55.7 1.0
O3G C:GNP500 2.0 52.6 1.0
O C:HOH903 2.2 55.5 1.0
OD2 C:ASP393 2.2 45.5 1.0
O C:HOH902 2.4 48.7 1.0
OD1 C:ASP393 2.5 45.5 1.0
CG C:ASP393 2.7 45.2 1.0
PG C:GNP500 3.1 55.1 1.0
O2B C:GNP500 3.1 50.5 1.0
O2G C:GNP500 3.2 55.6 1.0
O C:HOH901 3.3 48.0 1.0
N3B C:GNP500 3.9 50.5 1.0
PB C:GNP500 3.9 48.7 1.0
MG C:MG700 4.0 49.4 1.0
CB C:ASP393 4.2 44.4 1.0
OD2 C:ASP374 4.2 51.7 1.0
O C:HOH1083 4.3 61.3 1.0
O1G C:GNP500 4.3 55.2 1.0
NZ C:LYS226 4.5 53.9 1.0
O3A C:GNP500 4.5 46.8 1.0
O C:HOH991 4.5 60.2 1.0
OD2 C:ASP396 4.7 54.0 1.0
O2A C:GNP500 4.8 46.6 1.0
CA C:GLY395 4.8 50.0 1.0
O C:HOH921 4.8 46.7 1.0
OD1 C:ASP396 4.9 54.4 1.0
PA C:GNP500 4.9 45.9 1.0
N C:GLY395 4.9 47.8 1.0
CE1 C:HIS379 4.9 45.2 1.0
O C:HOH1571 5.0 65.2 1.0
CG C:ASP396 5.0 52.9 1.0

Magnesium binding site 7 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:52.7
occ:1.00
 O1A D:GNP500 1.8 49.8 1.0
O D:HOH900 1.8 58.9 1.0
O2G D:GNP500 1.9 51.8 0.5
OD2 D:ASP393 2.0 57.0 1.0
O D:HOH901 2.1 67.1 0.5
O2B D:GNP500 2.4 55.9 0.5
NE2 D:HIS379 2.6 57.0 1.0
PG D:GNP500 3.0 52.9 0.5
PA D:GNP500 3.0 50.7 1.0
N3B D:GNP500 3.1 52.0 0.5
CG D:ASP393 3.1 57.1 1.0
PB D:GNP500 3.3 55.5 0.5
O3A D:GNP500 3.4 50.7 0.5
O3A D:GNP500 3.4 52.6 0.5
PB D:GNP500 3.4 51.8 0.5
CD2 D:HIS379 3.5 56.4 1.0
CE1 D:HIS379 3.5 57.2 1.0
O1B D:GNP500 3.5 52.6 0.5
CB D:ASP393 3.6 55.9 1.0
MG D:MG702 3.6 72.0 1.0
O1G D:GNP500 3.7 53.2 0.5
O2A D:GNP500 4.0 50.1 1.0
O1B D:GNP500 4.2 58.9 0.5
OD1 D:ASP393 4.2 59.1 1.0
O D:84G600 4.2 87.3 1.0
O3G D:GNP500 4.2 53.9 0.5
O3' D:GNP500 4.3 52.1 1.0
O5' D:GNP500 4.3 52.7 1.0
C5' D:GNP500 4.4 53.4 1.0
O D:HOH902 4.5 69.5 1.0
ND1 D:HIS379 4.6 55.6 1.0
CG D:HIS379 4.6 56.3 1.0
N3B D:GNP500 4.7 57.5 0.5
C3' D:GNP500 4.7 52.7 1.0
OD1 D:ASN378 4.9 77.5 1.0
O2B D:GNP500 4.9 52.7 0.5
C1 D:84G600 4.9 90.5 1.0
C2 D:84G600 4.9 88.0 1.0

Magnesium binding site 8 out of 8 in 6cgg

Go back to Magnesium Binding Sites List in 6cgg
Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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

b:72.0
occ:1.00
 O1B D:GNP500 1.9 52.6 0.5
O D:HOH902 2.1 69.5 1.0
OD2 D:ASP393 2.1 57.0 1.0
O1G D:GNP500 2.3 53.2 0.5
O D:HOH903 2.3 60.3 1.0
OD1 D:ASP393 2.4 59.1 1.0
CG D:ASP393 2.6 57.1 1.0
O3G D:GNP500 2.8 61.1 0.5
O2B D:GNP500 3.0 55.9 0.5
O1G D:GNP500 3.1 60.7 0.5
PG D:GNP500 3.2 60.3 0.5
PB D:GNP500 3.3 51.8 0.5
O D:HOH901 3.3 67.1 0.5
PG D:GNP500 3.3 52.9 0.5
N3B D:GNP500 3.6 52.0 0.5
MG D:MG700 3.6 52.7 1.0
N3B D:GNP500 3.7 57.5 0.5
O2G D:GNP500 3.7 51.8 0.5
PB D:GNP500 3.7 55.5 0.5
CB D:ASP393 4.1 55.9 1.0
O2B D:GNP500 4.1 52.7 0.5
O D:HOH1083 4.2 69.3 1.0
O3A D:GNP500 4.3 52.6 0.5
OD2 D:ASP374 4.3 57.4 1.0
O3A D:GNP500 4.3 50.7 0.5
NZ D:LYS226 4.5 68.2 1.0
O1A D:GNP500 4.6 49.8 1.0
O3G D:GNP500 4.6 53.9 0.5
O D:HOH909 4.7 35.3 0.5
CA D:GLY395 4.7 56.0 1.0
O2G D:GNP500 4.7 59.8 0.5
PA D:GNP500 4.8 50.7 1.0
CE1 D:HIS379 4.9 57.2 1.0
OD2 D:ASP396 4.9 55.6 1.0
NE2 D:HIS379 4.9 57.0 1.0
N D:GLY395 4.9 56.3 1.0

Reference:

S.J.Caldwell, A.M.Berghuis. Plasticity of Aminoglycoside Binding to Antibiotic Kinase Aph(2′′)-Ia. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 29661878
DOI: 10.1128/AAC.00202-18
Page generated: Mon Sep 30 22:16:00 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