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

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin, PDB code: 6cav 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) 89.94 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.990, 98.340, 93.220, 90.00, 105.24, 90.00
R / Rfree (%) 19.2 / 24.4

Other elements in 6cav:

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

Magnesium binding site 1 out of 8 in 6cav

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Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:48.3
occ:1.00
 OD2 A:ASP393 1.9 51.3 1.0
O2B A:GNP500 2.0 47.9 1.0
O A:HOH900 2.1 39.9 1.0
NE2 A:HIS379 2.3 45.7 1.0
O2A A:GNP500 2.3 47.0 1.0
O A:HOH904 2.4 43.8 1.0
CG A:ASP393 3.1 47.9 1.0
CE1 A:HIS379 3.1 45.6 1.0
PB A:GNP500 3.3 45.7 1.0
CD2 A:HIS379 3.4 46.0 1.0
PA A:GNP500 3.5 45.7 1.0
MG A:MG702 3.6 53.9 1.0
O3A A:GNP500 3.6 47.0 1.0
CB A:ASP393 3.8 44.0 1.0
O3G A:GNP500 4.1 53.3 1.0
O A:HOH1221 4.1 41.2 1.0
OD1 A:ASP393 4.1 47.5 1.0
O1B A:GNP500 4.1 48.7 1.0
O1A A:GNP500 4.3 47.5 1.0
O7 A:84D600 4.3 57.2 1.0
ND1 A:HIS379 4.3 44.5 1.0
CG A:HIS379 4.5 44.8 1.0
ND2 A:ASN378 4.5 52.8 1.0
N3B A:GNP500 4.5 48.7 1.0
OD2 A:ASP374 4.6 55.3 1.0
O5' A:GNP500 4.6 45.0 1.0
O A:HOH902 4.7 62.8 1.0
C5' A:GNP500 4.8 46.5 1.0
O3' A:GNP500 4.8 52.7 1.0
PG A:GNP500 4.9 53.1 1.0

Magnesium binding site 2 out of 8 in 6cav

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Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:53.9
occ:1.00
 O3G A:GNP500 1.9 53.3 1.0
O A:HOH902 2.1 62.8 1.0
OD2 A:ASP393 2.3 51.3 1.0
OD1 A:ASP393 2.3 47.5 1.0
O A:HOH903 2.4 50.1 1.0
CG A:ASP393 2.7 47.9 1.0
PG A:GNP500 3.1 53.1 1.0
O2G A:GNP500 3.2 55.2 1.0
O2B A:GNP500 3.3 47.9 1.0
O A:HOH904 3.4 43.8 1.0
MG A:MG700 3.6 48.3 1.0
N1 A:84D600 3.7 61.4 1.0
OD2 A:ASP374 3.7 55.3 1.0
N3B A:GNP500 4.0 48.7 1.0
PB A:GNP500 4.1 45.7 1.0
O1G A:GNP500 4.2 55.5 1.0
CB A:ASP393 4.3 44.0 1.0
OD1 A:ASP396 4.5 55.5 1.0
OD2 A:ASP396 4.6 53.2 1.0
O A:HOH921 4.7 56.5 1.0
NZ A:LYS226 4.7 51.1 1.0
CG A:ASP396 4.7 52.7 1.0
O3A A:GNP500 4.7 47.0 1.0
CE1 A:HIS379 4.8 45.6 1.0
O7 A:84D600 4.8 57.2 1.0
CA A:GLY395 4.8 46.7 1.0
NE2 A:HIS379 4.8 45.7 1.0
O2A A:GNP500 4.9 47.0 1.0
CG A:ASP374 4.9 49.9 1.0
C14 A:84D600 5.0 60.5 1.0
N A:GLY395 5.0 44.3 1.0

Magnesium binding site 3 out of 8 in 6cav

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Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:52.8
occ:1.00
 NE2 B:HIS379 2.4 46.0 1.0
O1B B:GNP500 2.4 65.3 1.0
OD2 B:ASP393 2.5 48.6 1.0
O1A B:GNP500 2.6 56.0 1.0
CE1 B:HIS379 3.2 42.4 1.0
O7 B:84D600 3.3 52.5 1.0
CD2 B:HIS379 3.5 45.1 1.0
PB B:GNP500 3.6 63.0 1.0
CG B:ASP393 3.7 47.1 1.0
MG B:MG702 3.8 69.4 1.0
PA B:GNP500 3.9 55.6 1.0
ND2 B:ASN378 4.0 48.5 1.0
O3A B:GNP500 4.2 59.3 1.0
O2B B:GNP500 4.2 65.5 1.0
ND1 B:HIS379 4.4 41.8 1.0
CB B:ASP393 4.4 46.7 1.0
CG B:HIS379 4.5 43.4 1.0
OD1 B:ASP393 4.7 43.1 1.0
OD2 B:ASP374 4.7 52.1 1.0
C13 B:84D600 4.7 55.6 1.0
O5' B:GNP500 4.8 55.9 1.0
O3' B:GNP500 4.8 57.1 1.0
O1G B:GNP500 4.8 64.1 1.0
C5' B:GNP500 4.8 57.8 1.0
N3B B:GNP500 4.9 65.8 1.0

Magnesium binding site 4 out of 8 in 6cav

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Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:69.4
occ:1.00
 O B:HOH903 2.2 74.7 1.0
OD2 B:ASP393 2.2 48.6 1.0
O1G B:GNP500 2.4 64.1 1.0
O B:HOH902 2.5 57.0 1.0
OD1 B:ASP393 2.6 43.1 1.0
CG B:ASP393 2.7 47.1 1.0
N1 B:84D600 3.1 58.2 1.0
O1B B:GNP500 3.3 65.3 1.0
PG B:GNP500 3.4 67.7 1.0
O3G B:GNP500 3.4 71.5 1.0
OD2 B:ASP374 3.4 52.1 1.0
MG B:MG700 3.8 52.8 1.0
O7 B:84D600 3.9 52.5 1.0
O B:HOH921 4.0 32.6 0.7
N3B B:GNP500 4.2 65.8 1.0
PB B:GNP500 4.2 63.0 1.0
CB B:ASP393 4.3 46.7 1.0
C14 B:84D600 4.3 55.4 1.0
OD1 B:ASP396 4.4 51.4 1.0
CE1 B:HIS379 4.5 42.4 1.0
C13 B:84D600 4.5 55.6 1.0
OD2 B:ASP396 4.6 54.1 1.0
O1A B:GNP500 4.6 56.0 1.0
NE2 B:HIS379 4.6 46.0 1.0
CG B:ASP374 4.6 49.0 1.0
CG B:ASP396 4.7 50.3 1.0
O3A B:GNP500 4.7 59.3 1.0
O2G B:GNP500 4.8 68.5 1.0

Magnesium binding site 5 out of 8 in 6cav

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Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:46.9
occ:1.00
 O C:HOH900 1.7 54.4 1.0
O2B C:GNP500 1.9 53.2 1.0
OD2 C:ASP393 2.1 50.5 1.0
O2A C:GNP500 2.3 49.7 1.0
NE2 C:HIS379 2.5 50.3 1.0
PB C:GNP500 3.2 50.5 1.0
CE1 C:HIS379 3.3 47.5 1.0
CG C:ASP393 3.3 51.3 1.0
PA C:GNP500 3.5 49.6 1.0
MG C:MG702 3.6 56.2 1.0
CD2 C:HIS379 3.6 51.2 1.0
O3A C:GNP500 3.7 50.3 1.0
O1B C:GNP500 3.9 51.7 1.0
CB C:ASP393 4.1 50.0 1.0
O3G C:GNP500 4.1 53.7 1.0
OD1 C:ASP393 4.3 53.7 1.0
ND2 C:ASN378 4.4 61.4 1.0
ND1 C:HIS379 4.5 49.6 1.0
N3B C:GNP500 4.5 50.8 1.0
O1A C:GNP500 4.5 49.9 1.0
O7 C:84D600 4.6 63.9 1.0
O5' C:GNP500 4.6 49.8 1.0
C5' C:GNP500 4.6 52.0 1.0
CG C:HIS379 4.7 50.9 1.0
OD2 C:ASP374 4.7 54.7 1.0
O C:HOH902 4.8 51.2 1.0
PG C:GNP500 4.9 53.9 1.0
O3' C:GNP500 5.0 56.6 1.0

Magnesium binding site 6 out of 8 in 6cav

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Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:56.2
occ:1.00
 O3G C:GNP500 2.0 53.7 1.0
O C:HOH902 2.1 51.2 1.0
O C:HOH903 2.3 43.6 1.0
OD2 C:ASP393 2.4 50.5 1.0
OD1 C:ASP393 2.6 53.7 1.0
CG C:ASP393 2.8 51.3 1.0
O2B C:GNP500 3.1 53.2 1.0
PG C:GNP500 3.2 53.9 1.0
O2G C:GNP500 3.2 56.0 1.0
N1 C:84D600 3.4 67.8 1.0
MG C:MG700 3.6 46.9 1.0
OD2 C:ASP374 3.7 54.7 1.0
N3B C:GNP500 4.1 50.8 1.0
PB C:GNP500 4.1 50.5 1.0
CB C:ASP393 4.4 50.0 1.0
O1G C:GNP500 4.4 55.7 1.0
OD2 C:ASP396 4.5 54.2 1.0
O3A C:GNP500 4.7 50.3 1.0
OD1 C:ASP396 4.7 52.7 1.0
CE1 C:HIS379 4.7 47.5 1.0
CG C:ASP396 4.7 54.3 1.0
NE2 C:HIS379 4.8 50.3 1.0
C14 C:84D600 4.8 64.6 1.0
O2A C:GNP500 4.9 49.7 1.0
CG C:ASP374 4.9 51.2 1.0
NZ C:LYS226 4.9 54.2 1.0
CA C:GLY395 5.0 52.8 1.0

Magnesium binding site 7 out of 8 in 6cav

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Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:64.0
occ:1.00
 N3B D:GNP500 1.9 72.6 1.0
NE2 D:HIS379 2.4 62.6 1.0
O1A D:GNP500 2.5 61.3 1.0
OD2 D:ASP393 2.5 62.7 1.0
PB D:GNP500 3.2 67.4 1.0
O7 D:84D600 3.3 47.5 1.0
CE1 D:HIS379 3.3 58.3 1.0
CD2 D:HIS379 3.5 58.3 1.0
O D:HOH1119 3.6 57.4 1.0
CG D:ASP393 3.6 58.1 1.0
O3A D:GNP500 3.8 63.9 1.0
PA D:GNP500 3.8 60.5 1.0
O2B D:GNP500 3.8 72.7 1.0
ND2 D:ASN378 4.1 65.1 1.0
MG D:MG702 4.2 59.7 1.0
CB D:ASP393 4.3 57.2 1.0
O1B D:GNP500 4.4 70.1 1.0
C5' D:GNP500 4.4 65.6 1.0
ND1 D:HIS379 4.4 55.0 1.0
OD1 D:ASP393 4.6 58.1 1.0
CG D:HIS379 4.6 55.4 1.0
O3' D:GNP500 4.6 64.4 1.0
O5' D:GNP500 4.7 63.4 1.0
C13 D:84D600 4.7 51.6 1.0
OD2 D:ASP374 4.8 70.7 1.0
O2A D:GNP500 5.0 57.1 1.0

Magnesium binding site 8 out of 8 in 6cav

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Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:59.7
occ:1.00
 OD1 D:ASP393 2.3 58.1 1.0
OD2 D:ASP393 2.5 62.7 1.0
CG D:ASP393 2.8 58.1 1.0
O1B D:GNP500 3.2 70.1 1.0
N3B D:GNP500 3.2 72.6 1.0
N1 D:84D600 3.2 56.2 1.0
OD2 D:ASP374 3.7 70.7 1.0
PB D:GNP500 3.8 67.4 1.0
OD1 D:ASP396 4.1 59.0 1.0
O7 D:84D600 4.2 47.5 1.0
MG D:MG700 4.2 64.0 1.0
CB D:ASP393 4.4 57.2 1.0
CA D:GLY395 4.5 56.6 1.0
CG D:ASP396 4.5 58.1 1.0
C14 D:84D600 4.6 52.7 1.0
OD2 D:ASP396 4.6 57.7 1.0
NZ D:LYS226 4.6 63.4 1.0
O3A D:GNP500 4.7 63.9 1.0
C D:GLY395 4.8 54.2 1.0
N D:GLY395 4.8 58.7 1.0
N D:ASP396 4.8 55.0 1.0
C13 D:84D600 4.9 51.6 1.0
O D:HOH951 4.9 50.9 1.0
CE1 D:HIS379 4.9 58.3 1.0
O1A D:GNP500 4.9 61.3 1.0
CG D:ASP374 5.0 65.5 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 20:25:58 2024

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