Magnesium in PDB 4n57: Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex

The structure of Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex, PDB code: 4n57 was solved by E.Kaplan, N.Leban, L.Chaloin, J.-F.Guichou, C.Lionne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.93 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.051, 65.802, 76.731, 90.00, 92.43, 90.00
R / Rfree (%)	18.2 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex (pdb code 4n57). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex, PDB code: 4n57:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:43.6 occ:1.00 O1A A:ADP403 1.9 47.8 1.0 O3B A:ADP403 2.3 57.0 1.0 O A:HOH599 2.4 44.5 1.0 OD2 A:ASP217 2.5 32.1 1.0 NE2 A:HIS202 2.5 30.8 1.0 O A:HOH557 2.6 44.7 1.0 PA A:ADP403 3.0 43.0 1.0 O3A A:ADP403 3.2 29.6 1.0 PB A:ADP403 3.3 48.6 1.0 CE1 A:HIS202 3.3 29.1 1.0 CG A:ASP217 3.4 38.9 1.0 CD2 A:HIS202 3.5 35.9 1.0 CB A:ASP217 3.9 36.7 1.0 O5' A:ADP403 4.1 49.8 1.0 O2A A:ADP403 4.1 46.2 1.0 O1B A:ADP403 4.2 56.4 1.0 C5' A:ADP403 4.3 40.7 1.0 MG A:MG402 4.3 41.2 1.0 OD1 A:ASP217 4.4 40.1 1.0 ND1 A:HIS202 4.5 31.1 1.0 O2B A:ADP403 4.5 41.8 1.0 O3' A:ADP403 4.5 41.9 1.0 CG A:HIS202 4.6 38.7 1.0 O A:HOH568 4.6 32.1 1.0 C3' A:ADP403 4.8 40.4 1.0 CA A:GLY31 4.8 51.9 1.0 ND2 A:ASN32 5.0 53.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:41.2 occ:1.00 O A:HOH574 2.0 40.0 1.0 O A:HOH568 2.1 32.1 1.0 OD1 A:ASP217 2.5 40.1 1.0 O1B A:ADP403 2.5 56.4 1.0 OD2 A:ASP217 2.6 32.1 1.0 O3B A:ADP403 2.8 57.0 1.0 CG A:ASP217 2.9 38.9 1.0 PB A:ADP403 3.1 48.6 1.0 OD2 A:ASP220 3.3 65.0 1.0 O A:HOH599 3.8 44.5 1.0 OD2 A:ASP197 4.1 45.2 1.0 O A:HOH584 4.1 38.6 1.0 CA A:GLY219 4.1 35.8 1.0 O2B A:ADP403 4.2 41.8 1.0 OD2 A:ASP33 4.3 34.2 1.0 MG A:MG401 4.3 43.6 1.0 N A:GLY219 4.4 35.6 1.0 CB A:ASP217 4.4 36.7 1.0 O3A A:ADP403 4.4 29.6 1.0 CG A:ASP220 4.5 57.1 1.0 N A:ASP220 4.5 30.7 1.0 C A:GLY219 4.5 36.8 1.0 NZ A:LYS46 4.8 34.9 1.0 O A:HOH580 4.8 52.6 1.0 O2A A:ADP403 4.8 46.2 1.0 PA A:ADP403 4.9 43.0 1.0 O A:HOH534 4.9 32.1 1.0 O1A A:ADP403 5.0 47.8 1.0 CB A:ASP33 5.0 34.3 1.0 CG A:ASP33 5.0 34.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:33.2 occ:1.00 O1A B:ADP403 2.1 30.8 1.0 O1B B:ADP403 2.1 35.0 1.0 OD2 B:ASP217 2.2 27.1 1.0 O B:HOH571 2.3 46.7 1.0 NE2 B:HIS202 2.4 23.1 1.0 O B:HOH611 2.4 47.4 1.0 CE1 B:HIS202 3.0 27.4 1.0 PA B:ADP403 3.3 47.1 1.0 PB B:ADP403 3.3 32.3 1.0 CG B:ASP217 3.4 36.0 1.0 CD2 B:HIS202 3.5 21.5 1.0 O3A B:ADP403 3.6 44.3 1.0 MG B:MG402 3.8 37.3 1.0 O2B B:ADP403 4.0 42.8 1.0 CB B:ASP217 4.1 26.8 1.0 ND1 B:HIS202 4.3 23.2 1.0 OD1 B:ASP217 4.3 45.7 1.0 O2A B:ADP403 4.3 32.0 1.0 O5' B:ADP403 4.4 37.6 1.0 OD2 B:ASP197 4.5 27.6 1.0 O B:HOH557 4.5 44.5 1.0 CG B:HIS202 4.5 25.4 1.0 CA B:GLY31 4.5 30.9 1.0 O3B B:ADP403 4.5 26.3 1.0 C5' B:ADP403 4.6 28.8 1.0 O B:HOH581 4.8 38.5 1.0 O3' B:ADP403 5.0 39.6 1.0 N B:ASN32 5.0 34.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:37.3 occ:1.00 O2B B:ADP403 2.0 42.8 1.0 O B:HOH580 2.1 24.9 1.0 O B:HOH581 2.2 38.5 1.0 OD1 B:ASP217 2.3 45.7 1.0 OD2 B:ASP217 2.4 27.1 1.0 CG B:ASP217 2.7 36.0 1.0 O1B B:ADP403 3.0 35.0 1.0 PB B:ADP403 3.0 32.3 1.0 O B:HOH611 3.6 47.4 1.0 MG B:MG401 3.8 33.2 1.0 OD2 B:ASP33 4.0 40.5 1.0 OD2 B:ASP197 4.0 27.6 1.0 O3A B:ADP403 4.1 44.3 1.0 O3B B:ADP403 4.2 26.3 1.0 CB B:ASP217 4.2 26.8 1.0 OD1 B:ASP220 4.4 34.3 1.0 O1A B:ADP403 4.5 30.8 1.0 CA B:GLY219 4.5 35.4 1.0 PA B:ADP403 4.6 47.1 1.0 N B:GLY219 4.6 35.2 1.0 NZ B:LYS46 4.6 31.4 1.0 CG B:ASP33 4.6 33.0 1.0 O2A B:ADP403 4.6 32.0 1.0 CG B:ASP220 4.8 35.5 1.0 CB B:ASP33 4.9 31.9 1.0 N B:ASP220 4.9 25.7 1.0 C B:GLY219 4.9 38.9 1.0 CE1 B:HIS202 5.0 27.4 1.0 OD2 B:ASP220 5.0 47.7 1.0

E.Kaplan, N.Leban, L.Chaloin, J.-F.Guichou, C.Lionne. Crystal Structure of Aminoglycoside Phosphotransferase Aph(2'')-Iva Adp Complex To Be Published.