Magnesium in PDB 6fzb: Aada in Complex with Atp, Magnesium and Streptomycin

All present enzymatic activity of Aada in Complex with Atp, Magnesium and Streptomycin:
2.7.7.47;

The structure of Aada in Complex with Atp, Magnesium and Streptomycin, PDB code: 6fzb was solved by S.Kanchugal P, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.34 / 2.05
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	82.670, 82.670, 79.860, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.8

The structure of Aada in Complex with Atp, Magnesium and Streptomycin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Aada in Complex with Atp, Magnesium and Streptomycin (pdb code 6fzb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Aada in Complex with Atp, Magnesium and Streptomycin, PDB code: 6fzb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Aada in Complex with Atp, Magnesium and Streptomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aada in Complex with Atp, Magnesium and Streptomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:28.3 occ:1.00 O2B A:ATP304 1.9 32.2 1.0 O2G A:ATP304 2.0 29.3 1.0 O2A A:ATP304 2.0 35.7 1.0 OD1 A:ASP47 2.1 41.0 1.0 O A:HOH407 2.1 28.1 1.0 OD2 A:ASP49 2.2 36.9 1.0 PB A:ATP304 3.1 34.9 1.0 CG A:ASP47 3.2 38.8 1.0 CG A:ASP49 3.2 35.6 1.0 PA A:ATP304 3.3 38.3 1.0 PG A:ATP304 3.3 32.7 1.0 MG A:MG303 3.4 47.1 1.0 OD1 A:ASP49 3.5 36.7 1.0 H A:SER36 3.6 36.7 1.0 OD2 A:ASP47 3.6 41.5 1.0 H A:ASP47 3.6 42.5 1.0 O3A A:ATP304 3.6 38.1 1.0 O3B A:ATP304 3.7 32.6 1.0 O A:ASP47 3.9 38.2 1.0 O A:HOH483 4.0 55.0 1.0 O3G A:ATP304 4.0 32.6 1.0 OG A:SER36 4.1 33.2 1.0 HG A:SER36 4.1 39.9 1.0 HA3 A:GLY35 4.2 41.3 1.0 O1A A:ATP304 4.2 38.7 1.0 N A:ASP47 4.3 35.4 1.0 O A:HOH444 4.3 30.8 1.0 C A:ASP47 4.4 36.1 1.0 HB3 A:SER46 4.4 37.5 1.0 CB A:ASP47 4.4 34.9 1.0 N A:SER36 4.5 30.6 1.0 O1B A:ATP304 4.5 33.2 1.0 O5' A:ATP304 4.5 44.2 1.0 CB A:ASP49 4.5 35.9 1.0 O1G A:ATP304 4.5 32.7 1.0 HB2 A:ASP49 4.5 43.1 1.0 HB3 A:SER36 4.6 41.2 1.0 CA A:ASP47 4.6 34.4 1.0 H A:ASP49 4.8 43.3 1.0 CB A:SER36 4.8 34.4 1.0 CA A:GLY35 5.0 34.4 1.0 HB3 A:ASP47 5.0 41.9 1.0 N A:ASP49 5.0 36.1 1.0

Magnesium binding site 2 out of 4 in the Aada in Complex with Atp, Magnesium and Streptomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aada in Complex with Atp, Magnesium and Streptomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:47.1 occ:1.00 OE1 A:GLU87 2.0 66.9 1.0 OD1 A:ASP49 2.2 36.7 1.0 OD2 A:ASP47 2.3 41.5 1.0 O2A A:ATP304 2.4 35.7 1.0 O A:HOH425 3.1 49.6 1.0 CD A:GLU87 3.1 62.3 1.0 CG A:ASP47 3.2 38.8 1.0 CG A:ASP49 3.2 35.6 1.0 OD1 A:ASP47 3.3 41.0 1.0 HN23 A:SRY301 3.4 0.5 1.0 HO33 A:SRY301 3.4 0.6 1.0 PA A:ATP304 3.4 38.3 1.0 MG A:MG302 3.4 28.3 1.0 OD2 A:ASP49 3.5 36.9 1.0 HB3 A:GLU87 3.6 53.5 1.0 O5' A:ATP304 3.7 44.2 1.0 HB2 A:GLU87 3.8 53.5 1.0 OE2 A:GLU87 3.8 65.8 1.0 O33 A:SRY301 3.9 86.3 1.0 O1A A:ATP304 3.9 38.7 1.0 O A:HOH411 3.9 42.0 1.0 CB A:GLU87 4.0 44.6 1.0 CG A:GLU87 4.1 54.4 1.0 N23 A:SRY301 4.4 87.1 1.0 O A:HOH483 4.5 55.0 1.0 CB A:ASP47 4.6 34.9 1.0 CB A:ASP49 4.6 35.9 1.0 HG2 A:GLU87 4.6 65.3 1.0 O2G A:ATP304 4.6 29.3 1.0 O2B A:ATP304 4.6 32.2 1.0 HA A:ASP49 4.7 42.4 1.0 HB3 A:ASP49 4.8 43.1 1.0 HB2 A:ASP47 4.8 41.9 1.0 O3A A:ATP304 4.8 38.1 1.0 HG3 A:GLU87 4.8 65.3 1.0 HB3 A:ASP47 4.9 41.9 1.0 C33 A:SRY301 4.9 86.0 1.0 HI32 A:SRY301 5.0 0.5 1.0

Magnesium binding site 3 out of 4 in the Aada in Complex with Atp, Magnesium and Streptomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aada in Complex with Atp, Magnesium and Streptomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:28.0 occ:1.00 O1B B:ATP304 1.9 33.4 1.0 O1A B:ATP304 2.0 36.0 1.0 O2G B:ATP304 2.1 30.0 1.0 OD1 B:ASP47 2.1 39.1 1.0 O B:HOH405 2.2 27.0 1.0 OD2 B:ASP49 2.2 38.7 1.0 PB B:ATP304 3.1 34.1 1.0 CG B:ASP47 3.2 37.6 1.0 CG B:ASP49 3.2 36.8 1.0 PA B:ATP304 3.3 39.6 1.0 PG B:ATP304 3.4 33.4 1.0 MG B:MG303 3.4 45.4 1.0 OD1 B:ASP49 3.5 41.2 1.0 H B:SER36 3.6 39.9 1.0 OD2 B:ASP47 3.6 40.8 1.0 O3A B:ATP304 3.6 35.4 1.0 O3B B:ATP304 3.7 33.5 1.0 H B:ASP47 3.7 43.6 1.0 O B:ASP47 3.9 35.8 1.0 O B:HOH484 3.9 36.6 1.0 O B:HOH472 4.0 53.8 1.0 O1G B:ATP304 4.0 32.2 1.0 OG B:SER36 4.1 32.1 1.0 HA3 B:GLY35 4.1 37.8 1.0 HG B:SER36 4.1 38.5 1.0 O2A B:ATP304 4.1 40.0 1.0 N B:ASP47 4.4 36.3 1.0 O B:HOH423 4.4 31.3 1.0 C B:ASP47 4.4 35.5 1.0 N B:SER36 4.4 33.2 1.0 CB B:ASP47 4.5 36.6 1.0 O2B B:ATP304 4.5 32.5 1.0 O5' B:ATP304 4.5 46.0 1.0 CB B:ASP49 4.5 34.6 1.0 HB3 B:SER46 4.5 39.9 1.0 HB2 B:ASP49 4.5 41.6 1.0 HB3 B:SER36 4.5 42.3 1.0 O3G B:ATP304 4.5 31.9 1.0 CA B:ASP47 4.6 35.8 1.0 CB B:SER36 4.8 35.3 1.0 H B:ASP49 4.9 38.9 1.0 CA B:GLY35 4.9 31.5 1.0 HA2 B:GLY35 5.0 37.8 1.0 HB2 B:ASP47 5.0 43.9 1.0

Magnesium binding site 4 out of 4 in the Aada in Complex with Atp, Magnesium and Streptomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aada in Complex with Atp, Magnesium and Streptomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:45.4 occ:1.00 OE1 B:GLU87 2.1 69.4 1.0 OD2 B:ASP47 2.2 40.8 1.0 O1A B:ATP304 2.4 36.0 1.0 OD1 B:ASP49 2.4 41.2 1.0 CD B:GLU87 3.0 63.9 1.0 CG B:ASP47 3.1 37.6 1.0 O B:HOH462 3.3 51.6 1.0 CG B:ASP49 3.3 36.8 1.0 OD1 B:ASP47 3.3 39.1 1.0 PA B:ATP304 3.4 39.6 1.0 MG B:MG302 3.4 28.0 1.0 HO33 B:SRY301 3.5 97.2 1.0 OD2 B:ASP49 3.6 38.7 1.0 OE2 B:GLU87 3.6 68.5 1.0 HB3 B:GLU87 3.6 53.4 1.0 O5' B:ATP304 3.7 46.0 1.0 HB2 B:GLU87 3.7 53.4 1.0 O2A B:ATP304 3.9 40.0 1.0 O B:HOH439 4.0 42.3 1.0 CB B:GLU87 4.0 44.5 1.0 HN23 B:SRY301 4.0 98.0 1.0 CG B:GLU87 4.1 54.5 1.0 O33 B:SRY301 4.1 81.0 1.0 O B:HOH484 4.3 36.6 1.0 N23 B:SRY301 4.3 81.6 1.0 O B:HOH472 4.4 53.8 1.0 CB B:ASP47 4.5 36.6 1.0 HG2 B:GLU87 4.5 65.4 1.0 O2G B:ATP304 4.6 30.0 1.0 HB2 B:ASP47 4.7 43.9 1.0 CB B:ASP49 4.7 34.6 1.0 O1B B:ATP304 4.7 33.4 1.0 HG3 B:GLU87 4.8 65.4 1.0 HI31 B:SRY301 4.8 97.6 1.0 O3A B:ATP304 4.8 35.4 1.0 HB3 B:ASP47 4.8 43.9 1.0 HA B:ASP49 4.9 40.6 1.0 HB3 B:ASP49 4.9 41.6 1.0 H33 B:SRY301 4.9 98.1 1.0

A.L.Stern, S.E.Van Der Verren, S.Kanchugal P, J.Nasvall, H.Gutierrez-De-Teran, M.Selmer. Structural Mechanism of Aada, A Dual-Specificity Aminoglycoside Adenylyltransferase Fromsalmonella Enterica. J. Biol. Chem. V. 293 11481 2018.
ISSN: ESSN 1083-351X
PubMed: 29871922
DOI: 10.1074/JBC.RA118.003989