Calcium in PDB 5lpa: Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin

All present enzymatic activity of Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin:
2.7.7.47;

The structure of Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin, PDB code: 5lpa was solved by A.L.Stern, S.E.Van Der Verren, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.44 / 1.40
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	82.885, 82.885, 79.782, 90.00, 90.00, 120.00
R / Rfree (%)	14.6 / 17.8

The structure of Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin (pdb code 5lpa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin, PDB code: 5lpa:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:10.8 occ:1.00 OD1 A:ASP47 2.2 14.1 1.0 O2G A:ATP301 2.4 10.6 1.0 O A:HOH454 2.4 11.1 1.0 O2A A:ATP301 2.4 11.2 1.0 OD2 A:ASP49 2.4 14.7 1.0 O2B A:ATP301 2.4 10.8 1.0 OD1 A:ASP49 2.7 16.5 1.0 CG A:ASP49 2.9 12.8 1.0 CG A:ASP47 3.4 15.1 1.0 PB A:ATP301 3.4 9.8 1.0 CA A:CA305 3.5 15.9 0.5 PA A:ATP301 3.5 10.8 1.0 PG A:ATP301 3.6 9.6 1.0 O3A A:ATP301 3.7 11.3 1.0 O3B A:ATP301 3.8 10.6 1.0 OD2 A:ASP47 3.9 17.8 1.0 O A:HOH604 4.0 16.2 1.0 O A:ASP47 4.1 13.9 1.0 O A:HOH528 4.2 20.2 1.0 O A:HOH411 4.2 17.8 1.0 O3G A:ATP301 4.2 10.4 1.0 OG A:SER36 4.3 9.6 1.0 O A:HOH482 4.4 10.8 1.0 CB A:ASP49 4.4 11.5 1.0 N A:ASP47 4.4 11.8 1.0 N A:SER36 4.5 8.2 1.0 C A:ASP47 4.5 12.5 1.0 O1A A:ATP301 4.6 13.6 1.0 O5' A:ATP301 4.6 12.2 1.0 O A:HOH583 4.6 18.2 0.5 CB A:ASP47 4.6 12.8 1.0 CA A:ASP47 4.7 11.5 1.0 O1B A:ATP301 4.8 11.2 1.0 O1G A:ATP301 4.8 11.9 1.0 N A:ASP49 5.0 10.5 1.0 OE1 A:GLN87 5.0 21.2 0.7

Calcium binding site 2 out of 4 in the Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:15.9 occ:0.52 OE1 A:GLN87 1.7 21.2 0.7 OE1 A:GLN87 2.4 18.1 0.3 O A:HOH411 2.5 17.8 1.0 O2A A:ATP301 2.5 11.2 1.0 OD1 A:ASP49 2.6 16.5 1.0 OD2 A:ASP47 2.6 17.8 1.0 O A:HOH583 2.7 18.2 0.5 CD A:GLN87 2.9 21.5 0.7 CD A:GLN87 2.9 19.2 0.3 NE2 A:GLN87 3.3 19.9 0.3 CG A:ASP47 3.4 15.1 1.0 OD1 A:ASP47 3.4 14.1 1.0 CA A:CA303 3.5 10.8 1.0 O A:HOH560 3.6 30.6 1.0 CG A:ASP49 3.6 12.8 1.0 PA A:ATP301 3.7 10.8 1.0 NE2 A:GLN87 3.7 22.1 0.7 CB A:GLN87 3.9 16.4 0.7 CB A:GLN87 3.9 16.6 0.3 O05 A:71R302 3.9 26.3 1.0 CG A:GLN87 3.9 19.8 0.7 CG A:GLN87 3.9 18.9 0.3 OD2 A:ASP49 4.0 14.7 1.0 O A:HOH517 4.0 25.2 1.0 O5' A:ATP301 4.1 12.2 1.0 O A:HOH413 4.3 24.3 1.0 O1A A:ATP301 4.3 13.6 1.0 O A:HOH604 4.5 16.2 1.0 N02 A:71R302 4.6 23.1 1.0 O A:HOH528 4.7 20.2 1.0 CB A:ASP49 4.8 11.5 1.0 CB A:ASP47 4.8 12.8 1.0 O2G A:ATP301 4.9 10.6 1.0 C04 A:71R302 4.9 24.7 1.0 O A:HOH583 4.9 17.2 0.5

Calcium binding site 3 out of 4 in the Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:10.9 occ:1.00 OD1 B:ASP47 2.2 13.7 1.0 O B:HOH468 2.3 10.8 1.0 O1A B:ATP301 2.4 11.5 1.0 O2G B:ATP301 2.4 10.5 1.0 O1B B:ATP301 2.4 11.2 1.0 OD2 B:ASP49 2.4 13.3 1.0 OD1 B:ASP49 2.7 17.1 1.0 CG B:ASP49 2.9 12.3 1.0 CG B:ASP47 3.4 14.1 1.0 PB B:ATP301 3.5 9.9 1.0 CA B:CA306 3.5 15.3 0.5 PA B:ATP301 3.5 10.9 1.0 PG B:ATP301 3.6 9.7 1.0 O3A B:ATP301 3.7 11.4 1.0 O3B B:ATP301 3.8 10.6 1.0 OD2 B:ASP47 3.9 17.3 1.0 O B:HOH616 4.1 16.8 1.0 O B:ASP47 4.1 13.4 1.0 O B:HOH524 4.2 20.1 1.0 O B:HOH416 4.2 18.4 1.0 O1G B:ATP301 4.2 9.8 1.0 OG B:SER36 4.3 9.5 1.0 O B:HOH480 4.4 10.6 1.0 CB B:ASP49 4.4 11.8 1.0 N B:ASP47 4.4 11.5 1.0 C B:ASP47 4.5 11.8 1.0 N B:SER36 4.5 8.1 1.0 O2A B:ATP301 4.6 14.2 1.0 CB B:ASP47 4.6 12.3 1.0 O5' B:ATP301 4.6 12.5 1.0 O B:HOH571 4.6 19.5 0.5 CA B:ASP47 4.7 11.6 1.0 O3G B:ATP301 4.8 12.2 1.0 O2B B:ATP301 4.8 10.7 1.0 OE1 B:GLN87 4.9 22.3 0.7 N B:ASP49 5.0 10.8 1.0

Calcium binding site 4 out of 4 in the Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Aada E87Q in Complex with Atp, Calcium and Dihydrostreptomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca306 b:15.3 occ:0.51 OE1 B:GLN87 1.7 22.3 0.7 OE1 B:GLN87 2.4 19.1 0.3 O B:HOH416 2.4 18.4 1.0 O1A B:ATP301 2.5 11.5 1.0 OD1 B:ASP49 2.6 17.1 1.0 OD2 B:ASP47 2.6 17.3 1.0 O B:HOH571 2.8 19.5 0.5 CD B:GLN87 2.9 21.6 0.7 CD B:GLN87 3.1 20.1 0.3 CG B:ASP47 3.4 14.1 1.0 OD1 B:ASP47 3.4 13.7 1.0 CA B:CA303 3.5 10.9 1.0 CG B:ASP49 3.6 12.3 1.0 NE2 B:GLN87 3.7 22.1 0.3 PA B:ATP301 3.7 10.9 1.0 NE2 B:GLN87 3.7 23.0 0.7 O B:HOH593 3.8 33.2 1.0 CB B:GLN87 3.8 16.0 0.7 O05 B:71R302 3.9 27.3 1.0 CB B:GLN87 3.9 16.7 0.3 CG B:GLN87 3.9 18.4 0.7 OD2 B:ASP49 4.0 13.3 1.0 CG B:GLN87 4.0 18.8 0.3 O B:HOH535 4.0 24.0 1.0 O5' B:ATP301 4.1 12.5 1.0 O B:HOH418 4.2 24.0 1.0 O2A B:ATP301 4.3 14.2 1.0 O B:HOH616 4.6 16.8 1.0 N02 B:71R302 4.6 23.4 1.0 O B:HOH524 4.7 20.1 1.0 CB B:ASP49 4.8 11.8 1.0 CB B:ASP47 4.8 12.3 1.0 O B:HOH571 4.8 17.9 0.5 C04 B:71R302 4.8 25.1 1.0 O2G B:ATP301 4.9 10.5 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