Magnesium in PDB 1kny: Kanamycin Nucleotidyltransferase

The structure of Kanamycin Nucleotidyltransferase, PDB code: 1kny was solved by L.C.Pedersen, M.M.Benning, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.300, 102.200, 108.800, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Kanamycin Nucleotidyltransferase (pdb code 1kny). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kanamycin Nucleotidyltransferase, PDB code: 1kny:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kanamycin Nucleotidyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kanamycin Nucleotidyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:45.1 occ:1.00 OE2 A:GLU52 2.0 0.0 1.0 O1G A:APC556 2.2 53.8 1.0 OE1 A:GLU52 2.6 35.8 1.0 CD A:GLU52 2.6 17.4 1.0 O2B A:APC556 2.6 38.3 1.0 OD1 A:ASP50 3.3 34.8 1.0 OG A:SER39 3.3 77.5 1.0 PB A:APC556 3.5 4.0 1.0 PG A:APC556 3.5 49.3 1.0 O A:ASP50 3.6 34.5 1.0 O3B A:APC556 3.6 23.1 1.0 C3A A:APC556 3.7 56.3 1.0 O5' A:APC556 3.8 52.3 1.0 O1A A:APC556 4.0 37.1 1.0 PA A:APC556 4.0 2.1 1.0 N A:SER39 4.0 23.5 1.0 N A:ASP50 4.1 29.4 1.0 CG A:GLU52 4.1 4.6 1.0 C A:ASP50 4.1 46.3 1.0 CG A:ASP50 4.1 33.3 1.0 O A:HOH604 4.1 12.9 1.0 CB A:SER39 4.3 2.6 1.0 O A:HOH631 4.3 36.8 1.0 CA A:ASP50 4.4 27.1 1.0 O3G A:APC556 4.5 35.5 1.0 O2G A:APC556 4.5 31.4 1.0 CA A:GLY38 4.5 8.7 1.0 CB A:ASP50 4.5 8.3 1.0 CB A:SER49 4.6 46.6 1.0 C A:GLY38 4.8 14.7 1.0 CA A:SER39 4.8 16.9 1.0 O1B A:APC556 4.9 51.9 1.0 N A:ILE51 4.9 3.5 1.0

Magnesium binding site 2 out of 2 in the Kanamycin Nucleotidyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kanamycin Nucleotidyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:59.2 occ:1.00 O2B B:APC557 2.0 57.9 1.0 O1G B:APC557 2.3 63.5 1.0 OE2 B:GLU52 2.6 0.0 1.0 PB B:APC557 2.8 64.3 1.0 OE1 B:GLU52 3.0 46.9 1.0 CD B:GLU52 3.2 38.3 1.0 C3A B:APC557 3.2 66.7 1.0 O B:HOH610 3.2 30.5 1.0 O3B B:APC557 3.2 49.4 1.0 PG B:APC557 3.3 68.7 1.0 O1A B:APC557 3.4 37.4 1.0 O B:ASP50 3.5 59.7 1.0 OG B:SER39 3.6 45.3 1.0 OD1 B:ASP50 3.7 0.0 1.0 N B:SER39 3.8 72.4 1.0 PA B:APC557 3.8 8.8 1.0 N B:ASP50 4.1 34.9 1.0 O2G B:APC557 4.1 36.5 1.0 CG B:ASP50 4.2 17.9 1.0 C B:ASP50 4.2 28.3 1.0 O1B B:APC557 4.2 38.0 1.0 CB B:SER39 4.3 40.4 1.0 O5' B:APC557 4.3 19.6 1.0 O B:HOH619 4.3 52.5 1.0 CA B:GLY38 4.4 22.6 1.0 CA B:ASP50 4.5 13.7 1.0 CA B:SER39 4.5 1.0 1.0 O3G B:APC557 4.6 49.4 1.0 CG B:GLU52 4.6 19.8 1.0 C B:GLY38 4.6 14.0 1.0 OD2 B:ASP50 4.6 89.4 1.0 CB B:SER49 4.8 39.9 1.0 C5' B:APC557 4.8 0.0 1.0 CB B:ASP50 4.9 48.5 1.0

L.C.Pedersen, M.M.Benning, H.M.Holden. Structural Investigation of the Antibiotic and Atp-Binding Sites in Kanamycin Nucleotidyltransferase. Biochemistry V. 34 13305 1995.
ISSN: ISSN 0006-2960
PubMed: 7577914
DOI: 10.1021/BI00041A005