Magnesium in PDB 6ctz: Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia

The structure of Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia, PDB code: 6ctz was solved by C.A.Smith, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.09 / 1.34
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.169, 58.982, 70.853, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.1

The structure of Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia (pdb code 6ctz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia, PDB code: 6ctz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:12.7 occ:1.00 O2A A:GDP401 2.0 12.5 1.0 O2B A:GDP401 2.0 12.4 1.0 O A:HOH788 2.1 13.6 1.0 O A:HOH636 2.1 13.1 1.0 OD2 A:ASP218 2.1 12.3 1.0 NE2 A:HIS201 2.2 11.5 1.0 CE1 A:HIS201 3.0 11.7 1.0 CG A:ASP218 3.1 11.4 1.0 PB A:GDP401 3.2 13.2 1.0 PA A:GDP401 3.3 12.8 1.0 CD2 A:HIS201 3.3 10.7 1.0 O3A A:GDP401 3.5 12.7 1.0 CB A:ASP218 3.6 11.4 1.0 O1B A:GDP401 3.8 13.7 1.0 MG A:MG403 3.9 14.3 1.0 O A:HOH677 4.0 21.7 1.0 O3' A:GDP401 4.1 15.0 1.0 O A:HOH623 4.2 13.5 1.0 O1A A:GDP401 4.2 12.6 1.0 ND1 A:HIS201 4.2 11.1 1.0 OD1 A:ASP218 4.2 12.3 1.0 OD2 A:ASP196 4.3 15.6 1.0 CG A:HIS201 4.4 10.6 1.0 O5' A:GDP401 4.5 13.4 1.0 O A:HOH799 4.5 18.5 1.0 O3B A:GDP401 4.5 14.4 1.0 OD2 A:ASP200 4.5 17.4 1.0 O A:HOH696 4.5 20.3 1.0 O A:HOH691 4.7 16.2 1.0 C5' A:GDP401 4.7 14.9 1.0 C3' A:GDP401 4.8 13.5 1.0

Magnesium binding site 2 out of 2 in the Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Gdp and Kanamycin Complex of Aph(2")-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:14.3 occ:1.00 O1B A:GDP401 2.0 13.7 1.0 O A:HOH799 2.0 18.5 1.0 O A:HOH691 2.2 16.2 1.0 O A:HOH808 2.2 17.5 1.0 OD1 A:ASP218 2.2 12.3 1.0 OD2 A:ASP218 2.3 12.3 1.0 CG A:ASP218 2.5 11.4 1.0 PB A:GDP401 3.2 13.2 1.0 O2B A:GDP401 3.4 12.4 1.0 MG A:MG402 3.9 12.7 1.0 O A:HOH757 4.0 20.2 1.0 CB A:ASP218 4.1 11.4 1.0 O A:HOH636 4.1 13.1 1.0 NH2 A:ARG45 4.2 12.9 1.0 O A:HOH677 4.2 21.7 1.0 O3A A:GDP401 4.2 12.7 1.0 O3B A:GDP401 4.3 14.4 1.0 ND2 A:ASN33 4.3 14.5 1.0 OD2 A:ASP196 4.4 15.6 1.0 CA A:GLY220 4.4 11.1 1.0 N A:GLY220 4.4 10.2 1.0 OD2 A:ASP221 4.5 17.1 1.0 O A:HOH620 4.5 21.9 1.0 O2A A:GDP401 4.6 12.5 1.0 CB A:ARG32 4.7 17.4 1.0 O1A A:GDP401 4.7 12.6 1.0 PA A:GDP401 4.7 12.8 1.0 OE1 A:GLU55 4.7 19.7 1.0 O A:ASP218 4.8 10.0 1.0 CA A:ASP218 4.8 10.0 1.0 C A:ASP218 4.9 9.5 1.0 C A:GLY220 5.0 10.2 1.0

C.A.Smith, H.Frase, M.Toth, L.Maltz, N.K.Stewart, S.B.Vakulenko. Structural Basis For Diversity of the Phosphorylation Mechanisms of Aminoglycoside 2" Phosphotransferases To Be Published.