Magnesium in PDB 3tdv: Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia

The structure of Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia, PDB code: 3tdv 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)	38.45 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.680, 54.650, 77.160, 89.94, 103.83, 106.84
R / Rfree (%)	20.4 / 29.1

The binding sites of Magnesium atom in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia (pdb code 3tdv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia, PDB code: 3tdv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-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 Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:16.1 occ:1.00 OD2 A:ASP218 2.1 13.0 1.0 O2A A:GDP500 2.1 26.7 1.0 O A:HOH512 2.1 20.3 1.0 O A:HOH511 2.1 18.5 1.0 O2B A:GDP500 2.2 18.3 1.0 NE2 A:HIS201 2.2 20.3 1.0 CE1 A:HIS201 3.0 25.3 1.0 PB A:GDP500 3.1 23.5 1.0 CG A:ASP218 3.1 18.8 1.0 PA A:GDP500 3.2 18.0 1.0 O3B A:GDP500 3.3 20.1 1.0 CD2 A:HIS201 3.4 23.4 1.0 O3A A:GDP500 3.5 19.9 1.0 CB A:ASP218 3.7 17.7 1.0 O A:HOH602 3.9 21.9 1.0 OD2 A:ASP196 4.1 24.8 1.0 MG A:MG502 4.1 20.5 1.0 O1A A:GDP500 4.1 19.9 1.0 OD1 A:ASP218 4.2 16.6 1.0 ND1 A:HIS201 4.2 21.4 1.0 O3' A:GDP500 4.3 21.6 1.0 O A:HOH576 4.4 21.4 1.0 O5' A:GDP500 4.4 19.6 1.0 CG A:HIS201 4.4 23.1 1.0 O1B A:GDP500 4.4 20.8 1.0 O A:HOH523 4.4 18.7 1.0 C5' A:GDP500 4.5 19.4 1.0 O A:HOH522 4.5 17.9 1.0 C3' A:GDP500 4.8 22.2 1.0 O A:HOH624 4.9 40.0 1.0 CG A:ASP196 4.9 27.2 1.0

Magnesium binding site 2 out of 6 in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-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 Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.5 occ:1.00 O A:HOH521 2.0 23.2 1.0 O3B A:GDP500 2.0 20.1 1.0 O A:HOH523 2.1 18.7 1.0 O A:HOH522 2.1 17.9 1.0 OD1 A:ASP218 2.2 16.6 1.0 OD2 A:ASP218 2.5 13.0 1.0 CG A:ASP218 2.7 18.8 1.0 PB A:GDP500 3.5 23.5 1.0 O A:HOH564 3.9 21.3 1.0 NH2 A:ARG45 3.9 22.7 1.0 OD2 A:ASP196 4.0 24.8 1.0 CA A:GLY220 4.1 18.4 1.0 O2B A:GDP500 4.1 18.3 1.0 MG A:MG501 4.1 16.1 1.0 OE1 A:GLU55 4.1 21.7 1.0 CG A:ARG32 4.2 18.9 1.0 N A:GLY220 4.2 10.6 1.0 CB A:ASP218 4.2 17.7 1.0 CB A:ARG32 4.2 21.6 1.0 O1B A:GDP500 4.3 20.8 1.0 ND2 A:ASN33 4.3 17.4 1.0 O A:HOH511 4.4 18.5 1.0 O3A A:GDP500 4.5 19.9 1.0 O A:HOH590 4.6 26.2 1.0 O A:HOH602 4.6 21.9 1.0 O1A A:GDP500 4.7 19.9 1.0 OD2 A:ASP221 4.7 31.7 1.0 C A:GLY220 4.8 20.7 1.0 CA A:ASP218 4.9 17.8 1.0 PA A:GDP500 4.9 18.0 1.0 O2A A:GDP500 4.9 26.7 1.0 O A:ASP218 5.0 12.1 1.0 C A:ASP218 5.0 17.3 1.0 N A:ASP221 5.0 14.9 1.0

Magnesium binding site 3 out of 6 in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:27.8 occ:1.00 O A:HOH531 2.0 23.6 1.0 OE2 A:GLU55 2.0 21.4 1.0 OE1 A:GLN51 2.1 25.9 1.0 O A:HOH532 2.1 28.0 1.0 O A:HOH533 2.1 24.2 1.0 CD A:GLN51 2.9 26.6 1.0 CD A:GLU55 3.2 24.3 1.0 CG A:GLN51 3.5 24.5 1.0 O A:HOH604 3.6 32.1 1.0 NH2 A:ARG32 3.6 25.7 1.0 NE A:ARG32 3.8 24.4 1.0 CG A:GLU55 3.9 19.8 1.0 NE2 A:GLN51 4.0 25.9 1.0 OD1 A:ASP221 4.1 25.1 1.0 CZ A:ARG32 4.2 27.2 1.0 OE1 A:GLU55 4.2 21.7 1.0 O A:HOH564 4.5 21.3 1.0 CB A:GLN51 4.8 19.1 1.0 CD A:ARG32 4.9 23.9 1.0

Magnesium binding site 4 out of 6 in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:18.3 occ:1.00 O2A B:GDP500 2.1 22.0 1.0 OD2 B:ASP218 2.1 12.0 1.0 O B:HOH512 2.1 21.8 1.0 O2B B:GDP500 2.1 15.4 1.0 O B:HOH511 2.1 17.2 1.0 NE2 B:HIS201 2.1 24.4 1.0 CE1 B:HIS201 3.0 26.4 1.0 CG B:ASP218 3.2 17.9 1.0 CD2 B:HIS201 3.2 17.9 1.0 PA B:GDP500 3.3 18.6 1.0 PB B:GDP500 3.4 20.1 1.0 CB B:ASP218 3.6 18.0 1.0 O B:HOH597 3.7 15.7 1.0 O3A B:GDP500 3.7 17.1 1.0 MG B:MG502 3.9 16.6 1.0 O B:HOH523 4.0 22.2 1.0 O3B B:GDP500 4.0 18.6 1.0 OD2 B:ASP196 4.0 24.5 1.0 ND1 B:HIS201 4.2 22.1 1.0 O1A B:GDP500 4.2 13.4 1.0 O3' B:GDP500 4.2 21.2 1.0 OD1 B:ASP218 4.3 12.6 1.0 CG B:HIS201 4.3 24.0 1.0 O5' B:GDP500 4.5 19.3 1.0 O1B B:GDP500 4.6 17.4 1.0 C5' B:GDP500 4.6 23.2 1.0 C3' B:GDP500 4.8 22.6 1.0 O B:HOH521 4.8 21.8 1.0 CG B:ASP196 5.0 35.0 1.0

Magnesium binding site 5 out of 6 in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:16.6 occ:1.00 O3B B:GDP500 2.1 18.6 1.0 O B:HOH523 2.1 22.2 1.0 OD1 B:ASP218 2.1 12.6 1.0 O B:HOH521 2.1 21.8 1.0 O B:HOH522 2.1 19.1 1.0 OD2 B:ASP218 2.3 12.0 1.0 CG B:ASP218 2.5 17.9 1.0 PB B:GDP500 3.2 20.1 1.0 O2B B:GDP500 3.2 15.4 1.0 NH2 B:ARG45 3.9 15.8 1.0 MG B:MG501 3.9 18.3 1.0 CB B:ASP218 4.0 18.0 1.0 O B:HOH511 4.1 17.2 1.0 O B:HOH597 4.2 15.7 1.0 O1B B:GDP500 4.2 17.4 1.0 OD2 B:ASP196 4.2 24.5 1.0 CG B:ARG32 4.2 19.4 1.0 O3A B:GDP500 4.3 17.1 1.0 CB B:ARG32 4.3 20.5 1.0 CA B:GLY220 4.3 17.7 1.0 ND2 B:ASN33 4.3 21.5 1.0 OE1 B:GLU55 4.3 22.2 1.0 N B:GLY220 4.4 12.7 1.0 O1A B:GDP500 4.4 13.4 1.0 O2A B:GDP500 4.6 22.0 1.0 PA B:GDP500 4.6 18.6 1.0 OD2 B:ASP221 4.7 31.8 1.0 CA B:ASP218 4.7 18.2 1.0 O B:HOH527 4.8 19.4 1.0 O B:ASP218 4.9 16.3 1.0 C B:ASP218 4.9 16.8 1.0

Magnesium binding site 6 out of 6 in the Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Gdp Complex of Wild-Type Aminoglycoside 2'- Phosphotransferase-Iiia within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:27.1 occ:1.00 OE2 B:GLU55 2.0 22.1 1.0 OE1 B:GLN51 2.2 23.8 1.0 O B:HOH533 2.2 24.2 1.0 O B:HOH531 2.2 26.0 1.0 O B:HOH532 2.3 23.8 1.0 CD B:GLU55 3.1 21.7 1.0 CD B:GLN51 3.1 27.5 1.0 CG B:GLN51 3.5 24.4 1.0 CG B:GLU55 3.7 18.0 1.0 NH2 B:ARG32 4.0 23.5 1.0 NE B:ARG32 4.1 27.2 1.0 OD1 B:ASP221 4.1 17.6 1.0 OE1 B:GLU55 4.1 22.2 1.0 NE2 B:GLN51 4.4 25.9 1.0 CZ B:ARG32 4.5 24.9 1.0 CB B:GLN51 5.0 22.6 1.0

C.A.Smith, M.Toth, H.Frase, L.J.Byrnes, S.B.Vakulenko. Aminoglycoside-2' Phosphotransferase-Iiia (Aph(2')-Iiia) Prefers Gtp Over Atp: Structural Templates For Nucleotide Recognition in the Bacterial Aminoglycoside-2' Kinases. J.Biol.Chem. V. 287 12893 2012.
ISSN: ISSN 0021-9258
PubMed: 22367198
DOI: 10.1074/JBC.M112.341206