Magnesium in PDB 3tdw: The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant

The structure of The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant, PDB code: 3tdw 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)	19.21 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.060, 54.690, 77.810, 90.00, 108.49, 90.00
R / Rfree (%)	17.4 / 22

The binding sites of Magnesium atom in the The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant (pdb code 3tdw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant, PDB code: 3tdw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:14.3 occ:1.00 O2A A:GDP500 2.1 12.6 1.0 O2B A:GDP500 2.1 11.2 1.0 OD2 A:ASP218 2.2 11.6 1.0 O A:HOH511 2.2 17.7 1.0 O A:HOH512 2.3 15.5 1.0 NE2 A:HIS201 2.3 13.6 1.0 CE1 A:HIS201 3.1 17.1 1.0 CG A:ASP218 3.2 9.8 1.0 PB A:GDP500 3.2 13.4 1.0 PA A:GDP500 3.3 13.4 1.0 CD2 A:HIS201 3.3 15.1 1.0 O3A A:GDP500 3.6 12.1 1.0 CB A:ASP218 3.7 13.3 1.0 O3B A:GDP500 3.8 12.3 1.0 MG A:MG502 3.9 14.4 1.0 O A:HOH597 4.0 22.1 1.0 O A:HOH776 4.2 34.5 1.0 O3' A:GDP500 4.2 17.9 1.0 O1A A:GDP500 4.2 13.9 1.0 O A:HOH521 4.2 13.7 1.0 OD1 A:ASP218 4.2 11.8 1.0 ND1 A:HIS201 4.3 18.0 1.0 OD2 A:ASP196 4.4 21.0 1.0 CG A:HIS201 4.4 13.0 1.0 OD2 A:ASP200 4.4 27.3 0.5 O5' A:GDP500 4.5 12.9 1.0 O1B A:GDP500 4.5 13.3 1.0 O A:HOH633 4.7 23.3 1.0 C5' A:GDP500 4.7 15.9 1.0 C3' A:GDP500 4.8 16.1 1.0 O A:HOH523 4.9 14.0 1.0

Magnesium binding site 2 out of 4 in the The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:14.4 occ:1.00 O3B A:GDP500 2.0 12.3 1.0 O A:HOH521 2.1 13.7 1.0 O A:HOH522 2.2 13.2 1.0 O A:HOH523 2.2 14.0 1.0 OD1 A:ASP218 2.3 11.8 1.0 OD2 A:ASP218 2.3 11.6 1.0 CG A:ASP218 2.6 9.8 1.0 PB A:GDP500 3.2 13.4 1.0 O2B A:GDP500 3.4 11.2 1.0 O A:HOH649 3.9 21.3 1.0 MG A:MG501 3.9 14.3 1.0 NH2 A:ARG45 4.1 15.7 1.0 CB A:ASP218 4.1 13.3 1.0 OD2 A:ASP196 4.2 21.0 1.0 O A:HOH512 4.2 15.5 1.0 O1B A:GDP500 4.2 13.3 1.0 O3A A:GDP500 4.3 12.1 1.0 OE1 A:GLU55 4.3 16.0 1.0 ND2 A:ASN33 4.4 13.0 1.0 CG A:ARG32 4.4 13.1 1.0 CB A:ARG32 4.4 14.2 1.0 CA A:GLY220 4.5 12.5 1.0 N A:GLY220 4.5 10.1 1.0 O A:HOH597 4.5 22.1 1.0 O A:HOH568 4.6 24.0 1.0 O2A A:GDP500 4.6 12.6 1.0 O1A A:GDP500 4.6 13.9 1.0 OD2 A:ASP221 4.7 23.6 1.0 PA A:GDP500 4.7 13.4 1.0 CA A:ASP218 4.9 11.3 1.0 O A:ASP218 4.9 12.2 1.0 C A:ASP218 5.0 10.8 1.0

Magnesium binding site 3 out of 4 in the The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:16.4 occ:1.00 NE2 A:GLN51 2.1 13.5 1.0 O A:HOH532 2.2 16.0 1.0 OE2 A:GLU55 2.2 13.7 1.0 O A:HOH531 2.2 18.2 1.0 O A:HOH533 2.2 15.9 1.0 CD A:GLN51 3.3 17.3 1.0 CD A:GLU55 3.3 15.6 1.0 CG A:GLN51 3.6 13.9 1.0 CG A:GLU55 3.8 14.0 1.0 OD1 A:ASP221 4.0 26.9 1.0 NH2 A:ARG32 4.1 15.8 1.0 O A:HOH528 4.1 34.9 1.0 O A:HOH690 4.2 23.8 1.0 NE A:ARG32 4.2 13.4 1.0 OE1 A:GLU55 4.3 16.0 1.0 OE1 A:GLN51 4.3 20.2 1.0 O A:HOH513 4.3 26.5 1.0 O A:HOH527 4.5 25.1 1.0 CZ A:ARG32 4.6 19.1 1.0 O A:HOH649 4.7 21.3 1.0 O A:HOH609 4.9 21.5 1.0

Magnesium binding site 4 out of 4 in the The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Gdp Complex of the Aminoglycoside 2'-Phosphotransfere-Iiia F108L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:41.7 occ:1.00 O A:HOH541 2.0 36.1 1.0 O A:HOH544 2.1 38.2 1.0 NE2 A:HIS258 2.2 35.3 1.0 O A:HOH542 2.2 43.3 1.0 O A:HOH543 2.6 34.6 1.0 CE1 A:HIS258 3.0 31.2 1.0 CD2 A:HIS258 3.3 26.4 1.0 O A:HOH561 3.9 20.9 1.0 OE1 A:GLU252 4.0 29.2 1.0 ND1 A:HIS258 4.2 29.6 1.0 OD2 A:ASP228 4.2 22.3 1.0 O A:HOH326 4.3 49.7 1.0 CG A:HIS258 4.3 24.3 1.0 O A:HOH802 4.4 30.7 1.0 CD A:GLU252 4.7 36.1 1.0 OE2 A:GLU252 4.8 31.1 1.0 OD1 A:ASP228 4.8 22.8 1.0 CG A:ASP228 5.0 20.5 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