Magnesium in PDB 1f6t: Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex

All present enzymatic activity of Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex:
2.7.4.6;

The structure of Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex, PDB code: 1f6t was solved by C.Guerreiro, J.Boretto, J.Janin, M.Veron, B.Canard, B.Schneider, S.Sarfati, D.Deville-Bonne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.92
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.359, 70.359, 153.792, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 27.4

The binding sites of Magnesium atom in the Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex (pdb code 1f6t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex, PDB code: 1f6t:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex


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 Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg163 b:31.4 occ:1.00 O A:HOH775 2.2 38.0 1.0 O2B A:TBD160 2.2 26.7 1.0 O2A A:TBD160 2.3 29.8 1.0 O A:HOH875 2.3 20.6 1.0 O A:HOH872 2.3 29.5 1.0 O A:HOH776 2.4 26.5 1.0 PA A:TBD160 3.5 28.9 1.0 PB A:TBD160 3.5 27.1 1.0 NH2 A:ARG92 3.7 37.6 1.0 O3A A:TBD160 3.7 29.0 1.0 NH1 A:ARG92 3.9 35.4 1.0 O A:HOH779 3.9 24.2 1.0 O A:HOH778 3.9 19.9 1.0 OD2 A:ASP125 4.0 24.4 1.0 O A:HOH585 4.1 23.7 1.0 NE2 A:HIS59 4.2 24.5 1.0 CZ A:ARG92 4.2 36.9 1.0 O1B A:TBD160 4.5 21.4 1.0 OE2 A:GLU58 4.6 31.9 1.0 O3B A:TBD160 4.6 23.3 1.0 O5' A:TBD160 4.7 28.9 1.0 B1A A:TBD160 4.7 29.9 1.0 CG A:ASP125 4.7 26.6 1.0 O A:HOH785 4.8 30.7 1.0 CB A:ASP125 4.9 24.4 1.0 O A:HOH669 4.9 24.5 1.0 C5' A:TBD160 5.0 27.1 1.0 CE1 A:HIS59 5.0 24.6 1.0

Magnesium binding site 2 out of 3 in the Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex


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 Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg164 b:40.9 occ:1.00 O B:HOH871 2.2 39.3 1.0 O2B B:TBD161 2.2 32.8 1.0 O2A B:TBD161 2.3 29.0 1.0 O B:HOH870 2.3 31.3 1.0 O B:HOH869 2.3 37.0 1.0 O B:HOH782 2.4 25.9 1.0 NH2 B:ARG92 3.3 31.6 1.0 PA B:TBD161 3.5 30.6 1.0 PB B:TBD161 3.5 31.9 1.0 O3A B:TBD161 3.7 33.0 1.0 O B:HOH674 3.8 27.1 1.0 OD2 B:ASP125 4.0 23.0 1.0 CZ B:ARG92 4.2 33.5 1.0 NE2 B:HIS59 4.3 24.2 1.0 O1B B:TBD161 4.3 31.1 1.0 NH1 B:ARG92 4.4 32.1 1.0 O B:HOH824 4.4 27.4 1.0 O B:HOH597 4.5 23.5 1.0 B1A B:TBD161 4.6 29.6 1.0 O3B B:TBD161 4.6 30.1 1.0 O5' B:TBD161 4.7 31.8 1.0 OE2 B:GLU58 4.7 40.7 1.0 O B:HOH769 4.8 37.8 1.0 CE1 B:HIS59 4.8 23.0 1.0 C5' B:TBD161 4.9 34.0 1.0 CG B:ASP125 4.9 26.6 1.0 O B:HOH526 5.0 18.6 1.0

Magnesium binding site 3 out of 3 in the Structure of the Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex


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 Nucleoside Diphosphate Kinase/Alpha-Borano(Rp)-Tdp.Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg165 b:46.1 occ:1.00 O C:HOH876 2.3 31.4 1.0 O C:HOH800 2.5 30.7 1.0 O C:HOH863 2.7 40.0 1.0 O C:HOH873 2.8 41.2 1.0 O2A C:TBD162 2.8 39.8 1.0 O2B C:TBD162 2.8 39.6 1.0 OE2 C:GLU58 3.3 42.9 1.0 O C:HOH874 3.3 33.8 1.0 NH1 C:ARG92 3.6 40.3 1.0 O C:HOH592 3.9 40.2 1.0 CB C:ASP125 4.1 40.7 1.0 CG C:ASP125 4.2 42.4 1.0 PA C:TBD162 4.2 42.6 1.0 PB C:TBD162 4.2 36.7 1.0 CD C:GLU58 4.3 45.3 1.0 OD2 C:ASP125 4.4 42.3 1.0 OD1 C:ASP125 4.5 41.5 1.0 NE2 C:HIS59 4.5 52.0 1.0 O3A C:TBD162 4.6 41.5 1.0 OE1 C:GLU58 4.6 47.2 1.0 CZ C:ARG92 4.7 39.5 1.0 O C:HOH623 4.8 34.0 1.0 NH2 C:ARG92 4.8 40.8 1.0

P.Meyer, B.Schneider, S.Sarfati, D.Deville-Bonne, C.Guerreiro, J.Boretto, J.Janin, M.Veron, B.Canard. Structural Basis For Activation of Alpha-Boranophosphate Nucleotide Analogues Targeting Drug-Resistant Reverse Transcriptase. Embo J. V. 19 3520 2000.
ISSN: ISSN 0261-4189
PubMed: 10899107
DOI: 10.1093/EMBOJ/19.14.3520