Magnesium in PDB 1f3f: Structure of the H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex

All present enzymatic activity of Structure of the H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex:
2.7.4.6;

The structure of Structure of the H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex, PDB code: 1f3f was solved by P.Meyer, B.Schneider, S.Sarfati, D.Deville-Bonne, C.Guerreiro, J.Boretto, J.Janin, M.Veron, B.Canard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.73 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.018, 70.018, 152.098, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.4

The binding sites of Magnesium atom in the Structure of the H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex (pdb code 1f3f). 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 H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex, PDB code: 1f3f:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.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 H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg165 b:21.2 occ:1.00 O1C A:D4T160 2.0 27.9 1.0 O1A A:D4T160 2.0 20.5 1.0 O A:HOH727 2.1 21.7 1.0 O1B A:D4T160 2.1 21.1 1.0 O A:HOH726 2.2 17.4 1.0 O A:HOH725 2.3 20.2 1.0 PB A:D4T160 3.1 23.8 1.0 PC A:D4T160 3.2 31.9 1.0 PA A:D4T160 3.3 22.3 1.0 O7' A:D4T160 3.3 27.4 1.0 O6' A:D4T160 3.5 23.4 1.0 O3C A:D4T160 3.8 31.7 1.0 NH1 A:ARG92 4.0 35.8 1.0 NE2 A:HIS59 4.1 20.7 1.0 C5' A:D4T160 4.2 20.4 1.0 O A:HOH809 4.2 34.3 1.0 O5' A:D4T160 4.2 21.6 1.0 O A:HOH710 4.2 21.5 1.0 O A:HOH810 4.3 35.2 1.0 O2A A:D4T160 4.3 21.1 1.0 O2C A:D4T160 4.4 28.0 1.0 O A:HOH606 4.4 19.8 1.0 OE2 A:GLU58 4.4 27.4 1.0 OD2 A:ASP125 4.5 26.4 1.0 O2B A:D4T160 4.5 25.4 1.0 O A:GLY123 4.6 15.9 1.0 CE1 A:TYR56 4.8 25.3 1.0 NH2 A:ARG92 4.8 35.1 1.0 CZ A:ARG92 4.9 34.8 1.0 CE1 A:HIS59 4.9 21.6 1.0

Magnesium binding site 2 out of 3 in the Structure of the H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.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 H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg166 b:28.9 occ:1.00 O B:HOH729 2.0 31.0 1.0 O1B B:D4D163 2.0 26.7 0.3 O1B B:D4T161 2.1 26.6 0.8 O B:HOH730 2.1 32.1 1.0 O1A B:D4T161 2.1 29.6 0.8 O1C B:D4T161 2.2 28.1 0.8 O1 B:PO4162 2.3 25.2 0.3 O1A B:D4D163 2.3 27.3 0.3 O B:HOH728 2.3 22.1 1.0 PB B:D4T161 3.1 26.9 0.8 O3 B:PO4162 3.1 25.4 0.3 PA B:D4T161 3.3 29.3 0.8 O7' B:D4T161 3.3 27.3 0.8 PC B:D4T161 3.4 28.9 0.8 P B:PO4162 3.4 23.4 0.3 PB B:D4D163 3.4 26.6 0.3 O6' B:D4T161 3.4 29.2 0.8 PA B:D4D163 3.5 28.9 0.3 O3A B:D4D163 3.7 27.4 0.3 O3C B:D4T161 3.9 28.2 0.8 O3B B:D4D163 4.0 26.8 0.3 NE2 B:HIS59 4.1 31.3 1.0 C5' B:D4T161 4.2 28.0 0.8 O5' B:D4T161 4.2 29.4 0.8 O4 B:PO4162 4.3 24.7 0.3 O2 B:PO4162 4.3 24.1 0.3 OD2 B:ASP125 4.4 29.7 1.0 OE1 B:GLU58 4.4 41.3 1.0 O B:HOH843 4.4 33.4 0.9 O B:HOH538 4.4 23.3 1.0 O2A B:D4T161 4.4 28.9 0.8 O B:HOH559 4.4 24.1 1.0 C5' B:D4D163 4.4 28.9 0.3 NH1 B:ARG92 4.5 39.2 1.0 O2B B:D4T161 4.5 28.0 0.8 O2B B:D4D163 4.5 26.3 0.3 NH2 B:ARG92 4.5 38.3 1.0 O5' B:D4D163 4.5 28.3 0.3 O2C B:D4T161 4.6 28.3 0.8 O2A B:D4D163 4.6 27.2 0.3 O B:GLY123 4.7 19.6 1.0 CZ B:ARG92 4.9 38.1 1.0 CE1 B:TYR56 4.9 26.5 1.0 CE1 B:HIS59 5.0 33.6 1.0 CD B:GLU58 5.0 39.9 1.0 CG B:ASP125 5.0 27.5 1.0

Magnesium binding site 3 out of 3 in the Structure of the H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.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 H122G Nucleoside Diphosphate Kinase / D4T- Triphosphate.Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg167 b:41.2 occ:1.00 O1C C:D4T164 2.0 44.8 1.0 O C:HOH731 2.2 36.9 1.0 O1B C:D4T164 2.2 40.7 1.0 O1A C:D4T164 2.3 43.4 1.0 O C:HOH732 2.4 28.9 1.0 PC C:D4T164 3.2 45.0 1.0 PB C:D4T164 3.3 41.1 1.0 O7' C:D4T164 3.4 43.7 1.0 PA C:D4T164 3.6 43.6 1.0 O3C C:D4T164 3.7 45.4 1.0 O6' C:D4T164 3.7 43.3 1.0 OD2 C:ASP125 4.3 36.7 1.0 C5' C:D4T164 4.3 42.3 1.0 O2C C:D4T164 4.4 43.1 1.0 O C:HOH603 4.4 23.6 1.0 OE2 C:GLU58 4.4 49.1 1.0 O C:GLY123 4.5 21.8 1.0 O5' C:D4T164 4.5 41.1 1.0 O C:HOH717 4.5 29.4 1.0 NE2 C:HIS59 4.6 46.6 1.0 O2B C:D4T164 4.6 42.5 1.0 O2A C:D4T164 4.7 43.0 1.0 NH1 C:ARG92 4.8 36.7 1.0 CE1 C:TYR56 4.8 35.4 1.0 CB C:ASP125 5.0 31.7 1.0 CG C:ASP125 5.0 35.0 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