Magnesium in PDB 3kk2: Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site:
2.7.7.49;

The structure of Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site, PDB code: 3kk2 was solved by E.B.Lansdon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.77 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	167.912, 168.922, 102.041, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 28.4

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site (pdb code 3kk2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site, PDB code: 3kk2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg600 b:5.1 occ:1.00 O A:VAL111 2.1 39.2 1.0 O1A A:DTP563 2.3 25.7 1.0 OD1 A:ASP110 2.4 41.6 1.0 OD1 A:ASP185 2.4 31.1 1.0 O1B A:DTP563 2.4 34.8 1.0 O1G A:DTP563 2.5 38.5 1.0 CG A:ASP110 2.8 39.6 1.0 OD2 A:ASP110 2.9 41.2 1.0 C A:VAL111 3.2 38.0 1.0 N A:VAL111 3.4 37.4 1.0 CG A:ASP185 3.5 30.0 1.0 PG A:DTP563 3.5 37.6 1.0 PB A:DTP563 3.5 33.9 1.0 PA A:DTP563 3.6 30.2 1.0 O2G A:DTP563 3.8 37.6 1.0 CA A:VAL111 3.8 37.7 1.0 O3B A:DTP563 4.0 37.0 1.0 OD2 A:ASP185 4.0 31.3 1.0 O3A A:DTP563 4.0 33.4 1.0 CB A:ASP110 4.1 37.3 1.0 C A:ASP110 4.1 36.8 1.0 C5' A:DTP563 4.3 32.8 1.0 NZ A:LYS219 4.3 37.3 1.0 N A:GLY112 4.3 37.3 1.0 CB A:VAL111 4.5 38.2 1.0 CA A:ASP110 4.5 35.2 1.0 N A:ASP113 4.6 35.5 1.0 CA A:GLY112 4.6 36.8 1.0 O5' A:DTP563 4.6 31.7 1.0 O2A A:DTP563 4.7 28.6 1.0 CB A:ASP185 4.7 28.8 1.0 N A:ALA114 4.7 35.1 1.0 C A:GLY112 4.7 37.0 1.0 CB A:ALA114 4.8 32.1 1.0 O2B A:DTP563 4.9 31.4 1.0 CE A:LYS219 4.9 37.6 1.0 O3G A:DTP563 4.9 36.6 1.0 O A:ASP110 4.9 37.0 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Reverse Transcriptase-Dna Complex with Datp Bound in the Nucleotide Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:1.9 occ:1.00 OD1 A:ASP498 2.2 26.1 1.0 OD1 A:ASP443 2.2 43.6 1.0 OE1 A:GLU478 2.2 38.4 1.0 OD2 A:ASP498 2.4 25.4 1.0 OE2 A:GLU478 2.5 37.7 1.0 CG A:ASP498 2.6 26.5 1.0 CD A:GLU478 2.7 39.5 1.0 CG A:ASP443 3.2 40.9 1.0 OD2 A:ASP443 3.5 43.2 1.0 O A:GLY444 3.7 40.4 1.0 CB A:ASP498 4.2 27.1 1.0 CG A:GLU478 4.2 40.9 1.0 N A:GLY444 4.3 34.7 1.0 CB A:ASP443 4.5 38.3 1.0 CA A:ASP443 4.7 33.8 1.0 O A:ASP498 4.7 34.9 1.0 C A:GLY444 4.8 39.0 1.0 CB A:ALA538 4.8 38.7 1.0 C A:ASP498 4.8 32.0 1.0 CA A:ASP498 5.0 30.8 1.0

E.B.Lansdon, D.Samuel, L.Lagpacan, K.M.Brendza, K.L.White, M.Hung, X.Liu, C.G.Boojamra, R.L.Mackman, T.Cihlar, A.S.Ray, M.E.Mcgrath, S.Swaminathan. Visualizing the Molecular Interactions of A Nucleotide Analog, Gs-9148, with Hiv-1 Reverse Transcriptase-Dna Complex. J.Mol.Biol. V. 397 967 2010.
ISSN: ISSN 0022-2836
PubMed: 20156454
DOI: 10.1016/J.JMB.2010.02.019