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Magnesium in PDB 3kk1: Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site

Enzymatic activity of Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site:
2.7.7.49;

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site, PDB code: 3kk1 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) 29.71 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.753, 169.239, 103.026, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 28.2

Other elements in 3kk1:

The structure of Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site (pdb code 3kk1). 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 Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site, PDB code: 3kk1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3kk1

Go back to Magnesium Binding Sites List in 3kk1
Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide 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 Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:15.8
occ:1.00
 O A:VAL111 2.2 38.8 1.0
OD1 A:ASP185 2.2 43.1 1.0
O3 A:914825 2.5 46.7 1.0
OD1 A:ASP110 2.6 51.4 1.0
O10 A:914825 2.6 51.0 1.0
O9 A:914825 2.8 52.2 1.0
CG A:ASP110 3.1 48.2 1.0
OD2 A:ASP110 3.2 54.6 1.0
O6 A:914825 3.3 51.3 1.0
P1 A:914825 3.3 46.9 1.0
O4 A:914825 3.4 48.1 1.0
C A:VAL111 3.4 40.0 1.0
P2 A:914825 3.4 49.4 1.0
CG A:ASP185 3.5 43.8 1.0
P3 A:914825 3.6 51.8 1.0
C10 A:914825 3.8 48.9 1.0
N A:VAL111 3.9 42.3 1.0
NZ A:LYS219 4.0 52.1 1.0
OD2 A:ASP185 4.1 44.5 1.0
CA A:VAL111 4.3 40.9 1.0
N A:GLY112 4.3 39.4 1.0
CB A:ASP110 4.4 45.7 1.0
CA A:GLY112 4.4 39.5 1.0
O11 A:914825 4.4 52.6 1.0
CB A:ASP185 4.5 41.0 1.0
C A:ASP110 4.6 43.2 1.0
CB A:ALA114 4.6 40.2 1.0
N A:ASP113 4.7 42.2 1.0
O7 A:914825 4.7 53.3 1.0
C A:GLY112 4.7 41.8 1.0
O8 A:914825 4.7 49.0 1.0
N A:ALA114 4.7 40.2 1.0
CB A:VAL111 4.9 41.3 1.0
O5 A:914825 4.9 52.8 1.0
CA A:ASP110 4.9 43.1 1.0

Magnesium binding site 2 out of 2 in 3kk1

Go back to Magnesium Binding Sites List in 3kk1
Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase-Dna Complex with Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide 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 Nuceotide Inhibitor Gs- 9148-Diphosphate Bound in Nucleotide Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:13.1
occ:1.00
 OE1 A:GLU478 2.2 45.2 1.0
OD2 A:ASP443 2.3 45.0 1.0
OD2 A:ASP498 2.3 29.3 1.0
OD1 A:ASP498 2.5 34.2 1.0
CG A:ASP498 2.8 30.9 1.0
OD1 A:ASP443 2.8 42.2 1.0
CG A:ASP443 2.9 41.5 1.0
CD A:GLU478 2.9 45.7 1.0
OE2 A:GLU478 2.9 47.1 1.0
O A:GLY444 3.8 41.2 1.0
O A:HOH626 4.0 43.1 1.0
CB A:ASP443 4.3 39.3 1.0
CB A:ASP498 4.3 30.0 1.0
CG A:GLU478 4.4 45.0 1.0
N A:GLY444 4.5 37.9 1.0
CB A:ALA538 4.8 42.3 1.0
CA A:ASP443 4.8 38.2 1.0
C A:GLY444 4.9 40.6 1.0

Reference:

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
Page generated: Wed Aug 14 18:09:08 2024

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