Magnesium in PDB 6wph: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc:
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc, PDB code: 6wph was solved by N.Bertoletti, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.52 / 2.72
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.980, 168.054, 101.916, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.7

Other elements in 6wph:

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc (pdb code 6wph). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc, PDB code: 6wph:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6wph

Go back to Magnesium Binding Sites List in 6wph
Magnesium binding site 1 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:56.0
occ:1.00
OE2 A:GLU478 2.5 68.2 1.0
OD1 A:ASP443 2.7 60.7 1.0
OD1 A:ASP498 2.8 63.2 1.0
OD2 A:ASP498 3.0 65.3 1.0
CG A:ASP498 3.2 61.3 1.0
OP1 T:DC723 3.4 80.2 1.0
CG A:ASP443 3.5 60.4 1.0
OD2 A:ASP443 3.5 60.2 1.0
CD A:GLU478 3.6 65.7 1.0
O A:GLY444 3.7 62.4 1.0
OE1 A:GLU478 4.1 67.5 1.0
P T:DC723 4.5 77.6 1.0
CB A:ALA538 4.5 46.1 1.0
CB A:ASP498 4.7 55.5 1.0
NE2 A:HIS539 4.8 67.8 1.0
O A:ASP498 4.8 53.1 1.0
CG A:GLU478 4.9 57.7 1.0
N A:GLY444 4.9 52.3 1.0
C A:GLY444 4.9 55.8 1.0
OP2 T:DC723 4.9 77.3 1.0
OD1 A:ASP549 4.9 73.2 1.0
O3' T:DA722 4.9 71.0 1.0
CB A:ASP443 5.0 53.6 1.0

Magnesium binding site 2 out of 2 in 6wph

Go back to Magnesium Binding Sites List in 6wph
Magnesium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:62.3
occ:0.50
O B:ILE274 3.1 79.4 1.0
O B:PRO272 3.2 80.6 1.0
C B:ILE274 4.0 76.0 1.0
O B:GLY273 4.2 80.4 1.0
C B:GLY273 4.2 77.0 1.0
CB B:LYS275 4.4 78.1 1.0
C B:PRO272 4.4 79.4 1.0
CA B:LYS275 4.4 78.1 1.0
N B:ILE274 4.5 74.8 1.0
N B:LYS275 4.5 74.5 1.0
CA B:GLY273 4.6 77.2 1.0
CA B:ILE274 4.9 73.9 1.0
N B:GLY273 5.0 78.1 1.0

Reference:

N.Bertoletti, A.H.Chan, R.F.Schinazi, K.S.Anderson. Post-Catalytic Complexes with Emtricitabine or Stavudine and Hiv-1 Reverse Transcriptase Reveal New Mechanistic Insights For Nucleotide Incorporation and Drug Resistance. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 33096918
DOI: 10.3390/MOLECULES25204868
Page generated: Tue Dec 15 01:37:06 2020

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