Atomistry » Magnesium » PDB 6k7j-6kft » 6kdj
Atomistry »
  Magnesium »
    PDB 6k7j-6kft »
      6kdj »

Magnesium in PDB 6kdj: Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex, PDB code: 6kdj was solved by Y.Yasutake, S.I.Hattori, N.Tamura, K.Maeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.79 / 2.51
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 285.114, 285.114, 96.004, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex (pdb code 6kdj). 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 with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex, PDB code: 6kdj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6kdj

Go back to Magnesium Binding Sites List in 6kdj
Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex


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 with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:0.6
occ:1.00
O1G A:1RZ601 2.0 0.6 1.0
O1A A:1RZ601 2.0 90.1 1.0
O A:VAL111 2.3 57.7 1.0
O2B A:1RZ601 2.3 0.6 1.0
OD2 A:ASP185 2.8 62.2 1.0
PG A:1RZ601 3.2 0.0 1.0
PA A:1RZ601 3.4 91.5 1.0
PB A:1RZ601 3.4 0.5 1.0
C A:VAL111 3.4 50.2 1.0
O3G A:1RZ601 3.6 92.7 1.0
O3B A:1RZ601 3.7 0.2 1.0
CG A:ASP185 3.7 61.2 1.0
O A:HOH702 3.7 83.2 1.0
O3A A:1RZ601 3.8 0.1 1.0
CA A:GLY112 3.9 53.5 1.0
C5' A:1RZ601 3.9 91.7 1.0
N A:GLY112 4.0 50.8 1.0
O5' A:1RZ601 4.2 94.9 1.0
CB A:ASP185 4.2 54.5 1.0
N A:ASP113 4.3 52.5 1.0
C A:GLY112 4.4 56.6 1.0
O2C A:1RZ601 4.4 0.1 1.0
O2A A:1RZ601 4.4 93.0 1.0
N A:VAL111 4.4 52.9 1.0
CB A:ASP110 4.4 66.9 1.0
OD2 A:ASP110 4.5 88.4 1.0
CA A:VAL111 4.5 53.2 1.0
OD1 A:ASP185 4.6 55.9 1.0
CB A:ALA114 4.6 51.1 1.0
O1B A:1RZ601 4.7 0.5 1.0
N A:ALA114 4.7 50.0 1.0
CG A:ASP110 4.7 76.4 1.0
C A:ASP110 4.9 59.6 1.0

Magnesium binding site 2 out of 2 in 6kdj

Go back to Magnesium Binding Sites List in 6kdj
Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex


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 with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:74.8
occ:1.00
O C:VAL111 1.9 0.3 1.0
O2A C:1RZ601 2.1 98.2 1.0
OD2 C:ASP185 2.3 57.2 1.0
OD2 C:ASP110 2.3 79.7 0.5
O3G C:1RZ601 2.6 0.6 1.0
O1B C:1RZ601 2.7 0.9 1.0
C C:VAL111 3.2 78.6 1.0
CG C:ASP185 3.4 56.7 1.0
CG C:ASP110 3.4 78.5 0.5
PA C:1RZ601 3.5 0.5 1.0
PG C:1RZ601 3.7 0.1 1.0
OD1 C:ASP110 3.8 76.8 0.5
CB C:ASP185 3.8 63.2 1.0
C5' C:1RZ601 3.8 96.8 1.0
PB C:1RZ601 3.9 0.1 1.0
O1G C:1RZ601 3.9 0.3 1.0
CA C:GLY112 4.0 66.5 1.0
N C:GLY112 4.0 77.7 1.0
N C:VAL111 4.1 68.7 1.0
O5' C:1RZ601 4.2 0.7 1.0
CA C:VAL111 4.2 67.7 1.0
O3A C:1RZ601 4.2 0.2 1.0
CB C:ALA114 4.2 56.0 1.0
O3B C:1RZ601 4.3 0.5 1.0
OD2 C:ASP110 4.3 77.2 0.5
C C:GLY112 4.3 67.4 1.0
N C:ASP113 4.3 72.2 1.0
N C:ALA114 4.4 63.0 1.0
OD1 C:ASP185 4.5 55.5 1.0
O1A C:1RZ601 4.5 0.9 1.0
CB C:ASP110 4.7 76.5 0.5
CB C:ASP110 4.7 76.4 0.5
C C:ASP110 4.7 71.6 0.5
CB C:VAL111 4.7 62.5 1.0
CG C:ASP110 4.8 76.5 0.5
C C:ASP110 4.8 71.6 0.5
O C:ASP185 4.9 67.8 1.0
CA C:ALA114 4.9 60.1 1.0
O2C C:1RZ601 5.0 0.1 1.0

Reference:

Y.Yasutake, S.I.Hattori, N.Tamura, K.Matsuda, S.Kohgo, K.Maeda, H.Mitsuya. Structural Features in Common of Hbv and Hiv-1 Resistance Against Chirally-Distinct Nucleoside Analogues Entecavir and Lamivudine. Sci Rep V. 10 3021 2020.
ISSN: ESSN 2045-2322
PubMed: 32080249
DOI: 10.1038/S41598-020-59775-W
Page generated: Tue Oct 1 06:53:17 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy