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Magnesium in PDB 6an8: Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0:
2.7.7.49; 2.7.7.7;

Protein crystallography data

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0, PDB code: 6an8 was solved by S.E.Martinez, K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.36 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.959, 132.824, 138.909, 90.00, 97.83, 90.00
R / Rfree (%) 17.8 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0 (pdb code 6an8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0, PDB code: 6an8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6an8

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Magnesium binding site 1 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0


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) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:82.7
occ:1.00
 OD2 A:ASP185 2.0 0.9 1.0
OD1 A:ASP110 2.1 0.9 1.0
O2B A:D4T603 2.1 0.0 1.0
O2C A:D4T603 2.1 0.1 1.0
O A:VAL111 2.3 92.2 1.0
O1A A:D4T603 2.4 0.5 1.0
PB A:D4T603 3.2 0.7 1.0
CG A:ASP185 3.3 0.8 1.0
CG A:ASP110 3.3 0.8 1.0
C A:VAL111 3.3 93.7 1.0
PC A:D4T603 3.4 0.7 1.0
PA A:D4T603 3.6 0.7 1.0
O7' A:D4T603 3.6 0.1 1.0
O6' A:D4T603 3.7 0.7 1.0
OD2 A:ASP110 3.9 0.9 1.0
N A:VAL111 3.9 88.2 1.0
CB A:ASP185 4.1 0.7 1.0
OD1 A:ASP185 4.2 0.7 1.0
N A:GLY112 4.2 95.5 1.0
C A:ASP110 4.2 95.6 1.0
O1C A:D4T603 4.2 0.2 1.0
CA A:VAL111 4.2 89.6 1.0
CA A:GLY112 4.3 89.6 1.0
C5' A:D4T603 4.3 0.9 1.0
CB A:ASP110 4.4 98.7 1.0
O3C A:D4T603 4.4 0.7 1.0
O5' A:D4T603 4.5 0.4 1.0
O1B A:D4T603 4.5 0.3 1.0
O A:ASP110 4.6 98.4 1.0
CA A:ASP110 4.7 92.1 1.0
O2A A:D4T603 4.7 0.3 1.0
NZ A:LYS220 4.8 0.9 1.0
N A:ASP113 4.8 0.6 1.0
CB A:VAL111 4.9 84.7 1.0
C A:GLY112 4.9 98.2 1.0
CB A:ALA114 5.0 0.2 1.0

Magnesium binding site 2 out of 4 in 6an8

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Magnesium binding site 2 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0


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) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:56.1
occ:1.00
 OD1 A:ASP443 2.1 59.2 1.0
OD1 A:ASP498 2.2 62.2 1.0
OD2 A:ASP498 2.3 68.5 1.0
OE2 A:GLU478 2.4 84.6 1.0
O A:HOH788 2.5 78.1 1.0
CG A:ASP498 2.6 51.0 1.0
O A:HOH746 3.0 61.0 1.0
CG A:ASP443 3.1 60.1 1.0
CD A:GLU478 3.4 76.1 1.0
O A:HOH767 3.4 62.9 1.0
OD2 A:ASP443 3.4 65.5 1.0
O A:HOH827 3.5 56.8 1.0
OE1 A:GLU478 3.8 73.1 1.0
O A:HOH740 4.0 56.2 1.0
CB A:ASP498 4.1 47.0 1.0
CB A:ASP443 4.3 52.7 1.0
O A:GLY444 4.3 57.3 1.0
N A:GLY444 4.5 50.3 1.0
CA A:ASP443 4.6 48.2 1.0
CG A:GLU478 4.7 59.2 1.0
CB A:ALA538 4.8 56.7 1.0
CA A:ASP498 4.9 40.5 1.0
C A:ASP498 4.9 49.8 1.0
N A:ASP498 4.9 35.6 1.0

Magnesium binding site 3 out of 4 in 6an8

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Magnesium binding site 3 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:79.9
occ:1.00
 OD2 C:ASP185 2.1 0.2 1.0
O C:VAL111 2.1 0.1 1.0
OD1 C:ASP110 2.1 0.7 1.0
O2C C:D4T603 2.1 0.5 1.0
O2B C:D4T603 2.2 0.5 1.0
O1A C:D4T603 2.3 0.1 1.0
C C:VAL111 3.1 0.3 1.0
CG C:ASP110 3.3 0.6 1.0
CG C:ASP185 3.3 0.5 1.0
PB C:D4T603 3.3 0.3 1.0
PC C:D4T603 3.5 1.0 1.0
PA C:D4T603 3.5 0.2 1.0
O6' C:D4T603 3.6 0.3 1.0
O7' C:D4T603 3.7 0.8 1.0
N C:VAL111 3.9 97.3 1.0
OD2 C:ASP110 3.9 0.4 1.0
N C:GLY112 4.0 0.6 1.0
CA C:GLY112 4.0 0.2 1.0
CA C:VAL111 4.1 0.7 1.0
OD1 C:ASP185 4.1 0.6 1.0
C C:ASP110 4.1 100.0 1.0
CB C:ASP185 4.2 0.5 1.0
O1C C:D4T603 4.3 0.3 1.0
C5' C:D4T603 4.3 99.7 1.0
CB C:ASP110 4.4 0.9 1.0
O3C C:D4T603 4.5 0.2 1.0
O5' C:D4T603 4.5 0.3 1.0
O C:ASP110 4.5 99.3 1.0
O2A C:D4T603 4.5 0.7 1.0
N C:ASP113 4.5 0.4 1.0
O1B C:D4T603 4.6 0.0 1.0
C C:GLY112 4.6 1.0 1.0
CA C:ASP110 4.7 0.8 1.0
CB C:VAL111 4.8 97.0 1.0
CB C:ALA114 4.8 99.7 1.0
N C:ALA114 4.9 0.1 1.0

Magnesium binding site 4 out of 4 in 6an8

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Magnesium binding site 4 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:49.1
occ:1.00
 OD1 C:ASP443 2.1 55.8 1.0
OD1 C:ASP498 2.2 69.6 1.0
O C:HOH758 2.2 69.3 1.0
OE2 C:GLU478 2.3 88.4 1.0
OD2 C:ASP498 2.4 63.9 1.0
O C:HOH732 2.5 39.1 1.0
CG C:ASP498 2.6 49.8 1.0
CG C:ASP443 3.1 57.9 1.0
O C:HOH751 3.3 58.2 1.0
O C:HOH750 3.3 46.5 1.0
CD C:GLU478 3.3 80.0 1.0
OD2 C:ASP443 3.5 69.1 1.0
OE1 C:GLU478 3.7 84.5 1.0
O C:GLY444 4.1 52.2 1.0
CB C:ASP498 4.1 46.6 1.0
CB C:ASP443 4.3 53.5 1.0
O C:HOH785 4.4 73.8 1.0
N C:GLY444 4.5 47.8 1.0
CA C:ASP443 4.6 45.0 1.0
CG C:GLU478 4.6 50.8 1.0
O C:HOH816 4.7 58.6 1.0
CB C:ALA538 4.8 46.0 1.0
C C:ASP498 4.8 39.5 1.0
CA C:ASP498 4.9 39.5 1.0

Reference:

S.E.Martinez, J.D.Bauman, K.Das, E.Arnold. Structure of Hiv-1 Reverse Transcriptase/D4TTP Complex: Novel Dna Cross-Linking Site and pH-Dependent Conformational Changes. Protein Sci. V. 28 587 2019.
ISSN: ESSN 1469-896X
PubMed: 30499174
DOI: 10.1002/PRO.3559
Page generated: Mon Sep 30 19:15:32 2024

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