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Magnesium in PDB 6anq: Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.5

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 8.5

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 8.5:
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 8.5, PDB code: 6anq 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) 43.45 / 2.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.853, 132.723, 139.471, 90.00, 98.06, 90.00
R / Rfree (%) 18 / 21.9

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 8.5 (pdb code 6anq). 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 8.5, PDB code: 6anq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6anq

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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 8.5


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 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:88.0
occ:1.00
 OD2 A:ASP185 2.0 0.0 1.0
OD1 A:ASP110 2.1 0.4 1.0
O2B A:D4T603 2.1 0.9 1.0
O2C A:D4T603 2.1 0.3 1.0
O A:VAL111 2.2 0.1 1.0
O1A A:D4T603 2.4 0.8 1.0
PB A:D4T603 3.2 0.6 1.0
CG A:ASP185 3.3 0.5 1.0
C A:VAL111 3.3 0.8 1.0
CG A:ASP110 3.3 0.5 1.0
PC A:D4T603 3.4 0.9 1.0
PA A:D4T603 3.5 0.1 1.0
O6' A:D4T603 3.6 1.0 1.0
O7' A:D4T603 3.6 0.7 1.0
N A:VAL111 3.9 95.3 1.0
OD2 A:ASP110 4.0 0.4 1.0
C A:ASP110 4.1 0.3 1.0
CB A:ASP185 4.1 99.2 1.0
N A:GLY112 4.1 0.7 1.0
CA A:VAL111 4.2 94.0 1.0
OD1 A:ASP185 4.2 0.6 1.0
O1C A:D4T603 4.2 0.6 1.0
CA A:GLY112 4.3 93.9 1.0
C5' A:D4T603 4.3 0.9 1.0
CB A:ASP110 4.3 0.2 1.0
O A:ASP110 4.4 0.2 1.0
O3C A:D4T603 4.4 0.9 1.0
O5' A:D4T603 4.5 0.2 1.0
O1B A:D4T603 4.5 0.7 1.0
CA A:ASP110 4.6 0.8 1.0
O2A A:D4T603 4.7 0.4 1.0
NZ A:LYS220 4.7 0.5 1.0
N A:ASP113 4.8 0.2 1.0
CB A:VAL111 4.9 81.1 1.0
C A:GLY112 4.9 96.1 1.0
CB A:ALA114 4.9 0.2 1.0

Magnesium binding site 2 out of 4 in 6anq

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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 8.5


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 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:65.2
occ:1.00
 OD1 A:ASP498 2.0 71.3 1.0
OE2 A:GLU478 2.2 75.3 1.0
OD1 A:ASP443 2.2 50.6 1.0
OD2 A:ASP498 2.3 74.4 1.0
CG A:ASP498 2.4 49.8 1.0
O T:HOH811 2.8 90.9 1.0
O A:HOH704 2.9 79.6 1.0
CG A:ASP443 3.1 56.4 1.0
O A:HOH758 3.2 53.7 1.0
CD A:GLU478 3.2 68.6 1.0
O A:HOH711 3.3 53.2 1.0
O A:HOH784 3.4 61.6 1.0
OD2 A:ASP443 3.5 67.8 1.0
OE1 A:GLU478 3.6 66.9 1.0
O A:HOH734 3.8 54.5 1.0
CB A:ASP498 3.9 54.1 1.0
CB A:ASP443 4.3 42.7 1.0
O A:GLY444 4.4 59.5 1.0
C A:ASP498 4.5 48.1 1.0
CG A:GLU478 4.6 56.2 1.0
CA A:ASP443 4.6 43.0 1.0
N A:GLY444 4.6 44.8 1.0
CA A:ASP498 4.6 36.5 1.0
N A:ASP498 4.7 35.8 1.0
N A:SER499 4.8 45.6 1.0
O A:ASP498 4.8 60.4 1.0
CB A:ALA538 4.9 57.4 1.0

Magnesium binding site 3 out of 4 in 6anq

Go back to Magnesium Binding Sites List in 6anq
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 8.5


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 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:72.5
occ:1.00
 OD2 C:ASP185 2.0 0.6 1.0
O C:VAL111 2.1 1.0 1.0
O2C C:D4T603 2.1 0.8 1.0
OD1 C:ASP110 2.1 0.6 1.0
O2B C:D4T603 2.3 1.0 1.0
O1A C:D4T603 2.3 96.5 1.0
C C:VAL111 3.2 0.6 1.0
CG C:ASP185 3.3 0.1 1.0
CG C:ASP110 3.3 0.7 1.0
PB C:D4T603 3.4 0.1 1.0
PC C:D4T603 3.4 0.6 1.0
PA C:D4T603 3.5 0.3 1.0
O6' C:D4T603 3.7 0.5 1.0
O7' C:D4T603 3.8 0.1 1.0
N C:VAL111 3.9 90.9 1.0
OD2 C:ASP110 3.9 0.5 1.0
N C:GLY112 4.0 0.1 1.0
CA C:GLY112 4.1 0.3 1.0
CA C:VAL111 4.1 97.2 1.0
OD1 C:ASP185 4.1 0.5 1.0
C C:ASP110 4.2 93.5 1.0
CB C:ASP185 4.2 92.7 1.0
O1C C:D4T603 4.3 0.0 1.0
C5' C:D4T603 4.3 81.0 1.0
O3C C:D4T603 4.4 0.6 1.0
CB C:ASP110 4.4 0.5 1.0
O5' C:D4T603 4.5 94.5 1.0
O C:ASP110 4.5 92.9 1.0
N C:ASP113 4.6 0.3 1.0
O2A C:D4T603 4.6 0.4 1.0
O C:HOH706 4.6 84.6 1.0
CB C:ALA114 4.7 96.3 1.0
C C:GLY112 4.7 0.7 1.0
O1B C:D4T603 4.7 98.8 1.0
CA C:ASP110 4.7 93.8 1.0
N C:ALA114 4.8 0.7 1.0
CB C:VAL111 4.8 88.0 1.0

Magnesium binding site 4 out of 4 in 6anq

Go back to Magnesium Binding Sites List in 6anq
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 8.5


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 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:46.1
occ:1.00
 OD1 C:ASP443 2.1 52.7 1.0
O C:HOH785 2.1 75.4 1.0
OE2 C:GLU478 2.2 80.3 1.0
OD1 C:ASP498 2.2 67.2 1.0
OD2 C:ASP498 2.5 62.1 1.0
O C:HOH713 2.6 72.4 1.0
O C:HOH741 2.6 39.3 1.0
CG C:ASP498 2.7 45.3 1.0
CG C:ASP443 3.1 52.9 1.0
CD C:GLU478 3.3 78.9 1.0
O C:HOH759 3.5 49.1 1.0
O C:HOH775 3.5 68.6 1.0
OD2 C:ASP443 3.5 69.3 1.0
OE1 C:GLU478 3.7 78.3 1.0
O C:GLY444 4.0 54.2 1.0
CB C:ASP498 4.2 39.3 1.0
O C:HOH723 4.3 0.2 1.0
CB C:ASP443 4.4 46.0 1.0
N C:GLY444 4.5 44.4 1.0
CG C:GLU478 4.5 55.9 1.0
CA C:ASP443 4.7 37.7 1.0
C C:ASP498 4.9 38.0 1.0
CB C:ALA538 4.9 40.1 1.0
CA C:ASP498 4.9 42.4 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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