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Magnesium in PDB 6avt: Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 9.5 with Cross- Linking to First Base Template Overhang

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 9.5 with Cross- Linking to First Base Template Overhang

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 9.5 with Cross- Linking to First Base Template Overhang:
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 9.5 with Cross- Linking to First Base Template Overhang, PDB code: 6avt 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) 25.89 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.197, 133.504, 140.129, 90.00, 97.49, 90.00
R / Rfree (%) 17.9 / 21.1

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 9.5 with Cross- Linking to First Base Template Overhang (pdb code 6avt). 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 9.5 with Cross- Linking to First Base Template Overhang, PDB code: 6avt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6avt

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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 9.5 with Cross- Linking to First Base Template Overhang


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 9.5 with Cross- Linking to First Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:81.7
occ:1.00
 O2C A:D4T603 1.9 0.3 1.0
OD2 A:ASP185 2.0 0.5 1.0
OD1 A:ASP110 2.1 0.2 1.0
O2B A:D4T603 2.1 1.0 1.0
O A:VAL111 2.3 95.5 1.0
O1A A:D4T603 2.4 99.2 1.0
PC A:D4T603 3.2 0.1 1.0
CG A:ASP110 3.2 0.5 1.0
PB A:D4T603 3.2 0.0 1.0
CG A:ASP185 3.3 0.1 1.0
C A:VAL111 3.4 94.8 1.0
O7' A:D4T603 3.6 0.6 1.0
PA A:D4T603 3.6 0.0 1.0
O6' A:D4T603 3.7 0.8 1.0
OD2 A:ASP110 3.9 0.3 1.0
N A:VAL111 3.9 94.3 1.0
OD1 A:ASP185 4.0 0.5 1.0
O1C A:D4T603 4.1 0.2 1.0
C A:ASP110 4.2 99.7 1.0
O3C A:D4T603 4.2 0.5 1.0
CA A:VAL111 4.2 88.5 1.0
CB A:ASP185 4.3 0.6 1.0
N A:GLY112 4.3 94.7 1.0
CB A:ASP110 4.4 0.8 1.0
C5' A:D4T603 4.4 94.3 1.0
CA A:GLY112 4.4 94.8 1.0
O1B A:D4T603 4.5 0.9 1.0
O5' A:D4T603 4.6 97.3 1.0
CA A:ASP110 4.6 98.1 1.0
O A:ASP110 4.6 0.1 1.0
O2A A:D4T603 4.7 0.2 1.0
CB A:VAL111 4.9 82.1 1.0
N A:ASP113 5.0 0.4 1.0

Magnesium binding site 2 out of 4 in 6avt

Go back to Magnesium Binding Sites List in 6avt
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 9.5 with Cross- Linking to First Base Template Overhang


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 9.5 with Cross- Linking to First Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:66.7
occ:1.00
 OD1 A:ASP498 2.1 74.6 1.0
OE2 A:GLU478 2.2 86.8 1.0
OD1 A:ASP443 2.2 55.2 1.0
OD2 A:ASP498 2.3 75.5 1.0
O A:HOH778 2.4 82.2 1.0
CG A:ASP498 2.5 55.2 1.0
O A:HOH768 2.8 67.5 1.0
CG A:ASP443 3.1 66.2 1.0
CD A:GLU478 3.2 79.5 1.0
O A:HOH764 3.3 53.8 1.0
OE1 A:GLU478 3.5 77.7 1.0
OD2 A:ASP443 3.6 73.1 1.0
O A:HOH714 3.9 56.1 1.0
CB A:ASP498 4.0 50.9 1.0
O A:HOH738 4.1 75.7 1.0
CB A:ASP443 4.3 52.7 1.0
O A:GLY444 4.4 67.2 1.0
N A:GLY444 4.4 47.9 1.0
CG A:GLU478 4.5 57.2 1.0
CA A:ASP443 4.5 51.2 1.0
O A:HOH816 4.6 54.7 1.0
C A:ASP498 4.7 50.8 1.0
CA A:ASP498 4.7 39.2 1.0
N A:ASP498 4.8 38.1 1.0
N A:SER499 4.8 51.0 1.0
CB A:ALA538 5.0 58.5 1.0

Magnesium binding site 3 out of 4 in 6avt

Go back to Magnesium Binding Sites List in 6avt
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 9.5 with Cross- Linking to First Base Template Overhang


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 9.5 with Cross- Linking to First Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:72.9
occ:1.00
 OD2 C:ASP185 2.0 0.9 1.0
OD1 C:ASP110 2.1 0.1 1.0
O2C C:D4T603 2.1 0.0 1.0
O C:VAL111 2.2 0.4 1.0
O2B C:D4T603 2.2 0.0 1.0
O1A C:D4T603 2.3 0.3 1.0
C C:VAL111 3.2 0.6 1.0
CG C:ASP110 3.3 0.8 1.0
CG C:ASP185 3.3 0.2 1.0
PB C:D4T603 3.4 1.0 1.0
PC C:D4T603 3.5 0.8 1.0
PA C:D4T603 3.6 0.7 1.0
O6' C:D4T603 3.8 0.9 1.0
O7' C:D4T603 3.8 0.8 1.0
N C:VAL111 3.9 0.6 1.0
OD2 C:ASP110 3.9 0.8 1.0
N C:GLY112 4.0 0.7 1.0
OD1 C:ASP185 4.1 0.3 1.0
CA C:GLY112 4.1 0.3 1.0
O C:HOH701 4.1 1.0 1.0
CA C:VAL111 4.1 0.7 1.0
C C:ASP110 4.2 0.5 1.0
C5' C:D4T603 4.2 97.4 1.0
CB C:ASP185 4.3 0.5 1.0
NZ C:LYS220 4.3 0.0 1.0
O1C C:D4T603 4.3 0.4 1.0
CB C:ASP110 4.4 0.7 1.0
O3C C:D4T603 4.4 0.5 1.0
O5' C:D4T603 4.4 0.2 1.0
O C:ASP110 4.6 0.2 1.0
O2A C:D4T603 4.6 0.5 1.0
O1B C:D4T603 4.6 0.8 1.0
CA C:ASP110 4.7 96.1 1.0
N C:ASP113 4.7 0.8 1.0
C C:GLY112 4.7 0.1 1.0
CB C:ALA114 4.8 0.0 1.0
CB C:VAL111 4.9 97.6 1.0
N C:ALA114 5.0 0.6 1.0

Magnesium binding site 4 out of 4 in 6avt

Go back to Magnesium Binding Sites List in 6avt
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 9.5 with Cross- Linking to First Base Template Overhang


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 9.5 with Cross- Linking to First Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:48.9
occ:1.00
 O C:HOH800 2.0 60.6 1.0
OD1 C:ASP443 2.1 56.4 1.0
OD1 C:ASP498 2.2 75.2 1.0
OE2 C:GLU478 2.2 90.8 1.0
OD2 C:ASP498 2.4 67.0 1.0
CG C:ASP498 2.6 48.1 1.0
O C:HOH721 3.0 45.0 1.0
CG C:ASP443 3.1 60.4 1.0
CD C:GLU478 3.3 84.6 1.0
O C:HOH746 3.3 48.7 1.0
OD2 C:ASP443 3.5 74.5 1.0
O C:HOH709 3.6 89.4 1.0
OE1 C:GLU478 3.6 86.6 1.0
O C:HOH790 3.7 65.5 1.0
O C:GLY444 4.1 57.8 1.0
CB C:ASP498 4.1 42.1 1.0
CB C:ASP443 4.3 52.9 1.0
N C:GLY444 4.5 47.1 1.0
CA C:ASP443 4.6 47.4 1.0
CG C:GLU478 4.6 58.7 1.0
C C:ASP498 4.9 38.2 1.0
CA C:ASP498 4.9 38.4 1.0
CB C:ALA538 4.9 45.7 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 19:22:52 2024

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