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Magnesium in PDB 6avm: 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 Second 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 Second 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 Second 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 Second Base Template Overhang, PDB code: 6avm 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) 34.37 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.264, 133.333, 140.203, 90.00, 97.63, 90.00
R / Rfree (%) 19.1 / 22.9

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

Magnesium binding site 1 out of 4 in 6avm

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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 Second 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 Second Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:86.7
occ:1.00
 OD2 A:ASP185 2.1 0.9 1.0
OD1 A:ASP110 2.1 0.7 1.0
O2B A:D4T603 2.1 0.9 1.0
O2C A:D4T603 2.2 0.4 1.0
O A:VAL111 2.4 95.7 1.0
O1A A:D4T603 2.4 0.5 1.0
CG A:ASP110 3.3 0.8 1.0
C A:VAL111 3.3 94.1 1.0
CG A:ASP185 3.3 0.2 1.0
PB A:D4T603 3.3 0.8 1.0
PC A:D4T603 3.5 0.5 1.0
PA A:D4T603 3.6 0.3 1.0
O7' A:D4T603 3.8 0.2 1.0
O6' A:D4T603 3.8 0.2 1.0
OD2 A:ASP110 3.9 0.6 1.0
N A:VAL111 3.9 93.2 1.0
N A:GLY112 4.0 98.8 1.0
CA A:GLY112 4.0 95.0 1.0
OD1 A:ASP185 4.1 0.3 1.0
C A:ASP110 4.1 98.6 1.0
CA A:VAL111 4.2 86.5 1.0
CB A:ASP185 4.3 96.5 1.0
CB A:ASP110 4.4 98.4 1.0
C5' A:D4T603 4.4 0.5 1.0
O1C A:D4T603 4.4 0.5 1.0
O3C A:D4T603 4.4 0.9 1.0
O A:ASP110 4.5 0.8 1.0
O5' A:D4T603 4.5 0.8 1.0
O1B A:D4T603 4.6 0.3 1.0
CA A:ASP110 4.6 91.7 1.0
O2A A:D4T603 4.7 0.9 1.0
N A:ASP113 4.7 0.3 1.0
C A:GLY112 4.8 95.6 1.0
CB A:VAL111 5.0 78.4 1.0

Magnesium binding site 2 out of 4 in 6avm

Go back to Magnesium Binding Sites List in 6avm
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 Second 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 Second Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:57.2
occ:1.00
 OD1 A:ASP498 2.1 70.7 1.0
OD1 A:ASP443 2.2 64.8 1.0
OE2 A:GLU478 2.3 82.3 1.0
OD2 A:ASP498 2.3 70.0 1.0
CG A:ASP498 2.5 54.0 1.0
O A:HOH723 2.7 91.2 1.0
O A:HOH726 2.8 62.4 1.0
CG A:ASP443 3.1 64.8 1.0
O A:HOH783 3.3 53.1 1.0
CD A:GLU478 3.4 76.4 1.0
OD2 A:ASP443 3.4 73.5 1.0
OE1 A:GLU478 3.8 80.1 1.0
O A:HOH737 3.9 58.9 1.0
O A:HOH820 4.0 75.0 1.0
CB A:ASP498 4.0 49.7 1.0
CB A:ASP443 4.3 55.4 1.0
O A:GLY444 4.5 72.0 1.0
O A:HOH816 4.5 63.2 1.0
N A:GLY444 4.6 52.0 1.0
CA A:ASP443 4.6 50.9 1.0
CG A:GLU478 4.6 64.9 1.0
C A:ASP498 4.7 56.7 1.0
CA A:ASP498 4.7 38.8 1.0
N A:ASP498 4.8 37.9 1.0
CB A:ALA538 4.8 53.9 1.0
N A:SER499 4.9 52.2 1.0
O A:ASP498 5.0 62.8 1.0

Magnesium binding site 3 out of 4 in 6avm

Go back to Magnesium Binding Sites List in 6avm
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 Second 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 Second Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:68.8
occ:1.00
 OD2 C:ASP185 2.1 0.5 1.0
OD1 C:ASP110 2.1 0.2 1.0
O C:VAL111 2.2 0.1 1.0
O2C C:D4T603 2.2 0.3 1.0
O2B C:D4T603 2.3 0.2 1.0
O1A C:D4T603 2.3 0.8 1.0
C C:VAL111 3.2 0.2 1.0
CG C:ASP110 3.3 0.4 1.0
CG C:ASP185 3.3 0.3 1.0
PB C:D4T603 3.4 0.8 1.0
PC C:D4T603 3.5 0.9 1.0
PA C:D4T603 3.6 0.1 1.0
O6' C:D4T603 3.8 0.5 1.0
O7' C:D4T603 3.8 0.1 1.0
O C:HOH703 3.9 0.2 1.0
N C:VAL111 3.9 0.0 1.0
OD2 C:ASP110 3.9 0.9 1.0
N C:GLY112 4.0 0.4 1.0
OD1 C:ASP185 4.1 0.9 1.0
CA C:GLY112 4.1 0.1 1.0
CA C:VAL111 4.1 0.0 1.0
C C:ASP110 4.2 0.6 1.0
NZ C:LYS220 4.2 0.8 1.0
C5' C:D4T603 4.3 97.5 1.0
O1C C:D4T603 4.3 0.0 1.0
CB C:ASP185 4.3 99.7 1.0
CB C:ASP110 4.4 0.6 1.0
O5' C:D4T603 4.5 0.5 1.0
O3C C:D4T603 4.5 0.4 1.0
O C:ASP110 4.6 98.0 1.0
N C:ASP113 4.6 0.7 1.0
O2A C:D4T603 4.6 0.1 1.0
O1B C:D4T603 4.7 0.0 1.0
CA C:ASP110 4.7 96.9 1.0
C C:GLY112 4.7 0.6 1.0
CB C:ALA114 4.8 92.5 1.0
CB C:VAL111 4.9 93.0 1.0
N C:ALA114 4.9 0.2 1.0
CD C:LYS220 5.0 0.2 1.0

Magnesium binding site 4 out of 4 in 6avm

Go back to Magnesium Binding Sites List in 6avm
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 Second 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 Second Base Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:49.3
occ:1.00
 O C:HOH764 1.9 51.7 1.0
OD1 C:ASP443 2.1 53.1 1.0
OE2 C:GLU478 2.2 80.5 1.0
OD1 C:ASP498 2.2 70.2 1.0
OD2 C:ASP498 2.4 62.4 1.0
CG C:ASP498 2.6 53.5 1.0
O C:HOH737 3.0 42.6 1.0
CG C:ASP443 3.2 55.0 1.0
O C:HOH717 3.2 81.9 1.0
CD C:GLU478 3.2 72.3 1.0
O C:HOH725 3.2 46.4 1.0
O C:HOH735 3.5 66.2 1.0
OE1 C:GLU478 3.5 77.7 1.0
OD2 C:ASP443 3.7 63.9 1.0
O C:HOH741 3.9 55.0 1.0
O C:GLY444 4.1 64.0 1.0
CB C:ASP498 4.1 45.9 1.0
CB C:ASP443 4.4 50.6 1.0
N C:GLY444 4.4 42.6 1.0
CG C:GLU478 4.5 52.7 1.0
CA C:ASP443 4.6 44.8 1.0
C C:ASP498 4.8 41.4 1.0
CA C:ASP498 4.9 40.8 1.0
CB C:ALA538 4.9 41.3 1.0
N C:SER499 5.0 40.5 1.0
N C:ASP498 5.0 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 19:22:40 2024

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