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Magnesium in PDB 6asw: Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 9.0

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 9.0

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 9.0:
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 9.0, PDB code: 6asw 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) 33.62 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.225, 133.218, 140.309, 90.00, 97.94, 90.00
R / Rfree (%) 17.9 / 22

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 9.0 (pdb code 6asw). 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 9.0, PDB code: 6asw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6asw

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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 9.0


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

b:89.0
occ:1.00
 OD2 A:ASP185 2.0 0.2 1.0
O2C A:D4T603 2.1 0.1 1.0
OD1 A:ASP110 2.1 0.2 1.0
O2B A:D4T603 2.1 0.5 1.0
O A:VAL111 2.3 93.3 1.0
O1A A:D4T603 2.5 0.8 1.0
CG A:ASP110 3.3 0.4 1.0
CG A:ASP185 3.3 0.2 1.0
PB A:D4T603 3.3 0.6 1.0
PC A:D4T603 3.4 0.6 1.0
C A:VAL111 3.4 95.8 1.0
PA A:D4T603 3.7 0.7 1.0
O7' A:D4T603 3.7 0.1 1.0
O6' A:D4T603 3.8 0.1 1.0
OD2 A:ASP110 3.9 0.1 1.0
N A:VAL111 3.9 91.6 1.0
O1C A:D4T603 4.1 0.0 1.0
CB A:ASP185 4.1 0.3 1.0
C A:ASP110 4.1 94.5 1.0
OD1 A:ASP185 4.2 0.7 1.0
C5' A:D4T603 4.2 0.9 1.0
CA A:VAL111 4.2 87.7 1.0
N A:GLY112 4.3 99.2 1.0
CB A:ASP110 4.4 0.2 1.0
CA A:GLY112 4.4 98.5 1.0
O3C A:D4T603 4.4 0.9 1.0
O5' A:D4T603 4.5 0.7 1.0
O A:ASP110 4.5 0.9 1.0
O1B A:D4T603 4.6 0.6 1.0
CA A:ASP110 4.6 89.7 1.0
NZ A:LYS220 4.7 0.6 1.0
O2A A:D4T603 4.8 0.8 1.0
N A:ASP113 4.9 0.6 1.0
CB A:VAL111 4.9 78.3 1.0
CB A:ALA114 4.9 0.5 1.0
C A:GLY112 5.0 1.0 1.0

Magnesium binding site 2 out of 4 in 6asw

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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 9.0


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

b:49.2
occ:1.00
 OD1 A:ASP498 2.0 65.2 1.0
O A:HOH801 2.0 69.9 1.0
OE2 A:GLU478 2.2 75.9 1.0
OD1 A:ASP443 2.2 51.3 1.0
OD2 A:ASP498 2.4 66.7 1.0
CG A:ASP498 2.5 49.4 1.0
CG A:ASP443 3.2 57.3 1.0
CD A:GLU478 3.2 71.7 1.0
O A:HOH703 3.4 65.4 1.0
O A:HOH721 3.4 77.5 1.0
OD2 A:ASP443 3.5 62.1 1.0
O A:HOH722 3.6 52.8 1.0
OE1 A:GLU478 3.6 67.8 1.0
O A:HOH738 3.8 54.0 1.0
O A:HOH758 3.9 58.8 1.0
CB A:ASP498 4.0 45.6 1.0
O A:GLY444 4.4 63.1 1.0
CB A:ASP443 4.4 43.6 1.0
CG A:GLU478 4.5 63.2 1.0
C A:ASP498 4.6 50.4 1.0
N A:GLY444 4.7 44.6 1.0
CA A:ASP498 4.7 37.7 1.0
CA A:ASP443 4.7 42.3 1.0
N A:ASP498 4.8 40.5 1.0
O A:ASP498 4.8 62.1 1.0
CB A:ALA538 4.9 60.7 1.0
N A:SER499 4.9 54.1 1.0

Magnesium binding site 3 out of 4 in 6asw

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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 9.0


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

b:72.6
occ:1.00
 OD2 C:ASP185 2.1 0.6 1.0
O C:VAL111 2.1 0.8 1.0
OD1 C:ASP110 2.1 0.6 1.0
O2C C:D4T603 2.2 0.7 1.0
O2B C:D4T603 2.3 0.8 1.0
O1A C:D4T603 2.3 0.2 1.0
C C:VAL111 3.1 0.5 1.0
CG C:ASP110 3.3 0.3 1.0
CG C:ASP185 3.3 0.8 1.0
PB C:D4T603 3.4 0.9 1.0
PC C:D4T603 3.5 0.5 1.0
PA C:D4T603 3.6 0.5 1.0
O6' C:D4T603 3.7 0.7 1.0
N C:VAL111 3.8 0.4 1.0
O7' C:D4T603 3.8 0.7 1.0
OD2 C:ASP110 4.0 0.4 1.0
N C:GLY112 4.0 0.1 1.0
CA C:VAL111 4.1 0.6 1.0
C C:ASP110 4.1 0.8 1.0
CA C:GLY112 4.1 0.4 1.0
OD1 C:ASP185 4.1 0.0 1.0
CB C:ASP185 4.3 0.5 1.0
C5' C:D4T603 4.3 1.0 1.0
CB C:ASP110 4.4 0.2 1.0
O1C C:D4T603 4.4 0.7 1.0
O C:ASP110 4.4 98.4 1.0
O3C C:D4T603 4.5 0.7 1.0
O5' C:D4T603 4.5 0.7 1.0
N C:ASP113 4.6 0.4 1.0
O2A C:D4T603 4.6 0.6 1.0
CA C:ASP110 4.6 0.6 1.0
O1B C:D4T603 4.7 0.8 1.0
C C:GLY112 4.7 0.3 1.0
CB C:ALA114 4.7 95.7 1.0
CB C:VAL111 4.8 100.0 1.0
N C:ALA114 4.8 0.8 1.0

Magnesium binding site 4 out of 4 in 6asw

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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 9.0


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

b:60.3
occ:1.00
 OE2 C:GLU478 2.1 65.0 1.0
O C:HOH751 2.2 54.5 1.0
OD1 C:ASP443 2.2 42.3 1.0
OD1 C:ASP498 2.4 67.4 1.0
OD2 C:ASP498 2.4 60.9 1.0
CG C:ASP498 2.7 54.2 1.0
CD C:GLU478 3.2 67.1 1.0
CG C:ASP443 3.3 59.3 1.0
O C:HOH706 3.3 55.0 1.0
OE1 C:GLU478 3.6 67.5 1.0
OD2 C:ASP443 3.7 68.7 1.0
O C:HOH704 3.9 49.4 1.0
O C:GLY444 4.0 52.6 1.0
CB C:ASP498 4.2 41.0 1.0
CG C:GLU478 4.4 53.6 1.0
N C:GLY444 4.5 48.9 1.0
CB C:ASP443 4.6 48.6 1.0
CA C:ASP443 4.8 41.2 1.0
C C:ASP498 4.9 39.3 1.0
CB C:ALA538 4.9 45.6 1.0
OP1 E:DC723 5.0 0.7 1.0
CA C:ASP498 5.0 46.1 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 19:22:07 2024

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