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Magnesium in PDB 6an2: Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 7.5

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 7.5

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 7.5:
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 7.5, PDB code: 6an2 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) 45.98 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.958, 132.606, 139.319, 90.00, 98.07, 90.00
R / Rfree (%) 17.3 / 21.6

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 7.5 (pdb code 6an2). 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 7.5, PDB code: 6an2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6an2

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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 7.5


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

b:0.7
occ:1.00
 OD2 A:ASP185 2.0 0.5 1.0
O2B A:D4T603 2.1 0.7 1.0
OD1 A:ASP110 2.1 0.4 1.0
O2C A:D4T603 2.1 0.6 1.0
O A:VAL111 2.3 0.7 1.0
O2A A:D4T603 2.4 0.5 1.0
CG A:ASP110 3.2 0.9 1.0
PB A:D4T603 3.3 0.6 1.0
CG A:ASP185 3.3 1.0 1.0
C A:VAL111 3.4 0.9 1.0
PC A:D4T603 3.4 0.9 1.0
PA A:D4T603 3.6 0.1 1.0
O7' A:D4T603 3.7 0.0 1.0
O6' A:D4T603 3.7 0.2 1.0
OD2 A:ASP110 3.9 0.5 1.0
N A:VAL111 4.0 97.5 1.0
OD1 A:ASP185 4.1 0.6 1.0
CB A:ASP185 4.2 95.7 1.0
C A:ASP110 4.2 94.8 1.0
C5' A:D4T603 4.2 1.0 1.0
N A:GLY112 4.3 0.3 1.0
CA A:VAL111 4.3 96.4 1.0
O1C A:D4T603 4.3 0.2 1.0
CA A:GLY112 4.3 0.8 1.0
CB A:ASP110 4.3 0.8 1.0
O3C A:D4T603 4.4 0.7 1.0
O5' A:D4T603 4.4 0.0 1.0
O1B A:D4T603 4.5 0.1 1.0
O A:ASP110 4.5 0.6 1.0
NZ A:LYS220 4.6 0.0 1.0
CA A:ASP110 4.7 0.1 1.0
O1A A:D4T603 4.8 0.8 1.0
N A:ASP113 4.9 0.5 1.0
CD A:LYS220 5.0 0.3 1.0
CB A:VAL111 5.0 86.2 1.0

Magnesium binding site 2 out of 4 in 6an2

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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 7.5


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

b:61.7
occ:1.00
 OD1 A:ASP498 2.1 75.5 1.0
OD1 A:ASP443 2.1 71.7 1.0
OE2 A:GLU478 2.2 96.7 1.0
OD2 A:ASP498 2.3 76.2 1.0
CG A:ASP498 2.5 43.7 1.0
O A:HOH781 2.7 76.7 1.0
O A:HOH768 2.9 0.3 1.0
CG A:ASP443 3.1 66.6 1.0
CD A:GLU478 3.2 84.5 1.0
O A:HOH759 3.2 57.4 1.0
OE1 A:GLU478 3.4 75.0 1.0
OD2 A:ASP443 3.6 79.4 1.0
O A:HOH790 3.6 60.0 1.0
O A:HOH745 4.0 65.0 1.0
CB A:ASP498 4.0 45.5 1.0
O A:GLY444 4.1 58.5 1.0
CB A:ASP443 4.3 45.8 1.0
N A:GLY444 4.4 52.2 1.0
CA A:ASP443 4.5 50.7 1.0
CG A:GLU478 4.5 60.8 1.0
C A:ASP498 4.7 49.3 1.0
CA A:ASP498 4.7 48.4 1.0
O A:HOH802 4.7 78.6 1.0
N A:ASP498 4.8 36.7 1.0
N A:SER499 4.8 44.4 1.0
CB A:ALA538 4.9 56.1 1.0
C A:ASP443 5.0 51.2 1.0

Magnesium binding site 3 out of 4 in 6an2

Go back to Magnesium Binding Sites List in 6an2
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 7.5


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

b:85.0
occ:1.00
 OD2 C:ASP185 2.1 0.2 1.0
OD1 C:ASP110 2.1 0.7 1.0
O C:VAL111 2.1 0.1 1.0
O2C C:D4T603 2.2 0.6 1.0
O2B C:D4T603 2.2 0.6 1.0
O1A C:D4T603 2.3 0.9 1.0
C C:VAL111 3.2 0.9 1.0
CG C:ASP110 3.3 0.5 1.0
CG C:ASP185 3.3 0.9 1.0
PB C:D4T603 3.3 0.5 1.0
PA C:D4T603 3.5 0.4 1.0
PC C:D4T603 3.5 0.4 1.0
O6' C:D4T603 3.7 0.1 1.0
O7' C:D4T603 3.8 0.6 1.0
OD2 C:ASP110 3.9 1.0 1.0
N C:GLY112 3.9 0.3 1.0
CA C:GLY112 3.9 0.6 1.0
N C:VAL111 3.9 0.1 1.0
CA C:VAL111 4.1 0.9 1.0
CB C:ASP185 4.2 85.8 1.0
OD1 C:ASP185 4.2 0.5 1.0
C C:ASP110 4.2 0.4 1.0
C5' C:D4T603 4.3 91.7 1.0
O1C C:D4T603 4.4 0.5 1.0
CB C:ASP110 4.4 0.4 1.0
N C:ASP113 4.5 1.0 1.0
O5' C:D4T603 4.5 0.8 1.0
O3C C:D4T603 4.5 0.6 1.0
O2A C:D4T603 4.5 0.5 1.0
C C:GLY112 4.5 0.8 1.0
O C:ASP110 4.5 0.7 1.0
O1B C:D4T603 4.6 94.0 1.0
CB C:ALA114 4.7 0.5 1.0
CA C:ASP110 4.8 0.2 1.0
N C:ALA114 4.8 0.9 1.0
CB C:VAL111 4.9 0.6 1.0

Magnesium binding site 4 out of 4 in 6an2

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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 7.5


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

b:57.3
occ:1.00
 OD1 C:ASP443 2.2 54.7 1.0
OD1 C:ASP498 2.2 82.6 1.0
OE2 C:GLU478 2.3 0.2 1.0
O C:HOH742 2.4 54.9 1.0
OD2 C:ASP498 2.4 74.2 1.0
CG C:ASP498 2.6 46.5 1.0
CG C:ASP443 3.2 67.2 1.0
O C:HOH784 3.2 67.6 1.0
O E:HOH805 3.2 85.1 1.0
CD C:GLU478 3.3 95.9 1.0
O C:HOH726 3.5 53.2 1.0
OE1 C:GLU478 3.6 94.9 1.0
OD2 C:ASP443 3.7 72.2 1.0
O C:HOH790 3.8 58.1 1.0
O C:GLY444 3.9 58.7 1.0
CB C:ASP498 4.1 36.9 1.0
N C:GLY444 4.3 61.5 1.0
CB C:ASP443 4.4 55.0 1.0
CA C:ASP443 4.6 38.7 1.0
CG C:GLU478 4.6 69.8 1.0
CB C:ALA538 4.8 42.0 1.0
C C:ASP498 4.9 44.8 1.0
OP1 E:DC723 4.9 0.6 1.0
C C:GLY444 4.9 48.0 1.0
CA C:ASP498 5.0 44.1 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 19:15:31 2024

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