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Magnesium in PDB 6amo: Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 7.0

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming D4TTP at pH 7.0

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 7.0:
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 7.0, PDB code: 6amo 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) 43.52 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.020, 132.674, 139.392, 90.00, 98.40, 90.00
R / Rfree (%) 18.1 / 21.7

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 7.0 (pdb code 6amo). 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 7.0, PDB code: 6amo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6amo

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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 7.0


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

b:93.2
occ:1.00
 OD2 A:ASP185 2.1 0.0 1.0
OD1 A:ASP110 2.1 0.8 1.0
O2B A:D4T603 2.1 0.7 1.0
O2C A:D4T603 2.1 0.5 1.0
O A:VAL111 2.3 96.9 1.0
O2A A:D4T603 2.4 0.3 1.0
CG A:ASP110 3.3 0.9 1.0
CG A:ASP185 3.3 0.0 1.0
PB A:D4T603 3.3 0.8 1.0
C A:VAL111 3.4 0.7 1.0
PC A:D4T603 3.4 0.8 1.0
PA A:D4T603 3.6 0.2 1.0
O7' A:D4T603 3.7 0.2 1.0
O6' A:D4T603 3.7 0.7 1.0
OD2 A:ASP110 3.9 0.2 1.0
N A:VAL111 4.0 98.4 1.0
CB A:ASP185 4.0 0.9 1.0
C A:ASP110 4.2 0.5 1.0
NZ A:LYS220 4.2 0.9 1.0
OD1 A:ASP185 4.2 0.1 1.0
N A:GLY112 4.3 0.9 1.0
CA A:VAL111 4.3 94.3 1.0
O1C A:D4T603 4.3 0.3 1.0
CA A:GLY112 4.3 0.1 1.0
CB A:ASP110 4.4 0.8 1.0
C5' A:D4T603 4.4 0.4 1.0
O3C A:D4T603 4.4 0.8 1.0
O1B A:D4T603 4.5 0.6 1.0
O A:ASP110 4.5 0.7 1.0
O5' A:D4T603 4.6 0.5 1.0
CA A:ASP110 4.7 0.8 1.0
O1A A:D4T603 4.7 0.6 1.0
CD A:LYS220 4.7 0.1 1.0
N A:ASP113 4.9 0.1 1.0
CB A:VAL111 5.0 86.7 1.0

Magnesium binding site 2 out of 4 in 6amo

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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 7.0


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

b:59.5
occ:1.00
 OD1 A:ASP498 2.1 64.9 1.0
OD1 A:ASP443 2.1 57.8 1.0
OE2 A:GLU478 2.3 70.5 1.0
OD2 A:ASP498 2.3 65.3 1.0
O A:HOH710 2.3 70.3 1.0
CG A:ASP498 2.5 51.1 1.0
O A:HOH774 3.0 62.7 1.0
CG A:ASP443 3.1 56.6 1.0
O A:HOH782 3.2 59.4 1.0
CD A:GLU478 3.3 63.9 1.0
OD2 A:ASP443 3.5 68.4 1.0
O A:HOH820 3.6 66.9 1.0
OE1 A:GLU478 3.7 65.4 1.0
CB A:ASP498 4.0 47.8 1.0
O A:HOH769 4.1 53.3 1.0
O A:GLY444 4.2 60.6 1.0
CB A:ASP443 4.3 49.5 1.0
N A:GLY444 4.5 47.8 1.0
CA A:ASP443 4.5 46.4 1.0
CG A:GLU478 4.6 58.3 1.0
CA A:ASP498 4.8 41.0 1.0
C A:ASP498 4.8 46.1 1.0
N A:ASP498 4.8 40.0 1.0
CB A:ALA538 4.8 41.4 1.0
N A:SER499 4.8 46.5 1.0
ND2 A:ASN545 5.0 51.3 1.0

Magnesium binding site 3 out of 4 in 6amo

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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 7.0


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

b:75.6
occ:1.00
 OD2 C:ASP185 2.1 0.2 1.0
O C:VAL111 2.1 0.0 1.0
OD1 C:ASP110 2.1 0.1 1.0
O2C C:D4T603 2.2 0.5 1.0
O1A C:D4T603 2.2 0.1 1.0
O2B C:D4T603 2.3 0.7 1.0
C C:VAL111 3.2 0.7 1.0
CG C:ASP110 3.3 0.6 1.0
CG C:ASP185 3.3 0.0 1.0
PB C:D4T603 3.4 0.2 1.0
PA C:D4T603 3.5 0.7 1.0
PC C:D4T603 3.5 0.5 1.0
O6' C:D4T603 3.7 0.9 1.0
N C:VAL111 3.9 99.7 1.0
O7' C:D4T603 3.9 0.8 1.0
OD2 C:ASP110 3.9 0.5 1.0
N C:GLY112 4.1 0.2 1.0
CA C:VAL111 4.1 1.0 1.0
OD1 C:ASP185 4.1 0.3 1.0
CA C:GLY112 4.2 0.0 1.0
C C:ASP110 4.2 0.1 1.0
NZ C:LYS220 4.2 0.7 1.0
CB C:ASP185 4.2 0.6 1.0
O1C C:D4T603 4.3 0.8 1.0
C5' C:D4T603 4.4 0.3 1.0
CB C:ASP110 4.5 0.2 1.0
O5' C:D4T603 4.5 0.8 1.0
O2A C:D4T603 4.5 0.3 1.0
O3C C:D4T603 4.5 0.5 1.0
O C:ASP110 4.6 0.3 1.0
N C:ASP113 4.6 0.8 1.0
CB C:ALA114 4.7 98.6 1.0
CA C:ASP110 4.7 0.8 1.0
O1B C:D4T603 4.7 0.4 1.0
C C:GLY112 4.7 0.4 1.0
CB C:VAL111 4.8 95.9 1.0
N C:ALA114 4.8 0.5 1.0
OD1 C:ASP186 4.9 0.4 1.0

Magnesium binding site 4 out of 4 in 6amo

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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 7.0


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

b:51.8
occ:1.00
 O C:HOH713 2.1 64.9 1.0
OD1 C:ASP498 2.1 71.4 1.0
OD1 C:ASP443 2.2 55.9 1.0
OE2 C:GLU478 2.3 80.9 1.0
OD2 C:ASP498 2.3 61.8 1.0
CG C:ASP498 2.5 53.5 1.0
O C:HOH727 2.7 45.5 1.0
CG C:ASP443 3.1 55.1 1.0
O C:HOH768 3.2 54.7 1.0
CD C:GLU478 3.3 77.3 1.0
OD2 C:ASP443 3.5 64.1 1.0
O C:HOH760 3.5 63.8 1.0
OE1 C:GLU478 3.7 76.4 1.0
O C:HOH735 3.7 75.9 1.0
CB C:ASP498 4.1 46.9 1.0
O C:GLY444 4.2 61.2 1.0
CB C:ASP443 4.3 46.5 1.0
N C:GLY444 4.5 44.5 1.0
O C:HOH769 4.5 95.2 1.0
CA C:ASP443 4.5 43.9 1.0
CG C:GLU478 4.6 61.7 1.0
CB C:ALA538 4.8 38.6 1.0
C C:ASP498 4.8 42.0 1.0
CA C:ASP498 4.8 44.2 1.0
N C:ASP498 4.9 45.8 1.0
O C:HOH795 4.9 62.9 1.0
N C:SER499 5.0 43.4 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 19:14:56 2024

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