Atomistry » Magnesium » PDB 6akp-6asw » 6an2
Atomistry »
  Magnesium »
    PDB 6akp-6asw »
      6an2 »

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

Go back to Magnesium Binding Sites List in 6an2
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

Go back to Magnesium Binding Sites List in 6an2
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

Go back to Magnesium Binding Sites List in 6an2
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

Last articles

Mg in 5H1Y
Mg in 5H1B
Mg in 5H1C
Mg in 5H0V
Mg in 5GZA
Mg in 5GZ9
Mg in 5GYN
Mg in 5GXV
Mg in 5GXT
Mg in 5GX5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy