Atomistry » Magnesium » PDB 6ako-6asu » 6amo
Atomistry »
  Magnesium »
    PDB 6ako-6asu »
      6amo »

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

Go back to Magnesium Binding Sites List in 6amo
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

Go back to Magnesium Binding Sites List in 6amo
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

Go back to Magnesium Binding Sites List in 6amo
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

Go back to Magnesium Binding Sites List in 6amo
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy