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Magnesium in PDB 5j1e: Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase

Enzymatic activity of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase

All present enzymatic activity of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase, PDB code: 5j1e was solved by K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.77 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.070, 89.310, 108.220, 105.47, 92.69, 110.80
R / Rfree (%) 25.4 / 29.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase (pdb code 5j1e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase, PDB code: 5j1e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5j1e

Go back to Magnesium Binding Sites List in 5j1e
Magnesium binding site 1 out of 3 in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.2
occ:1.00
OD2 A:ASP443 2.1 68.0 1.0
OD1 A:ASP443 2.1 63.0 1.0
OD2 A:ASP498 2.1 84.0 1.0
CG A:ASP443 2.3 61.8 1.0
CG A:ASP498 3.1 80.3 1.0
OD1 A:ASP498 3.4 88.3 1.0
OD1 A:ASP549 3.5 0.6 1.0
CB A:ASP443 3.8 59.2 1.0
OE2 A:GLU478 3.8 79.0 1.0
CG A:ASP549 4.4 0.0 1.0
CB A:ASP549 4.4 97.2 1.0
O A:GLY444 4.4 58.9 1.0
OD1 A:ASN545 4.4 64.8 1.0
CB A:ASP498 4.4 70.4 1.0
CA A:ASP443 4.7 53.8 1.0
CD A:GLU478 4.8 77.7 1.0
N A:GLY444 4.9 52.2 1.0
OE1 A:GLU478 4.9 76.1 1.0
CB A:ALA538 5.0 83.5 1.0
CA A:ASP549 5.0 91.0 1.0

Magnesium binding site 2 out of 3 in 5j1e

Go back to Magnesium Binding Sites List in 5j1e
Magnesium binding site 2 out of 3 in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:66.1
occ:1.00
OE2 C:GLU478 2.1 63.1 1.0
OD2 C:ASP498 2.1 67.8 1.0
OD1 C:ASP443 2.1 63.6 1.0
OD1 C:ASP498 2.1 77.2 1.0
O05 C:6FT603 2.2 60.8 0.7
O01 C:6FT603 2.2 73.6 0.7
CG C:ASP498 2.3 69.1 1.0
CD C:GLU478 3.1 65.8 1.0
CG C:ASP443 3.2 59.7 1.0
C02 C:6FT603 3.2 73.4 0.7
C04 C:6FT603 3.3 62.9 0.7
MG C:MG602 3.3 67.5 1.0
OE1 C:GLU478 3.5 68.3 1.0
OD2 C:ASP443 3.6 58.9 1.0
C03 C:6FT603 3.7 68.9 0.7
CB C:ASP498 3.8 60.5 1.0
O C:GLY444 4.3 67.8 1.0
O06 C:6FT603 4.3 60.6 0.7
CG C:GLU478 4.4 62.2 1.0
C C:ASP498 4.4 59.4 1.0
CB C:ASP443 4.4 58.1 1.0
C27 C:6FT603 4.5 77.3 0.7
CA C:ASP498 4.6 58.3 1.0
N C:SER499 4.7 56.8 1.0
N C:GLY444 4.7 61.6 1.0
O C:ASP498 4.7 63.3 1.0
CA C:ASP443 4.8 59.8 1.0
N C:ASP498 4.8 54.9 1.0
O28 C:6FT603 4.8 81.3 0.7
CB C:ALA538 4.9 61.8 1.0
CB C:SER499 5.0 55.2 1.0

Magnesium binding site 3 out of 3 in 5j1e

Go back to Magnesium Binding Sites List in 5j1e
Magnesium binding site 3 out of 3 in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:67.5
occ:1.00
OD1 C:ASP549 2.1 68.8 1.0
OD2 C:ASP443 2.1 58.9 1.0
O01 C:6FT603 2.3 73.6 0.7
O28 C:6FT603 2.4 81.3 0.7
C02 C:6FT603 3.0 73.4 0.7
CG C:ASP443 3.0 59.7 1.0
C27 C:6FT603 3.1 77.3 0.7
CG C:ASP549 3.2 69.8 1.0
OD1 C:ASP443 3.2 63.6 1.0
MG C:MG601 3.3 66.1 1.0
OD2 C:ASP498 3.4 67.8 1.0
CB C:ASP549 3.7 69.8 1.0
O C:GLY444 4.2 67.8 1.0
NE2 C:HIS539 4.2 68.2 1.0
OD2 C:ASP549 4.3 67.6 1.0
CA C:ASP549 4.3 64.6 1.0
C03 C:6FT603 4.4 68.9 0.7
CB C:ASP443 4.5 58.1 1.0
CG C:ASP498 4.5 69.1 1.0
C26 C:6FT603 4.6 76.6 0.7
O05 C:6FT603 4.7 60.8 0.7
OE2 C:GLU478 4.7 63.1 1.0
CD2 C:HIS539 4.8 68.9 1.0
OD1 C:ASP498 4.9 77.2 1.0
CG2 C:VAL552 5.0 76.7 1.0

Reference:

J.Kankanala, K.A.Kirby, F.Liu, L.Miller, E.Nagy, D.J.Wilson, M.A.Parniak, S.G.Sarafianos, Z.Wang. Design, Synthesis, and Biological Evaluations of Hydroxypyridonecarboxylic Acids As Inhibitors of Hiv Reverse Transcriptase Associated Rnase H. J.Med.Chem. V. 59 5051 2016.
ISSN: ISSN 0022-2623
PubMed: 27094954
DOI: 10.1021/ACS.JMEDCHEM.6B00465
Page generated: Mon Dec 14 20:32:16 2020

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