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Magnesium in PDB 4ju1: Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6:
2.7.7.48; 3.4.21.98; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6, PDB code: 4ju1 was solved by R.Coulombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.820, 107.760, 135.860, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4ju1:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6 also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6 (pdb code 4ju1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6, PDB code: 4ju1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ju1

Go back to Magnesium Binding Sites List in 4ju1
Magnesium binding site 1 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 Hcv NS5B Polymerase in Complex with Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:36.7
occ:1.00
 O A:PHE551 2.6 50.9 1.0
O A:GLN194 2.6 46.4 1.0
O A:HOH3175 2.6 23.9 1.0
O A:HOH3169 2.6 35.5 1.0
C A:GLN194 3.7 45.8 1.0
C A:PHE551 3.8 49.5 1.0
CA A:GLN194 4.2 45.0 1.0
CB A:PHE551 4.2 51.9 1.0
CB A:GLN194 4.4 43.0 1.0
O A:HOH3230 4.4 43.9 1.0
OE1 A:GLN199 4.6 42.1 1.0
CA A:PHE551 4.6 50.2 1.0
O A:SER548 4.7 74.3 1.0
N A:VAL552 4.7 48.0 1.0
CA A:VAL552 4.9 44.8 1.0
N A:TYR195 4.9 45.9 1.0

Magnesium binding site 2 out of 4 in 4ju1

Go back to Magnesium Binding Sites List in 4ju1
Magnesium binding site 2 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 Hcv NS5B Polymerase in Complex with Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:64.7
occ:1.00
 O A:THR221 2.7 46.0 1.0
N A:CYS223 3.4 48.1 1.0
O A:HOH3102 3.4 36.8 1.0
OD2 A:ASP318 3.5 46.0 1.0
O A:HOH3114 3.6 48.9 1.0
N A:PHE224 3.6 43.0 1.0
CA A:CYS223 3.7 48.1 1.0
OD1 A:ASP220 3.8 49.7 1.0
C A:THR221 3.9 45.2 1.0
C A:ARG222 4.2 49.2 1.0
C A:CYS223 4.2 46.3 1.0
O A:HOH3164 4.2 36.6 1.0
CB A:PHE224 4.5 37.0 1.0
CA A:ARG222 4.6 49.2 1.0
CA A:PHE224 4.7 39.3 1.0
N A:ARG222 4.7 48.0 1.0
CG A:ASP318 4.7 45.2 1.0
CA A:THR221 4.9 43.4 1.0
N A:THR221 4.9 42.8 1.0

Magnesium binding site 3 out of 4 in 4ju1

Go back to Magnesium Binding Sites List in 4ju1
Magnesium binding site 3 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 Hcv NS5B Polymerase in Complex with Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:57.1
occ:1.00
 O B:PHE551 2.6 54.4 1.0
O B:GLN194 2.7 53.2 1.0
C B:PHE551 3.6 54.3 1.0
CB B:PHE551 3.8 53.7 1.0
C B:GLN194 3.9 51.3 1.0
O B:SER548 4.0 81.5 1.0
CA B:PHE551 4.2 54.8 1.0
CA B:GLN194 4.4 50.9 1.0
OE1 B:GLN199 4.4 56.1 1.0
N B:VAL552 4.6 52.5 1.0
N B:PHE551 4.7 57.0 1.0
CB B:GLN194 4.8 50.6 1.0
CA B:VAL552 5.0 51.1 1.0
C B:SER548 5.0 82.0 1.0
N B:TYR195 5.0 49.9 1.0

Magnesium binding site 4 out of 4 in 4ju1

Go back to Magnesium Binding Sites List in 4ju1
Magnesium binding site 4 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:77.2
occ:1.00
 O B:THR221 2.5 47.2 1.0
OD1 B:ASP220 3.2 60.5 1.0
O B:HOH1118 3.3 51.1 1.0
N B:CYS223 3.4 51.8 1.0
C B:THR221 3.6 48.3 1.0
OD2 B:ASP220 3.7 62.4 1.0
CG B:ASP220 3.8 58.6 1.0
CA B:ARG222 4.0 51.8 1.0
O B:HOH1141 4.0 49.6 1.0
O B:HOH1020 4.2 49.0 1.0
C B:ARG222 4.2 52.0 1.0
N B:ARG222 4.3 49.9 1.0
CA B:CYS223 4.3 51.2 1.0
N B:THR221 4.8 49.0 1.0
CA B:THR221 4.8 47.8 1.0
N B:PHE224 4.9 46.0 1.0
C B:ASP220 4.9 49.5 1.0

Reference:

O.Hucke, R.Coulombe, P.Bonneau, M.Bertrand-Laperle, C.Brochu, J.Gillard, M.A.Joly, S.Landry, O.Lepage, M.Llinas-Brunet, M.Pesant, M.Poirier, M.Poirier, G.Mckercher, M.Marquis, G.Kukolj, P.L.Beaulieu, T.A.Stammers. Molecular Dynamics Simulations and Structure-Based Rational Design Lead to Allosteric Hcv NS5B Polymerase Thumb Pocket 2 Inhibitor with Picomolar Cellular Replicon Potency. J.Med.Chem. V. 57 1932 2014.
ISSN: ISSN 0022-2623
PubMed: 23773186
DOI: 10.1021/JM4004522
Page generated: Sat Aug 17 03:17:06 2024

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