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Magnesium in PDB 4ju2: Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12:
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 12, PDB code: 4ju2 was solved by R.Coulombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.540, 107.740, 135.820, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4ju2:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12 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 12 (pdb code 4ju2). 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 12, PDB code: 4ju2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ju2

Go back to Magnesium Binding Sites List in 4ju2
Magnesium binding site 1 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:65.5
occ:1.00
 O A:PHE551 2.6 52.1 1.0
O A:GLN194 2.6 48.3 1.0
O A:HOH3110 2.9 47.3 1.0
O A:HOH3205 3.0 55.0 1.0
C A:GLN194 3.6 47.5 1.0
C A:PHE551 3.7 52.3 1.0
CA A:GLN194 4.0 45.8 1.0
CB A:GLN194 4.3 43.6 1.0
CB A:PHE551 4.4 55.9 1.0
N A:VAL552 4.6 52.4 1.0
CA A:VAL552 4.6 50.8 1.0
CA A:PHE551 4.7 53.3 1.0
OE1 A:GLN199 4.7 49.7 1.0
N A:TYR195 4.8 49.4 1.0
O A:SER548 4.9 77.1 1.0

Magnesium binding site 2 out of 4 in 4ju2

Go back to Magnesium Binding Sites List in 4ju2
Magnesium binding site 2 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:66.2
occ:1.00
 O A:THR221 2.5 49.2 1.0
O A:HOH3233 3.0 40.5 1.0
O A:HOH3207 3.1 63.2 1.0
N A:CYS223 3.6 48.3 1.0
OD1 A:ASP220 3.6 57.0 1.0
OD2 A:ASP318 3.6 53.7 1.0
N A:PHE224 3.7 45.7 1.0
C A:THR221 3.7 47.2 1.0
CA A:CYS223 4.0 49.0 1.0
C A:ARG222 4.3 49.2 1.0
C A:CYS223 4.4 48.3 1.0
O A:HOH3120 4.5 48.3 1.0
CB A:PHE224 4.5 41.0 1.0
N A:THR221 4.5 47.7 1.0
N A:ARG222 4.6 49.5 1.0
CA A:ARG222 4.6 50.5 1.0
CA A:THR221 4.6 45.4 1.0
CA A:PHE224 4.7 42.0 1.0
CG A:ASP220 4.8 54.6 1.0
CG A:ASP318 4.8 54.4 1.0
CB A:THR221 4.9 43.7 1.0

Magnesium binding site 3 out of 4 in 4ju2

Go back to Magnesium Binding Sites List in 4ju2
Magnesium binding site 3 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:77.4
occ:1.00
 O B:PHE551 2.7 60.6 1.0
O B:GLN194 2.7 54.9 1.0
O B:HOH713 2.8 59.9 1.0
C B:PHE551 3.6 61.4 1.0
CB B:PHE551 3.8 63.2 1.0
O B:SER548 3.8 89.6 1.0
C B:GLN194 3.9 53.8 1.0
CA B:PHE551 4.2 62.8 1.0
OE1 B:GLN199 4.3 61.3 1.0
CA B:GLN194 4.6 52.0 1.0
N B:PHE551 4.6 65.5 1.0
N B:VAL552 4.6 60.1 1.0
C B:SER548 4.8 89.2 1.0
CA B:SER548 4.8 91.8 1.0
CG B:PHE551 4.9 63.1 1.0
CA B:VAL552 5.0 57.8 1.0
CD2 B:PHE551 5.0 63.7 1.0
N B:TYR195 5.0 53.5 1.0

Magnesium binding site 4 out of 4 in 4ju2

Go back to Magnesium Binding Sites List in 4ju2
Magnesium binding site 4 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:83.0
occ:1.00
 O B:THR221 3.1 49.0 1.0
CA B:ARG222 3.3 52.8 1.0
N B:CYS223 3.3 53.5 1.0
OD2 B:ASP220 3.4 66.5 1.0
O B:HOH824 3.4 66.1 1.0
OD1 B:ASP220 3.7 65.7 1.0
C B:ARG222 3.9 53.1 1.0
C B:THR221 3.9 50.0 1.0
CG B:ASP220 3.9 62.7 1.0
N B:ARG222 4.1 50.5 1.0
CG B:ARG222 4.2 59.8 1.0
CB B:ARG222 4.3 55.8 1.0
CA B:GLY351 4.4 67.8 1.0
CA B:CYS223 4.5 53.6 1.0
SG B:CYS223 4.7 62.9 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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