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

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 4

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 4:
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 4, PDB code: 4jtz 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 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.090, 106.910, 135.930, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4jtz:

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

Magnesium binding site 1 out of 4 in 4jtz

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


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

b:44.5
occ:1.00
 O A:HOH3270 2.4 29.6 1.0
O A:PHE551 2.8 52.5 1.0
O A:GLN194 2.8 35.7 1.0
C A:PHE551 4.0 52.7 1.0
C A:GLN194 4.0 36.4 1.0
CB A:PHE551 4.4 54.9 1.0
CA A:GLN194 4.5 36.0 1.0
OE1 A:GLN199 4.6 37.0 1.0
CB A:GLN194 4.7 35.7 1.0
O A:SER548 4.7 78.9 1.0
CA A:PHE551 4.8 54.5 1.0
N A:VAL552 4.9 49.8 1.0
CA A:VAL552 4.9 47.2 1.0

Magnesium binding site 2 out of 4 in 4jtz

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


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

b:57.7
occ:1.00
 O A:THR221 2.6 37.4 1.0
OD1 A:ASP220 2.6 47.9 1.0
O A:HOH3130 3.1 47.3 1.0
CG A:ASP220 3.6 45.2 1.0
C A:THR221 3.7 36.8 1.0
N A:CYS223 4.0 35.8 1.0
OD2 A:ASP220 4.0 44.9 1.0
O A:HOH3250 4.1 35.9 1.0
OD2 A:ASP318 4.2 40.9 1.0
N A:THR221 4.3 37.4 1.0
N A:ARG222 4.5 37.4 1.0
CA A:ARG222 4.5 39.5 1.0
C A:ASP220 4.6 36.6 1.0
CA A:THR221 4.6 36.3 1.0
C A:ARG222 4.8 38.6 1.0
CB A:ASP220 4.8 40.5 1.0
CA A:CYS223 4.8 34.6 1.0
CA A:ASP220 4.9 36.3 1.0
N A:PHE224 4.9 31.9 1.0

Magnesium binding site 3 out of 4 in 4jtz

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


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

b:73.0
occ:1.00
 O B:GLN194 2.6 46.3 1.0
O B:HOH1100 2.8 46.6 1.0
O B:HOH1098 3.2 48.5 1.0
O B:PHE551 3.4 60.1 1.0
OE1 B:GLN199 3.6 63.9 1.0
C B:GLN194 3.7 46.5 1.0
CA B:GLN194 4.4 46.2 1.0
CB B:PHE551 4.4 63.4 1.0
CB B:GLN194 4.4 46.3 1.0
C B:PHE551 4.5 60.5 1.0
N B:TYR195 4.6 47.7 1.0
CD B:GLN199 4.7 60.9 1.0
CA B:TYR195 4.9 46.8 1.0
NE2 B:GLN199 4.9 61.1 1.0

Magnesium binding site 4 out of 4 in 4jtz

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


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

b:70.0
occ:1.00
 O B:HOH1160 2.5 46.1 1.0
OD2 B:ASP220 3.1 55.6 1.0
O B:HOH1117 3.4 38.8 1.0
O B:THR221 4.0 47.6 1.0
O B:HOH1134 4.2 44.2 1.0
O B:HOH1039 4.2 23.9 1.0
CG B:ASP220 4.3 53.6 1.0
CB B:ASP220 4.9 51.1 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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