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Magnesium in PDB 4jtw: Crystal Structure of Hcv NS5B Polymerase in Complex with Coupound 1

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Coupound 1

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Coupound 1:
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 Coupound 1, PDB code: 4jtw 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 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.430, 108.000, 134.920, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4jtw:

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

Magnesium binding site 1 out of 4 in 4jtw

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


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 Coupound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:46.5
occ:1.00
 O A:PHE551 2.7 46.5 1.0
O A:GLN194 2.7 38.4 1.0
O A:HOH3248 3.2 34.0 1.0
C A:PHE551 3.8 45.6 1.0
C A:GLN194 3.9 36.5 1.0
CB A:PHE551 4.1 46.4 1.0
OE1 A:GLN199 4.1 36.1 1.0
O A:SER548 4.2 63.7 1.0
CA A:PHE551 4.5 45.6 1.0
CA A:GLN194 4.6 36.3 1.0
N A:VAL552 4.8 44.7 1.0
NE2 A:GLN199 4.9 32.0 1.0
CD A:GLN199 4.9 31.5 1.0
N A:TYR195 5.0 35.0 1.0
N A:PHE551 5.0 45.6 1.0
CB A:GLN194 5.0 35.1 1.0

Magnesium binding site 2 out of 4 in 4jtw

Go back to Magnesium Binding Sites List in 4jtw
Magnesium binding site 2 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Coupound 1


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 Coupound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:44.5
occ:1.00
 O A:HOH3188 2.6 33.8 1.0
O A:THR221 2.7 35.8 1.0
N A:PHE224 3.4 36.1 1.0
N A:CYS223 3.6 38.4 1.0
C A:THR221 3.8 36.0 1.0
OD1 A:ASP220 3.9 43.4 1.0
OD1 A:ASP318 3.9 28.8 1.0
CA A:CYS223 3.9 39.9 1.0
O A:HOH3112 4.0 33.1 1.0
CB A:PHE224 4.0 33.2 1.0
C A:CYS223 4.2 38.5 1.0
CG A:ASP318 4.3 31.2 1.0
CA A:PHE224 4.3 33.7 1.0
C A:ARG222 4.4 38.2 1.0
CA A:THR221 4.6 34.5 1.0
N A:THR221 4.7 35.5 1.0
CB A:THR221 4.7 34.9 1.0
N A:ARG222 4.7 37.6 1.0
OD2 A:ASP318 4.7 33.9 1.0
CA A:ARG222 4.8 38.2 1.0
CB A:ASP318 4.9 32.1 1.0

Magnesium binding site 3 out of 4 in 4jtw

Go back to Magnesium Binding Sites List in 4jtw
Magnesium binding site 3 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Coupound 1


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 Coupound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:46.6
occ:1.00
 O B:PHE551 2.5 53.0 1.0
O B:GLN194 2.6 46.3 1.0
C B:PHE551 3.5 54.1 1.0
C B:GLN194 3.7 45.5 1.0
O B:SER548 4.0 80.5 1.0
CB B:PHE551 4.0 54.6 1.0
CA B:PHE551 4.2 55.2 1.0
CA B:GLN194 4.3 44.4 1.0
N B:VAL552 4.4 53.5 1.0
CA B:VAL552 4.6 52.3 1.0
N B:PHE551 4.7 57.6 1.0
CB B:GLN194 4.8 44.1 1.0
N B:TYR195 4.8 45.3 1.0
C B:SER548 4.9 81.2 1.0
OE1 B:GLN199 4.9 56.5 1.0
CA B:SER548 5.0 83.3 1.0
NE2 B:GLN199 5.0 53.3 1.0

Magnesium binding site 4 out of 4 in 4jtw

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


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 Coupound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:56.7
occ:1.00
 O B:HOH744 2.9 50.5 1.0
O B:HOH819 3.0 54.4 1.0
O B:HOH823 3.1 34.0 1.0
O B:HOH724 3.8 42.9 1.0
OD1 B:ASP318 4.0 48.6 1.0
OD2 B:ASP220 4.0 52.6 1.0
O B:HOH792 4.4 42.8 1.0
CG B:ASP318 4.6 47.1 1.0
O B:THR221 4.8 45.8 1.0
OD2 B:ASP318 4.9 49.6 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 03:16:27 2024

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