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Magnesium in PDB 4jju: Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29:
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 29, PDB code: 4jju 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 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.070, 108.390, 134.880, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4jju:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29 also contains other interesting chemical elements:

Fluorine (F) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29 (pdb code 4jju). 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 29, PDB code: 4jju:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4jju

Go back to Magnesium Binding Sites List in 4jju
Magnesium binding site 1 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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

b:30.9
occ:1.00
 O A:PHE551 2.4 21.5 1.0
O A:GLN194 2.5 17.6 1.0
C A:GLN194 3.4 18.1 1.0
O A:HOH3172 3.6 29.3 1.0
C A:PHE551 3.6 20.6 1.0
CA A:GLN194 3.9 18.0 1.0
CB A:PHE551 4.1 22.5 1.0
CB A:GLN194 4.2 17.8 1.0
O A:HOH3338 4.3 29.6 1.0
O A:HOH3509 4.4 47.7 1.0
CA A:PHE551 4.4 21.4 1.0
O A:SER548 4.5 41.6 1.0
OE1 A:GLN199 4.5 17.5 1.0
N A:TYR195 4.6 18.5 1.0
N A:VAL552 4.6 20.7 1.0
CA A:VAL552 4.7 20.9 1.0
CA A:TYR195 5.0 18.4 1.0

Magnesium binding site 2 out of 4 in 4jju

Go back to Magnesium Binding Sites List in 4jju
Magnesium binding site 2 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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

b:35.9
occ:1.00
 O A:THR221 2.4 22.6 1.0
OD1 A:ASP220 2.5 24.9 1.0
O A:HOH3214 2.6 29.2 1.0
O A:HOH3314 2.8 34.4 1.0
C A:THR221 3.5 21.6 1.0
CG A:ASP220 3.7 25.1 1.0
N A:THR221 3.8 19.4 1.0
O A:HOH3393 4.0 35.3 1.0
O A:HOH3322 4.2 33.9 1.0
OD2 A:ASP318 4.2 31.8 1.0
N A:CYS223 4.2 22.1 1.0
CA A:THR221 4.2 20.4 1.0
O A:HOH3252 4.3 38.8 1.0
OD2 A:ASP220 4.4 26.7 1.0
C A:ASP220 4.4 19.5 1.0
N A:PHE224 4.5 18.8 1.0
N A:ARG222 4.6 21.8 1.0
CA A:ASP220 4.6 18.3 1.0
CB A:THR221 4.7 18.4 1.0
CB A:ASP220 4.7 21.2 1.0
CA A:ARG222 4.7 22.4 1.0
C A:ARG222 4.8 22.5 1.0
CA A:CYS223 4.9 23.1 1.0
CG A:ASP318 4.9 29.2 1.0
CB A:PHE224 5.0 19.0 1.0

Magnesium binding site 3 out of 4 in 4jju

Go back to Magnesium Binding Sites List in 4jju
Magnesium binding site 3 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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

b:35.6
occ:1.00
 O B:PHE551 2.5 25.4 1.0
O B:GLN194 2.6 25.6 1.0
O B:HOH845 2.6 30.5 1.0
C B:GLN194 3.5 24.4 1.0
C B:PHE551 3.6 25.8 1.0
CA B:GLN194 3.9 23.7 1.0
O B:HOH817 4.0 33.5 1.0
CB B:PHE551 4.1 28.1 1.0
CB B:GLN194 4.2 22.9 1.0
O B:HOH923 4.4 38.9 1.0
O B:SER548 4.4 39.9 1.0
CA B:PHE551 4.5 26.7 1.0
N B:VAL552 4.5 26.1 1.0
O B:HOH1019 4.6 42.7 1.0
OE1 B:GLN199 4.6 28.4 1.0
CA B:VAL552 4.6 26.6 1.0
N B:TYR195 4.6 22.6 1.0

Magnesium binding site 4 out of 4 in 4jju

Go back to Magnesium Binding Sites List in 4jju
Magnesium binding site 4 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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

b:73.1
occ:1.00
 OD2 B:ASP318 3.1 35.8 1.0
O B:HOH1061 3.3 42.1 1.0
OD1 B:ASP318 3.8 35.2 1.0
CG B:ASP318 3.8 31.4 1.0
O B:HOH1060 3.8 40.9 1.0
O B:HOH1005 3.8 37.6 1.0
O B:HOH1056 3.8 41.4 1.0
O B:HOH799 4.1 27.6 1.0
O B:HOH893 4.6 35.0 1.0
O B:HOH961 5.0 48.9 1.0

Reference:

P.L.Beaulieu, R.Coulombe, J.Duan, G.Fazal, C.Godbout, O.Hucke, A.Jakalian, M.A.Joly, O.Lepage, M.Llinas-Brunet, J.Naud, M.Poirier, N.Rioux, B.Thavonekham, G.Kukolj, T.A.Stammers. Structure-Based Design of Novel Hcv NS5B Thumb Pocket 2 Allosteric Inhibitors with Submicromolar GT1 Replicon Potency: Discovery of A Quinazolinone Chemotype. Bioorg.Med.Chem.Lett. V. 23 4132 2013.
ISSN: ISSN 0960-894X
PubMed: 23768906
DOI: 10.1016/J.BMCL.2013.05.037
Page generated: Mon Dec 14 19:00:17 2020

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