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Sodium in PDB 4j02: Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid:
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 [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid, PDB code: 4j02 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.760, 108.340, 133.060, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4j02:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid (pdb code 4j02). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid, PDB code: 4j02:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4j02

Go back to Sodium Binding Sites List in 4j02
Sodium binding site 1 out of 2 in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:36.0
occ:1.00
 O A:THR221 2.5 20.1 1.0
OD1 A:ASP220 2.6 23.8 1.0
O A:HOH807 2.6 26.8 1.0
O A:HOH789 2.6 21.6 1.0
O A:HOH923 2.6 31.2 1.0
O A:HOH933 2.8 28.4 1.0
C A:THR221 3.6 21.3 1.0
CG A:ASP220 3.7 26.4 1.0
N A:THR221 3.8 20.6 1.0
O A:HOH995 3.9 36.7 1.0
OD2 A:ASP318 4.2 26.3 1.0
CA A:THR221 4.3 20.2 1.0
O A:HOH877 4.3 33.7 1.0
N A:CYS223 4.3 20.6 1.0
OD2 A:ASP220 4.3 26.9 1.0
O3 A:SO4602 4.3 74.5 1.0
C A:ASP220 4.4 20.9 1.0
O1 A:SO4602 4.4 74.2 1.0
O4 A:SO4602 4.6 73.7 1.0
CA A:ASP220 4.6 21.1 1.0
N A:PHE224 4.6 16.8 1.0
N A:ARG222 4.6 21.2 1.0
S A:SO4602 4.7 74.1 1.0
CB A:ASP220 4.7 22.4 1.0
CB A:THR221 4.8 19.3 1.0
CA A:ARG222 4.8 21.1 1.0
CG A:ASP318 4.9 25.2 1.0
C A:ARG222 4.9 21.2 1.0
CA A:CYS223 5.0 20.4 1.0

Sodium binding site 2 out of 2 in 4j02

Go back to Sodium Binding Sites List in 4j02
Sodium binding site 2 out of 2 in the Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hcv NS5B Polymerase in Complex with [(1R)-5,8- Dichloro-1-Propyl-1,3,4,9-Tetrahydropyrano[3,4-B]Indol-1-Yl]Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:39.4
occ:1.00
 O B:THR221 2.6 24.5 1.0
OD1 B:ASP220 2.6 33.5 1.0
O B:HOH1172 2.7 30.4 1.0
O B:HOH1248 2.9 30.8 1.0
O B:HOH1206 3.1 45.6 1.0
CG B:ASP220 3.6 34.3 1.0
C B:THR221 3.7 25.2 1.0
O B:HOH1285 4.0 42.9 1.0
N B:THR221 4.0 26.5 1.0
OD2 B:ASP220 4.2 36.4 1.0
O4 B:SO4602 4.2 68.6 1.0
O B:HOH1168 4.2 40.0 1.0
N B:CYS223 4.3 25.6 1.0
O3 B:SO4602 4.4 68.1 1.0
O2 B:SO4602 4.5 68.4 1.0
CA B:THR221 4.5 25.4 1.0
C B:ASP220 4.5 27.3 1.0
S B:SO4602 4.6 68.0 1.0
OD2 B:ASP318 4.6 32.6 1.0
N B:ARG222 4.7 26.1 1.0
CA B:ASP220 4.7 27.3 1.0
CB B:ASP220 4.8 29.9 1.0
CA B:ARG222 4.8 28.3 1.0
N B:PHE224 4.8 21.8 1.0
C B:ARG222 4.9 26.4 1.0
CB B:THR221 5.0 25.6 1.0

Reference:

T.A.Stammers, R.Coulombe, J.Rancourt, B.Thavonekham, G.Fazal, S.Goulet, A.Jakalian, D.Wernic, Y.Tsantrizos, M.A.Poupart, M.Bos, G.Mckercher, L.Thauvette, G.Kukolj, P.L.Beaulieu. Discovery of A Novel Series of Non-Nucleoside Thumb Pocket 2 Hcv NS5B Polymerase Inhibitors. Bioorg.Med.Chem.Lett. V. 23 2585 2013.
ISSN: ISSN 0960-894X
PubMed: 23545108
DOI: 10.1016/J.BMCL.2013.02.110
Page generated: Mon Oct 7 16:07:54 2024

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