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Manganese in PDB 4j04: Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic 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 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid, PDB code: 4j04 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 (°) 105.970, 107.970, 133.500, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4j04:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid (pdb code 4j04). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid, PDB code: 4j04:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4j04

Go back to Manganese Binding Sites List in 4j04
Manganese binding site 1 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:37.2
occ:1.00
 N10 A:1JF602 2.2 31.9 1.0
O22 A:1JF602 2.3 33.4 1.0
OD1 A:ASP359 2.3 36.6 1.0
O A:HOH851 2.3 41.4 1.0
O A:HOH788 2.3 36.4 1.0
O A:HOH760 2.4 32.5 1.0
C11 A:1JF602 3.1 32.5 1.0
CG A:ASP359 3.1 35.8 1.0
OD2 A:ASP359 3.2 32.6 1.0
C20 A:1JF602 3.3 34.1 1.0
S7 A:1JF602 3.5 33.9 1.0
C12 A:1JF602 3.5 33.9 1.0
O9 A:1JF602 3.5 35.8 1.0
C16 A:1JF602 4.2 30.8 1.0
O8 A:1JF602 4.2 33.3 1.0
O21 A:1JF602 4.4 35.7 1.0
CL1 A:1JF602 4.5 38.8 1.0
CB A:ASP359 4.5 33.3 1.0
OE2 A:GLU361 4.8 38.0 1.0
C13 A:1JF602 4.8 32.5 1.0
C1 A:1JF602 4.8 35.2 1.0

Manganese binding site 2 out of 4 in 4j04

Go back to Manganese Binding Sites List in 4j04
Manganese binding site 2 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:51.8
occ:1.00
 OD1 A:ASP318 2.3 32.3 1.0
OD2 A:ASP319 2.4 37.9 1.0
O A:HOH879 2.5 38.7 1.0
O A:HOH906 2.6 44.5 1.0
CG A:ASP319 3.2 34.4 1.0
CG A:ASP318 3.4 33.4 1.0
OD1 A:ASP319 3.5 33.8 1.0
OD2 A:ASP318 3.8 37.7 1.0
O A:HOH1023 4.3 45.3 1.0
O A:ASN316 4.4 24.7 1.0
N A:ASP319 4.4 27.3 1.0
CB A:ASP319 4.5 30.2 1.0
N A:ASP318 4.5 25.7 1.0
O A:HOH780 4.5 30.2 1.0
CB A:ASP318 4.7 29.1 1.0
C A:ASP318 4.9 27.8 1.0
CA A:ASP318 4.9 27.5 1.0
SG A:CYS366 5.0 45.0 1.0

Manganese binding site 3 out of 4 in 4j04

Go back to Manganese Binding Sites List in 4j04
Manganese binding site 3 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:55.0
occ:1.00
 O22 B:1JF601 2.2 41.7 1.0
O B:HOH974 2.2 46.6 1.0
N10 B:1JF601 2.3 48.2 1.0
OD2 B:ASP359 2.3 50.1 1.0
O B:HOH975 2.4 50.3 1.0
O B:HOH824 2.5 44.0 1.0
CG B:ASP359 3.1 47.2 1.0
OD1 B:ASP359 3.1 47.0 1.0
C11 B:1JF601 3.1 45.1 1.0
C20 B:1JF601 3.3 43.8 1.0
S7 B:1JF601 3.5 51.8 1.0
C12 B:1JF601 3.5 43.5 1.0
O9 B:1JF601 3.5 51.1 1.0
O8 B:1JF601 4.2 51.9 1.0
C16 B:1JF601 4.2 45.5 1.0
O21 B:1JF601 4.3 43.6 1.0
CB B:ASP359 4.5 46.2 1.0
CL1 B:1JF601 4.6 59.9 1.0
C13 B:1JF601 4.8 43.5 1.0
C1 B:1JF601 4.9 54.1 1.0
OE1 B:GLU361 5.0 50.0 1.0

Manganese binding site 4 out of 4 in 4j04

Go back to Manganese Binding Sites List in 4j04
Manganese binding site 4 out of 4 in the Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Hcv NS5B Polymerase in Complex with 4-Chloro-2- {[(2,4,5-Trichlorophenyl)Sulfonyl]Amino}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:54.8
occ:1.00
 OD1 B:ASP318 2.3 36.5 1.0
O B:HOH976 2.4 42.5 1.0
OD2 B:ASP319 2.5 43.5 1.0
O B:HOH725 2.5 41.2 1.0
CG B:ASP319 3.2 40.1 1.0
CG B:ASP318 3.3 34.9 1.0
OD1 B:ASP319 3.4 42.3 1.0
OD2 B:ASP318 3.7 37.1 1.0
N B:ASP319 4.3 33.1 1.0
O B:ASN316 4.4 26.5 1.0
N B:ASP318 4.4 29.1 1.0
CB B:ASP319 4.5 36.6 1.0
CB B:ASP318 4.6 30.4 1.0
O B:HOH814 4.7 37.9 1.0
C B:ASP318 4.9 31.8 1.0
CA B:ASP318 4.9 31.1 1.0
CA B:ASP319 5.0 34.1 1.0
SG B:CYS366 5.0 50.5 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: Sat Oct 5 19:56:23 2024

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