Manganese in PDB 4ry5: C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase

All present enzymatic activity of C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase:
2.7.7.48;

The structure of C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase, PDB code: 4ry5 was solved by J.Jaeger, A.Cherry, C.Dennis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.490, 107.946, 133.250, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 24.8

The binding sites of Manganese atom in the C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase (pdb code 4ry5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase, PDB code: 4ry5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:30.0 occ:0.85 O1B A:UTP1003 2.2 35.5 0.5 OD1 A:ASP319 2.3 48.7 1.0 O2B A:UTP1003 2.5 40.5 0.5 OD1 A:ASP220 2.6 40.0 1.0 O1G A:UTP1003 2.7 36.6 0.5 CG A:ASP319 2.9 49.6 1.0 OD2 A:ASP318 2.9 47.0 1.0 OD2 A:ASP319 3.2 58.5 1.0 PB A:UTP1003 3.3 41.7 0.5 CG A:ASP318 3.7 47.0 1.0 O2B A:UTP1003 3.7 48.6 0.5 PG A:UTP1003 3.7 36.7 0.5 O3B A:UTP1003 3.7 21.7 0.5 CG A:ASP220 3.8 48.0 1.0 PB A:UTP1003 3.9 45.2 0.5 CB A:ASP318 4.0 43.8 1.0 MN A:MN1002 4.0 31.4 0.8 CB A:ASP319 4.1 39.4 1.0 N A:ASP319 4.1 24.9 1.0 O3A A:UTP1003 4.1 53.4 0.5 O2G A:UTP1003 4.2 26.9 0.5 CA A:ASP319 4.3 31.2 1.0 C A:ASP318 4.4 32.5 1.0 OD2 A:ASP220 4.5 49.5 1.0 O3A A:UTP1003 4.6 47.3 0.5 OD1 A:ASP318 4.6 58.6 1.0 CA A:ASP318 4.7 38.5 1.0 O1B A:UTP1003 4.7 48.0 0.5 O A:ASP318 4.9 40.7 1.0 CB A:ASP220 4.9 45.4 1.0 O3B A:UTP1003 4.9 70.1 0.5

Manganese binding site 2 out of 4 in the C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:31.4 occ:0.84 OD2 A:ASP318 2.1 47.0 1.0 O A:THR221 2.2 38.5 1.0 O3B A:UTP1003 2.3 70.1 0.5 O2B A:UTP1003 2.5 40.5 0.5 O1A A:UTP1003 2.6 54.8 0.5 O1B A:UTP1003 2.7 35.5 0.5 OD2 A:ASP220 2.8 49.5 1.0 PB A:UTP1003 2.8 45.2 0.5 OD1 A:ASP220 3.1 40.0 1.0 PA A:UTP1003 3.1 59.4 0.5 CG A:ASP318 3.1 47.0 1.0 O3A A:UTP1003 3.2 53.4 0.5 CG A:ASP220 3.2 48.0 1.0 C A:THR221 3.3 27.9 1.0 O2A A:UTP1003 3.5 61.1 0.5 O2A A:UTP1003 3.5 61.6 0.5 OD1 A:ASP318 3.6 58.6 1.0 N A:THR221 3.6 28.1 1.0 O1A A:UTP1003 3.6 56.5 0.5 O3A A:UTP1003 3.7 47.3 0.5 PA A:UTP1003 3.7 63.5 0.5 PG A:UTP1003 3.8 51.8 0.5 PB A:UTP1003 3.8 41.7 0.5 O3G A:UTP1003 3.9 38.6 0.5 CA A:THR221 4.0 28.6 1.0 MN A:MN1001 4.0 30.0 0.8 N A:CYS223 4.3 37.9 1.0 O1B A:UTP1003 4.3 48.0 0.5 N A:ARG222 4.3 19.5 1.0 CB A:ASP318 4.3 43.8 1.0 C A:ASP220 4.4 29.3 1.0 N A:PHE224 4.4 31.1 1.0 O2G A:UTP1003 4.5 46.5 0.5 CB A:ASP220 4.6 45.4 1.0 CB A:THR221 4.6 34.2 1.0 O5' A:UTP1003 4.7 75.6 0.5 CA A:ARG222 4.7 24.2 1.0 CB A:PHE224 4.7 26.4 1.0 O1G A:UTP1003 4.8 52.7 0.5 C A:ARG222 4.8 32.6 1.0 CA A:ASP220 4.8 35.3 1.0 O3B A:UTP1003 4.9 21.7 0.5 CA A:CYS223 5.0 37.8 1.0 O2B A:UTP1003 5.0 48.6 0.5

Manganese binding site 3 out of 4 in the C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:25.9 occ:0.89 OD1 B:ASP319 2.2 48.4 1.0 O1B B:UTP1003 2.3 49.5 0.5 O2B B:UTP1003 2.3 50.9 0.6 OD1 B:ASP220 2.3 47.4 1.0 O B:HOH1188 2.6 24.4 1.0 O1G B:UTP1003 2.6 34.0 0.5 OD1 B:ASP318 2.7 33.9 1.0 OD2 B:ASP318 2.8 19.3 1.0 CG B:ASP319 2.9 40.4 1.0 OD2 B:ASP319 3.0 44.8 1.0 CG B:ASP318 3.1 23.6 1.0 O1A B:UTP1003 3.2 65.8 0.6 CG B:ASP220 3.5 47.8 1.0 PB B:UTP1003 3.5 45.7 0.5 PB B:UTP1003 3.7 48.7 0.6 MN B:MN1002 3.7 21.3 0.8 O3A B:UTP1003 3.7 67.7 0.5 PG B:UTP1003 3.9 37.7 0.5 OD2 B:ASP220 4.0 52.5 1.0 O3B B:UTP1003 4.1 63.3 0.5 O3B B:UTP1003 4.2 32.8 0.6 CB B:ASP319 4.2 19.9 1.0 N B:ASP319 4.2 9.2 1.0 CA B:ASP319 4.4 16.1 1.0 C B:ASP318 4.4 27.8 1.0 PA B:UTP1003 4.5 62.7 0.6 O3A B:UTP1003 4.5 51.3 0.6 CB B:ASP318 4.6 24.4 1.0 CB B:ASP220 4.7 35.2 1.0 O3G B:UTP1003 4.7 24.4 0.5 O B:ASP318 4.7 25.6 1.0 O2B B:UTP1003 4.8 49.1 0.5 O1B B:UTP1003 4.8 50.9 0.6

Manganese binding site 4 out of 4 in the C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of C-Terminal Mutant (W550N) of Hcv/J4 Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:21.3 occ:0.83 O B:THR221 2.2 30.1 1.0 OD2 B:ASP220 2.3 52.5 1.0 O3B B:UTP1003 2.5 32.8 0.6 O1A B:UTP1003 2.5 65.8 0.6 O3A B:UTP1003 2.8 67.7 0.5 OD2 B:ASP318 2.9 19.3 1.0 O1A B:UTP1003 2.9 47.0 0.5 CG B:ASP220 3.1 47.8 1.0 O2G B:UTP1003 3.2 24.5 0.6 PA B:UTP1003 3.2 49.3 0.5 OD1 B:ASP220 3.3 47.4 1.0 PA B:UTP1003 3.3 62.7 0.6 O2B B:UTP1003 3.4 50.9 0.6 C B:THR221 3.4 27.4 1.0 PB B:UTP1003 3.4 48.7 0.6 O1B B:UTP1003 3.4 49.5 0.5 O2A B:UTP1003 3.5 49.3 0.6 PG B:UTP1003 3.5 43.5 0.6 PB B:UTP1003 3.6 45.7 0.5 O2A B:UTP1003 3.6 44.6 0.5 O3A B:UTP1003 3.7 51.3 0.6 MN B:MN1001 3.7 25.9 0.9 CG B:ASP318 3.9 23.6 1.0 N B:THR221 4.0 19.2 1.0 CA B:ARG222 4.1 29.6 1.0 O2B B:UTP1003 4.2 49.1 0.5 N B:ARG222 4.2 27.0 1.0 N B:CYS223 4.2 20.2 1.0 O3G B:UTP1003 4.3 44.6 0.6 CA B:THR221 4.4 22.7 1.0 OD1 B:ASP318 4.4 33.9 1.0 N B:PHE224 4.5 19.2 1.0 CB B:ASP220 4.5 35.2 1.0 C B:ASP220 4.5 13.5 1.0 C B:ARG222 4.6 26.8 1.0 O1G B:UTP1003 4.7 47.2 0.6 O5' B:UTP1003 4.7 53.9 0.5 CB B:PHE224 4.8 8.8 1.0 O5' B:UTP1003 4.8 75.0 0.6 OG1 B:THR221 4.8 38.9 1.0 O1B B:UTP1003 4.8 50.9 0.6 CA B:ASP220 4.9 19.4 1.0 O B:HOH1188 5.0 24.4 1.0

A.L.Cherry, C.A.Dennis, A.Baron, L.E.Eisele, P.A.Thommes, J.Jaeger. Hydrophobic and Charged Residues in the C-Terminal Arm of Hepatitis C Virus Rna-Dependent Rna Polymerase Regulate Initiation and Elongation. J.Virol. V. 89 2052 2015.
ISSN: ISSN 0022-538X
PubMed: 25428878
DOI: 10.1128/JVI.01106-14