Manganese in PDB 1nb6: Hc-J4 Rna Polymerase Complexed with Utp

All present enzymatic activity of Hc-J4 Rna Polymerase Complexed with Utp:
2.7.7.48;

The structure of Hc-J4 Rna Polymerase Complexed with Utp, PDB code: 1nb6 was solved by D.J.O'farrell, R.Trowbridge, D.J.Rowlands, J.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.430, 107.740, 133.200, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 24.9

The binding sites of Manganese atom in the Hc-J4 Rna Polymerase Complexed with Utp (pdb code 1nb6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Hc-J4 Rna Polymerase Complexed with Utp, PDB code: 1nb6:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Hc-J4 Rna Polymerase Complexed with Utp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hc-J4 Rna Polymerase Complexed with Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:24.6 occ:1.00 O A:HOH1961 2.5 46.7 1.0 OD2 A:ASP319 2.6 37.4 1.0 OD1 A:ASP220 2.8 54.0 1.0 OD2 A:ASP318 2.8 48.7 1.0 OD1 A:ASP319 3.0 44.4 1.0 CG A:ASP319 3.1 41.2 1.0 O1A A:UTP1700 3.1 70.8 1.0 O2A A:UTP1700 3.2 70.7 1.0 OD1 A:ASP318 3.2 61.1 1.0 PA A:UTP1700 3.3 70.1 1.0 CG A:ASP318 3.4 56.2 1.0 C5' A:UTP1700 3.5 70.8 1.0 O5' A:UTP1700 3.9 70.7 1.0 CG A:ASP220 3.9 64.0 1.0 O A:HOH1947 3.9 38.7 1.0 MN A:MN1002 4.4 26.5 1.0 CB A:ASP319 4.4 29.6 1.0 OD2 A:ASP220 4.4 67.9 1.0 N A:ASP319 4.5 28.1 1.0 CA A:ASP319 4.6 27.8 1.0 C A:ASP318 4.7 34.9 1.0 C4' A:UTP1700 4.7 66.6 1.0 CB A:ASP318 4.8 42.7 1.0 O3A A:UTP1700 4.8 67.0 1.0 O A:ASP318 4.9 31.7 1.0

Manganese binding site 2 out of 4 in the Hc-J4 Rna Polymerase Complexed with Utp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hc-J4 Rna Polymerase Complexed with Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:26.5 occ:1.00 O1A A:UTP1700 2.0 70.8 1.0 O1B A:UTP1700 2.2 62.5 1.0 O A:THR221 2.5 31.3 1.0 OD2 A:ASP220 2.6 67.9 1.0 OD2 A:ASP318 2.6 48.7 1.0 CG A:ASP220 3.3 64.0 1.0 OD1 A:ASP220 3.3 54.0 1.0 PA A:UTP1700 3.4 70.1 1.0 C4' A:UTP1700 3.5 66.6 1.0 PB A:UTP1700 3.6 70.5 1.0 CG A:ASP318 3.6 56.2 1.0 C A:THR221 3.6 31.7 1.0 O5' A:UTP1700 3.6 70.7 1.0 C5' A:UTP1700 3.7 70.8 1.0 N A:PHE224 3.8 17.6 1.0 OG1 A:THR221 3.9 44.6 1.0 O3' A:UTP1700 3.9 62.4 1.0 O3A A:UTP1700 4.0 67.0 1.0 N A:THR221 4.0 34.6 1.0 CB A:PHE224 4.0 14.4 1.0 N A:CYS223 4.1 34.9 1.0 CA A:THR221 4.3 33.3 1.0 CB A:ASP318 4.3 42.7 1.0 C3' A:UTP1700 4.3 60.1 1.0 OD1 A:ASP318 4.4 61.1 1.0 MN A:MN1001 4.4 24.6 1.0 O2B A:UTP1700 4.5 70.6 1.0 O3B A:UTP1700 4.5 70.4 1.0 CA A:CYS223 4.5 32.9 1.0 CA A:PHE224 4.5 16.1 1.0 O4' A:UTP1700 4.5 64.7 1.0 O A:HOH1966 4.6 54.6 1.0 C A:ASP220 4.6 39.2 1.0 N A:ARG222 4.6 38.2 1.0 CB A:ASP220 4.6 50.4 1.0 C A:CYS223 4.7 25.2 1.0 O2A A:UTP1700 4.7 70.7 1.0 C A:ARG222 4.7 41.1 1.0 CB A:THR221 4.8 31.4 1.0 CA A:ARG222 4.9 41.3 1.0 CA A:ASP220 5.0 42.5 1.0

Manganese binding site 3 out of 4 in the Hc-J4 Rna Polymerase Complexed with Utp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hc-J4 Rna Polymerase Complexed with Utp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:22.4 occ:1.00 OD2 B:ASP319 2.3 44.9 1.0 OD1 B:ASP220 2.5 42.8 1.0 O1A B:UTP2700 2.5 61.6 1.0 OD2 B:ASP318 2.6 33.6 1.0 O B:HOH2976 2.6 45.5 1.0 OD1 B:ASP318 2.9 28.3 1.0 CG B:ASP318 3.1 36.6 1.0 CG B:ASP319 3.3 44.8 1.0 MN B:MN2002 3.4 31.2 1.0 PA B:UTP2700 3.4 68.1 1.0 CG B:ASP220 3.5 50.1 1.0 OD2 B:ASP220 3.7 55.5 1.0 OD1 B:ASP319 3.9 50.5 1.0 O5' B:UTP2700 4.2 62.3 1.0 N B:ASP319 4.2 23.1 1.0 O2A B:UTP2700 4.2 58.1 1.0 C5' B:UTP2700 4.3 65.7 1.0 CA B:ASP319 4.4 23.8 1.0 CB B:ASP319 4.4 35.7 1.0 C B:ASP318 4.5 19.5 1.0 CB B:ASP318 4.5 25.9 1.0 O3A B:UTP2700 4.8 64.8 1.0 O B:ASP318 4.8 21.7 1.0 CB B:ASP220 4.8 36.0 1.0 O B:HOH2845 4.9 12.4 1.0

Manganese binding site 4 out of 4 in the Hc-J4 Rna Polymerase Complexed with Utp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hc-J4 Rna Polymerase Complexed with Utp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:31.2 occ:1.00 OD2 B:ASP318 2.4 33.6 1.0 O B:THR221 2.5 24.4 1.0 OD2 B:ASP220 2.5 55.5 1.0 O1A B:UTP2700 2.7 61.6 1.0 O1B B:UTP2700 3.3 63.7 1.0 CG B:ASP220 3.4 50.1 1.0 MN B:MN2001 3.4 22.4 1.0 O2B B:UTP2700 3.5 52.7 1.0 CG B:ASP318 3.5 36.6 1.0 OD1 B:ASP220 3.6 42.8 1.0 C B:THR221 3.6 26.1 1.0 PA B:UTP2700 3.8 68.1 1.0 PB B:UTP2700 3.8 70.8 1.0 O5' B:UTP2700 4.0 62.3 1.0 O3A B:UTP2700 4.0 64.8 1.0 OD1 B:ASP318 4.1 28.3 1.0 CB B:PHE224 4.2 25.6 1.0 N B:THR221 4.3 23.2 1.0 N B:PHE224 4.3 30.8 1.0 N B:CYS223 4.4 39.3 1.0 CA B:ARG222 4.4 40.7 1.0 CB B:ASP318 4.5 25.9 1.0 N B:ARG222 4.5 31.3 1.0 CA B:THR221 4.6 25.1 1.0 C B:ARG222 4.6 40.5 1.0 CB B:ASP220 4.7 36.0 1.0 C B:ASP220 4.7 25.6 1.0 C5' B:UTP2700 4.7 65.7 1.0 O B:HOH3018 4.8 59.4 1.0 CA B:PHE224 4.9 26.2 1.0

D.O'farrell, R.Trowbridge, D.Rowlands, J.Jager. Substrate Complexes of Hepatitis C Virus Rna Polymerase (Hc-J4): Structural Evidence For Nucleotide Import and De-Novo Initiation. J.Mol.Biol. V. 326 1025 2003.
ISSN: ISSN 0022-2836
PubMed: 12589751
DOI: 10.1016/S0022-2836(02)01439-0