Manganese in PDB 1nb7: Hc-J4 Rna Polymerase Complexed with Short Rna Template Strand

All present enzymatic activity of Hc-J4 Rna Polymerase Complexed with Short Rna Template Strand:
2.7.7.48;

The structure of Hc-J4 Rna Polymerase Complexed with Short Rna Template Strand, PDB code: 1nb7 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)	22.00 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.660, 108.500, 134.950, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 29.5

The binding sites of Manganese atom in the Hc-J4 Rna Polymerase Complexed with Short Rna Template Strand (pdb code 1nb7). 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 Short Rna Template Strand, PDB code: 1nb7:
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 Short Rna Template Strand


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 Short Rna Template Strand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:1.0 occ:1.00 OD1 B:ASP319 3.1 42.8 1.0 OD1 B:ASP220 3.2 65.3 1.0 OD1 B:ASP318 3.2 22.9 1.0 CG B:ASP319 3.3 42.8 1.0 OD2 B:ASP319 3.4 42.8 1.0 N B:ASP319 3.6 6.6 1.0 CG B:ASP318 3.7 22.9 1.0 CA B:ASP319 3.8 6.6 1.0 C B:ASP318 3.9 20.8 1.0 CB B:ASP319 4.1 42.8 1.0 O B:ASP318 4.1 20.8 1.0 CB B:ASP318 4.2 22.9 1.0 CG B:ASP220 4.2 65.3 1.0 MN B:MN1002 4.3 1.0 1.0 OD2 B:ASP318 4.3 22.9 1.0 CA B:ASP318 4.6 20.8 1.0 OD2 B:ASP220 5.0 65.3 1.0

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


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 Short Rna Template Strand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:1.0 occ:1.00 O B:THR221 2.5 6.9 1.0 OD2 B:ASP318 3.4 22.9 1.0 C B:THR221 3.5 6.9 1.0 CB B:PHE224 3.6 18.0 1.0 OD2 B:ASP220 3.8 65.3 1.0 CA B:ARG222 3.9 40.2 1.0 CG B:ASP318 3.9 22.9 1.0 OG1 B:THR221 4.0 14.5 1.0 N B:PHE224 4.0 14.4 1.0 CB B:ASP318 4.1 22.9 1.0 N B:CYS223 4.1 19.6 1.0 OD1 B:ASP220 4.1 65.3 1.0 N B:ARG222 4.2 40.2 1.0 CG B:ASP220 4.2 65.3 1.0 C B:ARG222 4.2 40.2 1.0 MN B:MN1001 4.3 1.0 1.0 CA B:PHE224 4.4 14.4 1.0 N B:THR221 4.4 6.9 1.0 CA B:THR221 4.6 6.9 1.0 CG B:PHE224 4.6 18.0 1.0 CD2 B:PHE224 4.6 18.0 1.0 OD1 B:ASP318 4.7 22.9 1.0 CB B:THR221 4.9 14.5 1.0 C B:ASP220 4.9 1.8 1.0

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


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 Short Rna Template Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2001 b:1.0 occ:1.00 OD2 A:ASP319 3.9 30.7 1.0 OD2 A:ASP318 4.3 20.5 1.0 OD1 A:ASP220 4.4 56.0 1.0 CG A:ASP319 4.9 30.7 1.0

Manganese binding site 4 out of 4 in the Hc-J4 Rna Polymerase Complexed with Short Rna Template Strand


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 Short Rna Template Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2002 b:1.0 occ:1.00 N A:CYS223 2.9 2.4 1.0 N A:PHE224 3.0 12.1 1.0 CA A:CYS223 3.0 2.4 1.0 O A:THR221 3.5 1.0 1.0 C A:CYS223 3.5 2.4 1.0 C A:ARG222 3.8 11.0 1.0 CA A:PHE224 4.2 12.1 1.0 CB A:PHE224 4.3 7.0 1.0 CA A:ARG222 4.4 11.0 1.0 CB A:CYS223 4.5 17.7 1.0 C A:THR221 4.5 1.0 1.0 O A:ARG222 4.6 11.0 1.0 O A:CYS223 4.8 2.4 1.0 OD2 A:ASP220 4.9 56.0 1.0 N A:ARG222 4.9 11.0 1.0 OD2 A:ASP318 5.0 20.5 1.0 SG A:CYS223 5.0 17.7 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