Manganese in PDB 1hi0: Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex

The structure of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex, PDB code: 1hi0 was solved by J.M.Grimes, S.J.Butcher, E.V.Makeyev, D.H.Bamford, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.0 / 3.0
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.650, 92.700, 140.790, 90.00, 101.09, 90.00
R / Rfree (%)	21.4 / 23.9

The structure of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Manganese atom in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex (pdb code 1hi0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex, PDB code: 1hi0:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn665 b:67.3 occ:1.00 OE1 P:GLU491 1.9 53.4 1.0 OD1 P:ASP454 1.9 61.1 1.0 O P:ALA495 2.2 41.4 1.0 CD P:GLU491 2.8 54.4 1.0 CG P:ASP454 3.1 60.4 1.0 OE2 P:GLU491 3.1 45.6 1.0 C P:ALA495 3.4 44.0 1.0 OD2 P:ASP454 3.7 72.6 1.0 O P:THR323 3.9 65.8 1.0 CG P:GLU491 4.2 43.6 1.0 N P:ALA495 4.2 44.4 1.0 CB P:ASP454 4.2 58.3 1.0 CA P:PHE496 4.2 38.6 1.0 N P:PHE496 4.3 41.9 1.0 CA P:ALA495 4.4 45.6 1.0 CB P:GLU491 4.5 45.1 1.0 CA P:ASP454 4.5 56.9 1.0 O P:ALA455 4.5 42.3 1.0 N P:ALA455 4.5 53.0 1.0 CB P:PHE496 4.9 32.3 1.0 CB P:ALA495 5.0 32.0 1.0 C P:ASP454 5.0 57.0 1.0

Manganese binding site 2 out of 3 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mn665 b:67.3 occ:1.00 OE1 Q:GLU491 1.9 53.4 1.0 OD1 Q:ASP454 1.9 61.1 1.0 O Q:ALA495 2.2 41.4 1.0 CD Q:GLU491 2.8 54.4 1.0 CG Q:ASP454 3.1 60.4 1.0 OE2 Q:GLU491 3.1 45.6 1.0 C Q:ALA495 3.4 44.0 1.0 OD2 Q:ASP454 3.7 72.6 1.0 O Q:THR323 3.9 65.8 1.0 CG Q:GLU491 4.2 43.6 1.0 N Q:ALA495 4.2 44.4 1.0 CB Q:ASP454 4.2 58.3 1.0 CA Q:PHE496 4.2 38.6 1.0 N Q:PHE496 4.3 41.9 1.0 CA Q:ALA495 4.4 45.6 1.0 CB Q:GLU491 4.5 45.1 1.0 CA Q:ASP454 4.5 56.9 1.0 O Q:ALA455 4.5 42.3 1.0 N Q:ALA455 4.5 53.0 1.0 CB Q:PHE496 4.9 32.3 1.0 CB Q:ALA495 5.0 32.0 1.0 C Q:ASP454 5.0 57.0 1.0

Manganese binding site 3 out of 3 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Mn665 b:67.3 occ:1.00 OE1 R:GLU491 1.9 53.4 1.0 OD1 R:ASP454 1.9 61.1 1.0 O R:ALA495 2.2 41.4 1.0 CD R:GLU491 2.8 54.4 1.0 CG R:ASP454 3.1 60.4 1.0 OE2 R:GLU491 3.1 45.6 1.0 C R:ALA495 3.4 44.0 1.0 OD2 R:ASP454 3.7 72.6 1.0 O R:THR323 3.9 65.8 1.0 CG R:GLU491 4.2 43.6 1.0 N R:ALA495 4.2 44.4 1.0 CB R:ASP454 4.2 58.3 1.0 CA R:PHE496 4.2 38.6 1.0 N R:PHE496 4.3 41.9 1.0 CA R:ALA495 4.4 45.6 1.0 CB R:GLU491 4.5 45.1 1.0 CA R:ASP454 4.5 56.9 1.0 O R:ALA455 4.5 42.3 1.0 N R:ALA455 4.5 53.0 1.0 CB R:PHE496 4.9 32.3 1.0 CB R:ALA495 5.0 32.0 1.0 C R:ASP454 5.0 57.0 1.0

S.J.Butcher, J.M.Grimes, E.V.Makeyev, D.H.Bamford, D.I.Stuart. A Mechanism For Initiating Rna-Dependent Rna Polymerization Nature V. 410 235 2001.
ISSN: ISSN 0028-0836
PubMed: 11242087
DOI: 10.1038/35065653