Zinc in PDB 3ol6: Poliovirus Polymerase Elongation Complex

All present enzymatic activity of Poliovirus Polymerase Elongation Complex:
2.7.7.48;

The structure of Poliovirus Polymerase Elongation Complex, PDB code: 3ol6 was solved by P.Gong, O.B.Peersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.62 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.395, 60.410, 191.430, 83.72, 83.69, 77.85
R / Rfree (%)	21.2 / 26.9

The binding sites of Zinc atom in the Poliovirus Polymerase Elongation Complex (pdb code 3ol6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Poliovirus Polymerase Elongation Complex, PDB code: 3ol6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Poliovirus Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Poliovirus Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.3 occ:0.52 O A:HOH766 2.4 67.7 1.0 NE2 A:HIS270 2.7 0.2 1.0 NE2 A:HIS272 2.8 88.4 1.0 SG A:CYS281 3.1 74.7 1.0 CE1 A:HIS270 3.1 0.8 1.0 CE1 A:HIS272 3.4 86.2 1.0 NE1 A:TRP5 3.7 78.8 1.0 CZ2 A:TRP5 3.7 88.4 1.0 CB A:CYS281 3.8 67.6 1.0 CD2 A:HIS272 3.9 74.6 1.0 CD2 A:HIS270 3.9 0.7 1.0 CE2 A:TRP5 4.1 83.8 1.0 ND1 A:HIS270 4.4 0.7 1.0 ND1 A:HIS272 4.6 81.8 1.0 CG A:HIS270 4.8 0.5 1.0 CG A:HIS272 4.9 79.7 1.0 CH2 A:TRP5 5.0 87.0 1.0 CD1 A:TRP5 5.0 75.2 1.0

Zinc binding site 2 out of 4 in the Poliovirus Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Poliovirus Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2002 b:0.4 occ:0.40 NE2 E:HIS272 2.5 88.3 1.0 SG E:CYS281 2.7 77.0 1.0 NE2 E:HIS270 2.7 0.1 1.0 CE1 E:HIS272 3.1 86.2 1.0 CE1 E:HIS270 3.2 0.5 1.0 CB E:CYS281 3.4 66.8 1.0 CD2 E:HIS272 3.5 75.8 1.0 CZ2 E:TRP5 3.6 87.5 1.0 NE1 E:TRP5 3.7 77.0 1.0 CD2 E:HIS270 3.8 0.2 1.0 CE2 E:TRP5 4.0 81.4 1.0 ND1 E:HIS272 4.2 81.2 1.0 ND1 E:HIS270 4.3 0.3 1.0 CG E:HIS272 4.4 77.6 1.0 CG E:HIS270 4.7 0.4 1.0 CH2 E:TRP5 4.7 86.7 1.0 CA E:CYS281 4.8 73.6 1.0 CD1 E:TRP5 5.0 75.1 1.0

Zinc binding site 3 out of 4 in the Poliovirus Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Poliovirus Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2003 b:0.2 occ:0.52 O I:HOH488 2.4 56.7 1.0 SG I:CYS281 2.4 76.4 1.0 NE2 I:HIS272 2.9 81.8 1.0 NE2 I:HIS270 3.0 0.4 1.0 O I:HOH537 3.1 57.6 1.0 CB I:CYS281 3.4 46.7 1.0 NE1 I:TRP5 3.4 75.5 1.0 CD2 I:HIS272 3.8 76.1 1.0 O I:HOH851 3.8 51.5 1.0 CD2 I:HIS270 3.8 0.5 1.0 CE1 I:HIS272 3.8 81.2 1.0 CZ2 I:TRP5 3.9 84.6 1.0 CE1 I:HIS270 3.9 0.2 1.0 CE2 I:TRP5 4.0 84.6 1.0 CD1 I:TRP5 4.6 77.9 1.0 CA I:CYS281 4.8 65.7 1.0 ND1 I:HIS272 4.9 86.2 1.0 CG I:HIS272 4.9 74.5 1.0

Zinc binding site 4 out of 4 in the Poliovirus Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Poliovirus Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn2004 b:0.5 occ:0.57 SG M:CYS281 2.6 73.5 1.0 NE2 M:HIS272 2.9 80.7 1.0 NE2 M:HIS270 3.0 0.4 1.0 NE1 M:TRP5 3.4 75.4 1.0 CB M:CYS281 3.5 47.6 1.0 CD2 M:HIS272 3.8 75.6 1.0 CE1 M:HIS272 3.8 78.7 1.0 CZ2 M:TRP5 3.9 81.3 1.0 CD2 M:HIS270 3.9 0.5 1.0 CE1 M:HIS270 3.9 0.2 1.0 CE2 M:TRP5 4.0 82.3 1.0 CD1 M:TRP5 4.6 76.6 1.0 ND1 M:HIS272 4.9 86.7 1.0 CG M:HIS272 4.9 76.3 1.0 CA M:CYS281 4.9 66.6 1.0

P.Gong, O.B.Peersen. Structural Basis For Active Site Closure By the Poliovirus Rna-Dependent Rna Polymerase. Proc.Natl.Acad.Sci.Usa V. 107 22505 2010.
ISSN: ISSN 0027-8424
PubMed: 21148772
DOI: 10.1073/PNAS.1007626107