Zinc in PDB 3ol9: Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp

All present enzymatic activity of Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp:
2.7.7.48;

The structure of Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp, PDB code: 3ol9 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)	41.38 / 2.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.499, 60.555, 192.353, 83.69, 83.67, 77.45
R / Rfree (%)	20.3 / 24.9

The binding sites of Zinc atom in the Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp (pdb code 3ol9). 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 with 3'-Deoxy-Ctp, PDB code: 3ol9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp


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 with 3'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.9 occ:0.17 O2 A:IPA6032 2.3 73.6 1.0 CE1 A:HIS272 2.4 89.0 1.0 NE2 A:HIS272 2.4 0.2 1.0 NE2 A:HIS270 2.5 0.2 1.0 SG A:CYS281 2.5 96.8 1.0 CE1 A:HIS270 2.6 0.9 1.0 O A:HOH749 2.8 82.2 1.0 CB A:CYS281 3.4 80.1 1.0 C2 A:IPA6032 3.5 70.0 1.0 ND1 A:HIS272 3.5 81.8 1.0 CD2 A:HIS272 3.6 0.2 1.0 CD2 A:HIS270 3.7 0.8 1.0 ND1 A:HIS270 3.8 0.0 1.0 CZ2 A:TRP5 3.9 91.8 1.0 NE1 A:TRP5 4.0 80.9 1.0 C3 A:IPA6032 4.1 68.5 1.0 CG A:HIS272 4.1 88.8 1.0 CE2 A:TRP5 4.3 83.8 1.0 CG A:HIS270 4.3 0.8 1.0 C1 A:IPA6032 4.6 72.8 1.0 CA A:CYS281 4.8 71.4 1.0 CE A:LYS283 4.9 1.0 1.0

Zinc binding site 2 out of 4 in the Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp


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 with 3'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2002 b:0.1 occ:0.17 O2 E:IPA6030 2.3 72.4 1.0 SG E:CYS281 2.5 98.5 1.0 NE2 E:HIS270 2.5 0.7 1.0 CE1 E:HIS272 2.6 89.6 1.0 CE1 E:HIS270 2.6 0.0 1.0 NE2 E:HIS272 2.6 0.1 1.0 O E:HOH1082 2.8 86.0 1.0 CB E:CYS281 3.4 79.6 1.0 ND1 E:HIS272 3.7 80.8 1.0 C2 E:IPA6030 3.7 73.6 1.0 CD2 E:HIS272 3.7 0.3 1.0 CD2 E:HIS270 3.7 0.9 1.0 ND1 E:HIS270 3.8 0.3 1.0 NE1 E:TRP5 3.9 80.6 1.0 CZ2 E:TRP5 3.9 90.9 1.0 CE2 E:TRP5 4.2 83.6 1.0 CG E:HIS272 4.3 89.7 1.0 C3 E:IPA6030 4.3 74.1 1.0 CG E:HIS270 4.4 0.9 1.0 C1 E:IPA6030 4.7 77.3 1.0 CA E:CYS281 4.8 72.6 1.0 CE E:LYS283 4.8 0.5 1.0

Zinc binding site 3 out of 4 in the Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp


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 with 3'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2003 b:0.9 occ:0.40 O I:HOH560 2.3 65.0 1.0 SG I:CYS281 2.5 70.2 1.0 NE2 I:HIS272 2.7 87.6 1.0 NE2 I:HIS270 2.8 94.0 1.0 O I:HOH1112 3.3 69.1 1.0 O I:HOH1111 3.3 72.3 1.0 NE1 I:TRP5 3.4 77.0 1.0 CE1 I:HIS270 3.5 91.9 1.0 CE1 I:HIS272 3.5 86.6 1.0 CD2 I:HIS272 3.6 69.1 1.0 CB I:CYS281 3.6 60.0 1.0 CZ2 I:TRP5 3.8 76.1 1.0 CE2 I:TRP5 3.9 79.1 1.0 CD2 I:HIS270 4.0 92.3 1.0 ND1 I:HIS272 4.5 87.3 1.0 CD1 I:TRP5 4.6 75.9 1.0 CG I:HIS272 4.6 72.7 1.0 ND1 I:HIS270 4.7 89.7 1.0 CA I:CYS281 4.9 57.8 1.0 CG I:HIS270 4.9 81.1 1.0

Zinc binding site 4 out of 4 in the Poliovirus Polymerase Elongation Complex with 3'-Deoxy-Ctp


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 with 3'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn2004 b:0.2 occ:0.47 SG M:CYS281 2.4 72.9 1.0 NE2 M:HIS272 2.8 85.4 1.0 NE2 M:HIS270 2.9 93.5 1.0 NE1 M:TRP5 3.3 76.7 1.0 CB M:CYS281 3.5 62.4 1.0 CE1 M:HIS270 3.6 91.3 1.0 CE1 M:HIS272 3.6 87.2 1.0 CD2 M:HIS272 3.6 69.9 1.0 CZ2 M:TRP5 3.7 76.8 1.0 CE2 M:TRP5 3.8 79.5 1.0 CD2 M:HIS270 4.0 91.1 1.0 CD1 M:TRP5 4.5 77.0 1.0 ND1 M:HIS272 4.6 85.4 1.0 CG M:HIS272 4.7 72.1 1.0 ND1 M:HIS270 4.8 90.1 1.0 CA M:CYS281 4.9 57.5 1.0 CH2 M:TRP5 5.0 65.1 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