Zinc in PDB 3ola: Poliovirus Polymerase Elongation Complex with 2'-Deoxy-Ctp

All present enzymatic activity of Poliovirus Polymerase Elongation Complex with 2'-Deoxy-Ctp:
2.7.7.48;

The structure of Poliovirus Polymerase Elongation Complex with 2'-Deoxy-Ctp, PDB code: 3ola 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)	46.71 / 2.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.562, 60.560, 192.832, 83.57, 83.56, 77.59
R / Rfree (%)	22.6 / 28.4

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

Zinc binding site 1 out of 4 in the Poliovirus Polymerase Elongation Complex with 2'-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 2'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:80.1 occ:0.63 CE1 A:HIS272 2.2 95.0 1.0 SG A:CYS281 2.3 79.5 1.0 NE2 A:HIS270 2.3 97.9 1.0 CE1 A:HIS270 2.4 83.4 1.0 O2 A:GOL8002 2.5 0.8 1.0 NE2 A:HIS272 2.9 0.2 1.0 ND1 A:HIS272 3.0 87.7 1.0 CB A:CYS281 3.1 59.8 1.0 CD2 A:HIS270 3.5 91.7 1.0 O3 A:GOL8002 3.5 97.5 1.0 ND1 A:HIS270 3.6 89.3 1.0 C2 A:GOL8002 3.7 0.6 1.0 CD2 A:HIS272 3.9 94.8 1.0 CG A:HIS272 3.9 85.9 1.0 C3 A:GOL8002 4.1 0.9 1.0 NE1 A:TRP5 4.1 66.7 1.0 CG A:HIS270 4.1 90.2 1.0 CZ2 A:TRP5 4.2 87.1 1.0 CA A:CYS281 4.3 75.1 1.0 CE2 A:TRP5 4.4 85.2 1.0 C1 A:GOL8002 4.9 0.6 1.0 O1 A:GOL8002 4.9 98.0 1.0 O A:SER271 4.9 74.8 1.0 C A:CYS281 5.0 78.4 1.0

Zinc binding site 2 out of 4 in the Poliovirus Polymerase Elongation Complex with 2'-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 2'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2003 b:79.1 occ:0.57 SG E:CYS281 2.3 85.9 1.0 CE1 E:HIS272 2.3 94.2 1.0 NE2 E:HIS270 2.4 98.4 1.0 CE1 E:HIS270 2.5 83.3 1.0 NE2 E:HIS272 3.0 98.2 1.0 ND1 E:HIS272 3.0 87.8 1.0 CB E:CYS281 3.1 58.4 1.0 CD2 E:HIS270 3.6 93.8 1.0 ND1 E:HIS270 3.6 92.4 1.0 CD2 E:HIS272 3.9 93.9 1.0 CG E:HIS272 4.0 84.7 1.0 NE1 E:TRP5 4.0 68.9 1.0 CZ2 E:TRP5 4.2 85.2 1.0 CG E:HIS270 4.2 90.7 1.0 CA E:CYS281 4.3 73.0 1.0 CE2 E:TRP5 4.4 84.4 1.0 C E:CYS281 4.9 77.3 1.0 O E:SER271 5.0 76.3 1.0

Zinc binding site 3 out of 4 in the Poliovirus Polymerase Elongation Complex with 2'-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 2'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2002 b:70.1 occ:0.73 NE2 I:HIS270 2.3 86.5 1.0 SG I:CYS281 2.3 70.9 1.0 CE1 I:HIS272 2.3 90.7 1.0 NE2 I:HIS272 2.8 88.9 1.0 O3 I:GOL8001 3.0 63.5 1.0 CE1 I:HIS270 3.0 89.4 1.0 CB I:CYS281 3.2 51.5 1.0 CD2 I:HIS270 3.3 86.8 1.0 ND1 I:HIS272 3.4 83.5 1.0 C2 I:GOL8001 3.7 91.3 1.0 O1 I:GOL8001 3.9 88.5 1.0 C3 I:GOL8001 3.9 84.7 1.0 NE1 I:TRP5 3.9 66.8 1.0 CD2 I:HIS272 4.0 66.2 1.0 ND1 I:HIS270 4.1 78.7 1.0 CZ2 I:TRP5 4.2 75.3 1.0 C1 I:GOL8001 4.3 94.2 1.0 CG I:HIS270 4.3 76.0 1.0 CG I:HIS272 4.3 64.8 1.0 CE2 I:TRP5 4.3 81.7 1.0 CA I:CYS281 4.4 67.2 1.0 CE I:LYS283 4.8 91.8 1.0 O2 I:GOL8001 4.8 83.6 1.0 CD1 I:TRP5 5.0 63.6 1.0

Zinc binding site 4 out of 4 in the Poliovirus Polymerase Elongation Complex with 2'-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 2'-Deoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn2001 b:68.5 occ:0.69 SG M:CYS281 2.2 71.6 1.0 CE1 M:HIS272 2.3 91.5 1.0 NE2 M:HIS270 2.4 86.2 1.0 O M:HOH518 2.8 60.7 1.0 NE2 M:HIS272 2.8 87.6 1.0 CB M:CYS281 3.1 52.6 1.0 CE1 M:HIS270 3.2 89.4 1.0 CD2 M:HIS270 3.4 87.7 1.0 ND1 M:HIS272 3.4 84.5 1.0 NE1 M:TRP5 3.8 66.2 1.0 CD2 M:HIS272 4.0 66.9 1.0 CZ2 M:TRP5 4.1 71.7 1.0 O M:HOH522 4.2 67.5 1.0 CE2 M:TRP5 4.2 79.6 1.0 O M:HOH520 4.2 66.0 1.0 CG M:HIS272 4.3 66.1 1.0 ND1 M:HIS270 4.3 77.0 1.0 CA M:CYS281 4.3 65.6 1.0 CG M:HIS270 4.4 76.2 1.0 CE M:LYS283 4.8 89.5 1.0 CD1 M:TRP5 4.9 59.8 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