Zinc in PDB 3ol7: Poliovirus Polymerase Elongation Complex with Ctp

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

The structure of Poliovirus Polymerase Elongation Complex with Ctp, PDB code: 3ol7 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)	48.08 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.724, 60.769, 192.969, 83.01, 82.93, 77.12
R / Rfree (%)	22.6 / 29

The structure of Poliovirus Polymerase Elongation Complex with Ctp also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Poliovirus Polymerase Elongation Complex with Ctp (pdb code 3ol7). 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 Ctp, PDB code: 3ol7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Poliovirus Polymerase Elongation Complex with 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 Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.2 occ:0.41 NE2 A:HIS272 2.7 70.9 1.0 CE1 A:HIS272 3.3 80.4 1.0 SG A:CYS281 3.7 63.2 1.0 NE2 A:HIS270 3.7 74.0 1.0 CD2 A:HIS272 3.9 78.8 1.0 CZ2 A:TRP5 3.9 73.0 1.0 NE1 A:TRP5 4.0 64.6 1.0 CE1 A:HIS270 4.0 92.4 1.0 CE2 A:TRP5 4.3 73.5 1.0 CB A:CYS281 4.5 51.9 1.0 ND1 A:HIS272 4.6 80.0 1.0 CG A:HIS272 4.9 75.4 1.0 CD2 A:HIS270 4.9 98.4 1.0

Zinc binding site 2 out of 4 in the Poliovirus Polymerase Elongation Complex with 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 Ctp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2002 b:0.3 occ:0.42 NE1 E:TRP5 3.4 65.9 1.0 NE2 E:HIS272 3.4 69.9 1.0 SG E:CYS281 3.6 65.0 1.0 NE2 E:HIS270 3.8 73.5 1.0 CZ2 E:TRP5 4.0 69.0 1.0 CE2 E:TRP5 4.1 73.3 1.0 CE1 E:HIS270 4.1 92.6 1.0 CE1 E:HIS272 4.1 83.2 1.0 CB E:CYS281 4.5 50.6 1.0 CD2 E:HIS272 4.5 79.7 1.0 CD1 E:TRP5 4.6 64.8 1.0

Zinc binding site 3 out of 4 in the Poliovirus Polymerase Elongation Complex with 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 Ctp within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2003 b:78.5 occ:0.58 NE2 I:HIS270 2.4 0.6 1.0 NE2 I:HIS272 2.4 0.3 1.0 SG I:CYS281 2.4 68.8 1.0 CE1 I:HIS272 2.5 89.3 1.0 CB I:CYS281 2.8 52.8 1.0 O I:HOH504 2.9 52.4 1.0 CE1 I:HIS270 3.0 0.8 1.0 CD2 I:HIS272 3.3 91.8 1.0 ND1 I:HIS272 3.4 91.6 1.0 CD2 I:HIS270 3.4 0.7 1.0 CZ2 I:TRP5 3.6 90.7 1.0 NE1 I:TRP5 3.7 74.8 1.0 CG I:HIS272 3.8 86.8 1.0 CE2 I:TRP5 3.9 92.8 1.0 ND1 I:HIS270 4.0 0.3 1.0 CA I:CYS281 4.1 55.6 1.0 CG I:HIS270 4.3 0.6 1.0 CH2 I:TRP5 4.7 72.4 1.0 O I:SER271 4.7 69.0 1.0 C I:CYS281 4.9 67.5 1.0 CD1 I:TRP5 4.9 74.5 1.0 N I:VAL282 5.0 62.5 1.0

Zinc binding site 4 out of 4 in the Poliovirus Polymerase Elongation Complex with 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 Ctp within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn2004 b:76.6 occ:0.58 SG M:CYS281 2.3 67.1 1.0 NE2 M:HIS270 2.5 0.7 1.0 NE2 M:HIS272 2.5 0.1 1.0 O M:HOH523 2.6 59.4 1.0 CE1 M:HIS272 2.7 89.7 1.0 CB M:CYS281 2.7 52.1 1.0 CE1 M:HIS270 3.1 0.2 1.0 CD2 M:HIS272 3.4 91.7 1.0 CZ2 M:TRP5 3.5 87.5 1.0 CD2 M:HIS270 3.5 0.4 1.0 ND1 M:HIS272 3.5 89.9 1.0 NE1 M:TRP5 3.6 75.9 1.0 CE2 M:TRP5 3.8 90.4 1.0 CG M:HIS272 3.9 87.0 1.0 CA M:CYS281 4.0 53.5 1.0 ND1 M:HIS270 4.2 0.2 1.0 CG M:HIS270 4.4 100.0 1.0 CH2 M:TRP5 4.6 72.3 1.0 CD1 M:TRP5 4.7 72.7 1.0 O M:SER271 4.8 73.2 1.0 C M:CYS281 4.8 68.0 1.0 N M:VAL282 4.9 61.6 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