Zinc in PDB 3olb: Poliovirus Polymerase Elongation Complex with 2',3'-Dideoxy-Ctp

All present enzymatic activity of Poliovirus Polymerase Elongation Complex with 2',3'-Dideoxy-Ctp:
2.7.7.48;

The structure of Poliovirus Polymerase Elongation Complex with 2',3'-Dideoxy-Ctp, PDB code: 3olb 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)	45.23 / 2.41
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.528, 60.539, 192.936, 83.82, 83.84, 77.35
R / Rfree (%)	21.7 / 26.1

The binding sites of Zinc atom in the Poliovirus Polymerase Elongation Complex with 2',3'-Dideoxy-Ctp (pdb code 3olb). 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',3'-Dideoxy-Ctp, PDB code: 3olb:
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',3'-Dideoxy-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',3'-Dideoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.9 occ:0.42 NE2 A:HIS272 2.3 93.1 1.0 CE1 A:HIS272 2.5 95.8 1.0 SG A:CYS281 2.6 99.4 1.0 CB A:CYS281 2.6 69.3 1.0 CD2 A:HIS272 2.9 93.0 1.0 ND1 A:HIS272 3.1 90.1 1.0 NE2 A:HIS270 3.2 0.7 1.0 CG A:HIS272 3.4 88.5 1.0 CE1 A:HIS270 3.5 0.7 1.0 CA A:CYS281 3.7 64.1 1.0 CZ2 A:TRP5 3.8 92.4 1.0 CD2 A:HIS270 3.9 0.7 1.0 NE1 A:TRP5 4.1 82.0 1.0 O A:SER271 4.2 87.6 1.0 CE2 A:TRP5 4.2 88.6 1.0 ND1 A:HIS270 4.3 0.4 1.0 CG A:HIS270 4.5 0.9 1.0 C A:SER271 4.5 73.8 1.0 C A:CYS281 4.6 75.6 1.0 CB A:HIS272 4.6 76.9 1.0 N A:CYS281 4.7 62.6 1.0 CH2 A:TRP5 4.8 89.1 1.0 CA A:HIS272 4.8 77.6 1.0 N A:VAL282 4.8 59.5 1.0 N A:HIS272 4.8 53.5 1.0 O A:TYR280 4.9 73.9 1.0

Zinc binding site 2 out of 4 in the Poliovirus Polymerase Elongation Complex with 2',3'-Dideoxy-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',3'-Dideoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2002 b:0.7 occ:0.48 NE2 E:HIS272 2.4 91.2 1.0 SG E:CYS281 2.6 99.4 1.0 CB E:CYS281 2.6 68.4 1.0 CE1 E:HIS272 2.6 94.8 1.0 CD2 E:HIS272 3.0 91.7 1.0 NE2 E:HIS270 3.2 0.7 1.0 ND1 E:HIS272 3.3 90.3 1.0 O2 E:IPA6027 3.4 81.5 1.0 CG E:HIS272 3.5 85.8 1.0 CE1 E:HIS270 3.5 0.2 1.0 CA E:CYS281 3.6 67.3 1.0 CZ2 E:TRP5 3.7 92.9 1.0 CD2 E:HIS270 4.0 0.6 1.0 NE1 E:TRP5 4.0 81.7 1.0 CE2 E:TRP5 4.1 88.6 1.0 O E:SER271 4.3 88.7 1.0 ND1 E:HIS270 4.3 0.1 1.0 CG E:HIS270 4.6 0.4 1.0 C E:CYS281 4.6 75.8 1.0 N E:CYS281 4.7 64.0 1.0 C E:SER271 4.7 73.7 1.0 CB E:HIS272 4.7 78.2 1.0 CH2 E:TRP5 4.7 88.1 1.0 C2 E:IPA6027 4.7 88.5 1.0 N E:VAL282 4.8 55.6 1.0 CA E:HIS272 4.9 77.0 1.0 N E:HIS272 5.0 56.5 1.0 O E:TYR280 5.0 74.3 1.0

Zinc binding site 3 out of 4 in the Poliovirus Polymerase Elongation Complex with 2',3'-Dideoxy-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',3'-Dideoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2003 b:96.2 occ:0.52 NE2 I:HIS272 2.3 70.8 1.0 SG I:CYS281 2.4 72.0 1.0 O I:HOH675 2.7 57.2 1.0 CE1 I:HIS272 2.8 75.6 1.0 NE2 I:HIS270 2.9 1.0 1.0 CB I:CYS281 3.1 63.3 1.0 CD2 I:HIS272 3.3 73.0 1.0 CE1 I:HIS270 3.6 0.4 1.0 CD2 I:HIS270 3.7 0.4 1.0 ND1 I:HIS272 3.8 78.2 1.0 NE1 I:TRP5 3.9 71.8 1.0 CG I:HIS272 4.1 74.4 1.0 CZ2 I:TRP5 4.1 66.8 1.0 O I:HOH767 4.3 94.8 1.0 CE2 I:TRP5 4.3 73.2 1.0 CA I:CYS281 4.4 57.6 1.0 ND1 I:HIS270 4.5 1.0 1.0 CG I:HIS270 4.6 93.9 1.0

Zinc binding site 4 out of 4 in the Poliovirus Polymerase Elongation Complex with 2',3'-Dideoxy-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',3'-Dideoxy-Ctp within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn2004 b:93.8 occ:0.51 NE2 M:HIS272 2.4 69.5 1.0 SG M:CYS281 2.4 72.8 1.0 O M:HOH478 2.7 57.4 1.0 CE1 M:HIS272 2.9 73.2 1.0 NE2 M:HIS270 2.9 0.4 1.0 CB M:CYS281 3.2 63.8 1.0 CD2 M:HIS272 3.4 66.8 1.0 CE1 M:HIS270 3.6 0.6 1.0 CD2 M:HIS270 3.8 0.1 1.0 NE1 M:TRP5 3.9 71.5 1.0 ND1 M:HIS272 3.9 77.8 1.0 CZ2 M:TRP5 4.1 66.0 1.0 CG M:HIS272 4.2 72.5 1.0 CE2 M:TRP5 4.3 74.2 1.0 CA M:CYS281 4.5 58.8 1.0 ND1 M:HIS270 4.6 0.2 1.0 CG M:HIS270 4.7 93.4 1.0 CD1 M:TRP5 5.0 74.5 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