Zinc in PDB 3ol8: Poliovirus Polymerase Elongation Complex with Ctp-Mn

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

The structure of Poliovirus Polymerase Elongation Complex with Ctp-Mn, PDB code: 3ol8 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)	44.16 / 2.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.779, 60.863, 193.078, 83.06, 83.04, 76.81
R / Rfree (%)	22.4 / 27.7

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

Manganese

(Mn)

8 atoms

The binding sites of Zinc atom in the Poliovirus Polymerase Elongation Complex with Ctp-Mn (pdb code 3ol8). 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-Mn, PDB code: 3ol8:
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-Mn


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-Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:81.3 occ:0.52 NE2 A:HIS272 2.2 77.0 1.0 NE2 A:HIS270 2.4 78.7 1.0 SG A:CYS281 2.4 71.9 1.0 CE1 A:HIS272 2.5 80.9 1.0 CE1 A:HIS270 2.6 85.5 1.0 O2 A:GOL8012 3.1 81.4 1.0 CD2 A:HIS272 3.2 75.8 1.0 CB A:CYS281 3.3 62.6 1.0 ND1 A:HIS272 3.4 75.2 1.0 CD2 A:HIS270 3.4 96.9 1.0 ND1 A:HIS270 3.6 89.7 1.0 CG A:HIS272 3.8 75.6 1.0 C1 A:GOL8012 3.8 98.6 1.0 CG A:HIS270 4.0 83.9 1.0 C2 A:GOL8012 4.1 94.2 1.0 O A:SER271 4.4 52.2 1.0 CA A:CYS281 4.4 61.0 1.0 NE1 A:TRP5 4.5 59.2 1.0 CZ2 A:TRP5 4.5 70.0 1.0 CE2 A:TRP5 4.8 66.6 1.0 C A:SER271 4.9 57.2 1.0 O A:HOH570 5.0 86.7 1.0

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


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-Mn within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2003 b:88.3 occ:0.57 SG E:CYS281 2.2 79.5 1.0 NE2 E:HIS272 2.3 80.3 1.0 NE2 E:HIS270 2.4 77.3 1.0 CE1 E:HIS272 2.6 84.3 1.0 O2 E:GOL8011 2.6 94.3 1.0 CE1 E:HIS270 2.7 81.1 1.0 CB E:CYS281 3.0 64.8 1.0 CD2 E:HIS272 3.2 73.6 1.0 CD2 E:HIS270 3.5 97.1 1.0 ND1 E:HIS272 3.5 73.9 1.0 ND1 E:HIS270 3.8 89.9 1.0 CG E:HIS272 3.9 70.7 1.0 C2 E:GOL8011 3.9 88.6 1.0 CG E:HIS270 4.2 85.6 1.0 CA E:CYS281 4.2 62.0 1.0 NE1 E:TRP5 4.3 56.8 1.0 CZ2 E:TRP5 4.3 70.9 1.0 O E:SER271 4.4 55.8 1.0 CE2 E:TRP5 4.6 66.1 1.0 O1 E:GOL8011 4.6 79.7 1.0 O E:HOH555 4.8 71.1 1.0 C3 E:GOL8011 4.8 82.2 1.0 C E:CYS281 4.8 55.1 1.0 C1 E:GOL8011 4.9 89.0 1.0 N E:VAL282 4.9 51.5 1.0 C E:SER271 5.0 56.7 1.0 CE E:LYS283 5.0 88.5 1.0

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


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-Mn within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2002 b:70.5 occ:0.59 NE2 I:HIS270 2.3 74.5 1.0 CE1 I:HIS270 2.4 94.1 1.0 SG I:CYS281 2.4 73.4 1.0 NE2 I:HIS272 2.5 78.8 1.0 CE1 I:HIS272 2.7 71.4 1.0 CB I:CYS281 2.9 70.8 1.0 CZ2 I:TRP5 3.4 73.2 1.0 CD2 I:HIS272 3.4 74.0 1.0 CD2 I:HIS270 3.5 87.0 1.0 ND1 I:HIS270 3.6 99.9 1.0 ND1 I:HIS272 3.6 80.1 1.0 NE1 I:TRP5 3.8 67.5 1.0 CE2 I:TRP5 3.9 74.4 1.0 CG I:HIS272 4.0 79.6 1.0 CG I:HIS270 4.1 90.0 1.0 CA I:CYS281 4.3 61.2 1.0 CH2 I:TRP5 4.5 63.8 1.0 CE I:LYS283 4.8 95.5 1.0

Zinc binding site 4 out of 4 in the Poliovirus Polymerase Elongation Complex with Ctp-Mn


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-Mn within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn2001 b:70.2 occ:0.60 SG M:CYS281 2.4 69.2 1.0 NE2 M:HIS272 2.5 81.1 1.0 NE2 M:HIS270 2.5 73.2 1.0 CE1 M:HIS270 2.6 91.1 1.0 CE1 M:HIS272 2.8 73.4 1.0 CB M:CYS281 2.9 70.2 1.0 CZ2 M:TRP5 3.2 74.0 1.0 CD2 M:HIS272 3.3 73.7 1.0 ND1 M:HIS272 3.6 75.3 1.0 NE1 M:TRP5 3.7 63.0 1.0 CE2 M:TRP5 3.7 71.9 1.0 CD2 M:HIS270 3.7 84.9 1.0 ND1 M:HIS270 3.8 98.2 1.0 CG M:HIS272 3.9 76.0 1.0 CA M:CYS281 4.2 60.4 1.0 CH2 M:TRP5 4.2 66.7 1.0 CG M:HIS270 4.4 89.5 1.0 CD1 M:TRP5 4.9 59.2 1.0 CE M:LYS283 5.0 94.1 1.0 CD2 M:TRP5 5.0 73.6 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