Zinc in PDB 3auo: Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp

All present enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp:
2.7.7.7;

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp, PDB code: 3auo was solved by S.Nakane, N.Nakagawa, R.Masui, S.Kuramitsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.445, 96.941, 143.428, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 29.3

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp (pdb code 3auo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp, PDB code: 3auo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn579 b:70.2 occ:1.00 OE2 A:GLU413 2.2 31.3 1.0 NE2 A:HIS468 2.3 19.4 1.0 OE1 A:GLU413 2.9 31.5 1.0 CD A:GLU413 2.9 31.0 1.0 NE2 A:HIS440 2.9 23.3 1.0 CE1 A:HIS468 3.2 19.4 1.0 CD2 A:HIS468 3.2 19.4 1.0 CE1 A:HIS440 3.6 24.2 1.0 OE1 A:GLN342 3.9 29.8 1.0 OD2 A:ASP529 3.9 20.9 1.0 CD2 A:HIS440 4.0 23.1 1.0 NH2 A:ARG506 4.1 17.9 1.0 CZ A:ARG506 4.3 17.6 1.0 ND1 A:HIS468 4.3 18.9 1.0 CE1 A:HIS374 4.3 53.2 1.0 CG A:GLU413 4.3 30.3 1.0 CG A:HIS468 4.3 19.4 1.0 OG A:SER438 4.4 23.8 1.0 NE A:ARG506 4.5 18.3 1.0 NE2 A:HIS374 4.6 53.1 1.0 OD1 A:ASP529 4.6 22.5 1.0 CG A:ASP529 4.7 21.7 1.0 NH1 A:ARG506 4.8 17.5 1.0 ND1 A:HIS440 4.8 23.6 1.0 O A:HOH597 4.9 7.0 1.0 CD A:GLN342 4.9 29.5 1.0 O A:HOH617 4.9 23.7 1.0

Zinc binding site 2 out of 2 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn579 b:56.9 occ:1.00 OE2 B:GLU413 2.0 23.9 1.0 NE2 B:HIS468 2.1 18.3 1.0 NE2 B:HIS440 2.2 19.2 1.0 O B:HOH580 2.3 5.5 1.0 CE1 B:HIS440 2.9 19.8 1.0 CD2 B:HIS468 3.0 18.0 1.0 CD B:GLU413 3.0 23.3 1.0 CE1 B:HIS468 3.1 17.8 1.0 OE1 B:GLU413 3.3 23.5 1.0 CD2 B:HIS440 3.4 19.1 1.0 OG B:SER438 3.8 17.1 1.0 NH2 B:ARG506 4.1 17.8 1.0 ND1 B:HIS440 4.2 19.2 1.0 CG B:HIS468 4.2 17.1 1.0 ND1 B:HIS468 4.2 17.4 1.0 O B:HOH607 4.2 20.0 1.0 OD2 B:ASP529 4.3 24.8 1.0 OE1 B:GLN342 4.3 24.0 1.0 CG B:GLU413 4.3 23.0 1.0 CZ B:ARG506 4.4 18.3 1.0 CG B:HIS440 4.4 19.2 1.0 CB B:SER438 4.7 17.3 1.0 NE B:ARG506 4.7 18.3 1.0 NH1 B:ARG506 4.8 18.2 1.0

S.Nakane, H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. The Structural Basis of the Kinetic Mechanism of A Gap-Filling X-Family Dna Polymerase That Binds Mg(2+)-Dntp Before Binding to Dna. J.Mol.Biol. V. 417 179 2012.
ISSN: ISSN 0022-2836
PubMed: 22306405
DOI: 10.1016/J.JMB.2012.01.025