Zinc in PDB 3au2: Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp

All present enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp:
2.7.7.7;

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp, PDB code: 3au2 was solved by S.Nakane, H.Ishikawa, T.Wakamatsu, 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 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.189, 53.286, 84.877, 90.00, 107.52, 90.00
R / Rfree (%)	16.2 / 18.8

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp (pdb code 3au2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp, PDB code: 3au2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp


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 Complexed with Ca-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn577 b:22.8 occ:0.40 OD2 A:ASP349 1.8 30.2 1.0 NE2 A:HIS374 1.9 25.1 1.0 NE2 A:HIS531 2.3 19.0 1.0 CG A:ASP349 2.7 26.3 1.0 OD1 A:ASP349 2.9 27.5 1.0 CD2 A:HIS374 2.9 22.7 1.0 CE1 A:HIS374 2.9 27.2 1.0 O A:HOH1168 3.0 39.9 1.0 CE1 A:HIS531 3.2 19.6 1.0 CD2 A:HIS531 3.3 20.0 1.0 ND1 A:HIS374 4.0 25.8 1.0 CG A:HIS374 4.0 20.9 1.0 CB A:ASP349 4.1 24.6 1.0 ND1 A:HIS344 4.2 21.6 1.0 CE1 A:HIS344 4.2 22.3 1.0 ND1 A:HIS531 4.3 18.6 1.0 CG A:HIS531 4.4 17.1 1.0 O A:HOH1178 4.5 29.0 1.0 CG A:HIS344 4.7 16.8 1.0 NE2 A:HIS344 4.7 21.4 1.0 CD2 A:HIS344 5.0 19.9 1.0

Zinc binding site 2 out of 3 in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp


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 Complexed with Ca-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn578 b:13.5 occ:0.20 OE1 A:GLN342 1.6 21.6 1.0 O A:HOH1113 1.8 25.2 1.0 OD1 A:ASP529 2.3 18.8 1.0 NE2 A:HIS344 2.4 21.4 1.0 OE1 A:GLU413 2.4 24.7 1.0 CD A:GLN342 2.7 18.4 1.0 CE1 A:HIS344 2.9 22.3 1.0 O A:HOH1168 3.1 39.9 1.0 CG A:ASP529 3.2 15.6 1.0 CD A:GLU413 3.2 19.2 1.0 OD2 A:ASP529 3.4 16.0 1.0 ZN A:ZN579 3.5 14.6 0.5 OE2 A:GLU413 3.6 19.4 1.0 CD2 A:HIS344 3.6 19.9 1.0 NE2 A:GLN342 3.7 16.6 1.0 CG A:GLN342 3.7 13.4 1.0 CE1 A:HIS374 3.7 27.2 1.0 O A:HOH1178 3.8 29.0 1.0 ND1 A:HIS344 4.2 21.6 1.0 CG A:GLU413 4.3 16.1 1.0 ND1 A:HIS374 4.4 25.8 1.0 CB A:ASP529 4.5 13.4 1.0 CG A:HIS344 4.5 16.8 1.0 NE2 A:HIS468 4.5 20.1 1.0 CB A:GLU413 4.6 13.5 1.0 CE1 A:HIS531 4.6 19.6 1.0 NE2 A:HIS374 4.6 25.1 1.0 CD2 A:HIS468 4.7 19.5 1.0 CA A:ASP529 4.7 12.8 1.0

Zinc binding site 3 out of 3 in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn579 b:14.6 occ:0.50 OE2 A:GLU413 1.9 19.4 1.0 NE2 A:HIS468 2.0 20.1 1.0 O A:HOH1113 2.0 25.2 1.0 O A:HOH1178 2.1 29.0 1.0 NE2 A:HIS440 2.4 22.3 1.0 CD A:GLU413 2.8 19.2 1.0 CE1 A:HIS468 2.9 19.9 1.0 OE1 A:GLU413 3.0 24.7 1.0 CD2 A:HIS468 3.1 19.5 1.0 CE1 A:HIS440 3.2 22.4 1.0 CD2 A:HIS440 3.5 21.6 1.0 ZN A:ZN578 3.5 13.5 0.2 OG A:SER438 3.9 22.4 1.0 O A:HOH1168 4.0 39.9 1.0 ND1 A:HIS468 4.0 17.7 1.0 NH2 A:ARG506 4.1 23.2 1.0 CG A:GLU413 4.2 16.1 1.0 CG A:HIS468 4.2 15.0 1.0 OE1 A:GLN342 4.2 21.6 1.0 CE1 A:HIS374 4.3 27.2 1.0 ND1 A:HIS440 4.4 24.2 1.0 CZ A:ARG506 4.4 21.6 1.0 CG A:HIS440 4.6 21.6 1.0 CB A:SER438 4.6 15.4 1.0 OD2 A:ASP529 4.6 16.0 1.0 O A:HOH704 4.7 23.4 1.0 NH1 A:ARG506 4.7 17.4 1.0 ND1 A:HIS374 4.8 25.8 1.0 CG1 A:VAL378 4.9 21.1 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