Zinc in PDB 3b0x: K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp

All present enzymatic activity of K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp:
2.7.7.7;

The structure of K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0x was solved by S.Nakane, N.Nakagawa, R.Masui, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.088, 53.202, 84.859, 90.00, 107.65, 90.00
R / Rfree (%)	17.1 / 19.8

The structure of K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp (pdb code 3b0x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the K263A Mutant of Polx 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 K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn576 b:23.0 occ:0.20 OD2 A:ASP349 1.2 21.5 1.0 O A:HOH872 2.0 28.8 1.0 NE2 A:HIS374 2.3 21.9 1.0 CG A:ASP349 2.3 20.8 1.0 NE2 A:HIS531 2.4 15.3 1.0 OD1 A:ASP349 2.8 21.4 1.0 CD2 A:HIS374 3.0 20.4 1.0 CD2 A:HIS531 3.4 14.5 1.0 CE1 A:HIS531 3.4 13.6 1.0 CE1 A:HIS374 3.5 22.4 1.0 CB A:ASP349 3.6 20.2 1.0 ND1 A:HIS344 3.9 16.6 1.0 CE1 A:HIS344 4.1 17.3 1.0 CG A:HIS374 4.2 18.5 1.0 ND1 A:HIS374 4.4 21.2 1.0 ND1 A:HIS531 4.5 14.0 1.0 CG A:HIS531 4.5 13.2 1.0 CG A:HIS344 4.6 13.6 1.0 O A:HOH954 4.7 34.0 1.0 NE2 A:HIS344 4.8 16.7 1.0 O A:HOH639 4.8 22.8 1.0 CA A:ASP349 4.9 19.9 1.0

Zinc binding site 2 out of 2 in the K263A Mutant of Polx 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 K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn577 b:18.6 occ:0.30 OE2 A:GLU413 1.8 18.1 1.0 O A:HOH1051 2.0 29.1 1.0 NE2 A:HIS468 2.1 17.2 1.0 O A:HOH639 2.2 22.8 1.0 CE1 A:HIS468 2.6 16.7 1.0 CD A:GLU413 2.7 18.6 1.0 NE2 A:HIS440 2.8 24.8 1.0 OE1 A:GLU413 2.9 21.9 1.0 CD2 A:HIS468 3.3 14.6 1.0 CD2 A:HIS440 3.5 22.9 1.0 OG A:SER438 3.8 19.8 1.0 ND1 A:HIS468 3.9 15.7 1.0 CE1 A:HIS440 3.9 23.5 1.0 CE1 A:HIS374 3.9 22.4 1.0 CG A:GLU413 4.0 15.7 1.0 NH2 A:ARG506 4.1 24.5 1.0 CG A:HIS468 4.2 11.8 1.0 O A:HOH680 4.3 23.8 1.0 OE1 A:GLN342 4.4 18.2 1.0 O A:HOH872 4.4 28.8 1.0 O A:HOH954 4.5 34.0 1.0 CZ A:ARG506 4.5 22.9 1.0 CB A:SER438 4.6 13.0 1.0 NH1 A:ARG506 4.6 16.3 1.0 ND1 A:HIS374 4.7 21.2 1.0 OD2 A:ASP529 4.8 12.3 1.0 CG A:HIS440 4.8 19.9 1.0 NE2 A:HIS374 4.9 21.9 1.0 ND1 A:HIS440 4.9 23.9 1.0 CG1 A:VAL378 5.0 25.0 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