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Zinc in PDB 3b0y: K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp

Enzymatic activity of K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp

All present enzymatic activity of K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp:
2.7.7.7;

Protein crystallography data

The structure of K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0y 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 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.942, 53.224, 84.864, 90.00, 107.65, 90.00
R / Rfree (%) 17.5 / 20.5

Other elements in 3b0y:

The structure of K263D 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

Zinc Binding Sites:

The binding sites of Zinc atom in the K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp (pdb code 3b0y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0y:

Zinc binding site 1 out of 1 in 3b0y

Go back to Zinc Binding Sites List in 3b0y
Zinc binding site 1 out of 1 in the K263D 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 K263D 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:18.7
occ:0.20
 OE2 A:GLU413 1.8 18.9 1.0
O A:HOH894 1.9 26.9 1.0
NE2 A:HIS468 2.0 18.5 1.0
O A:HOH615 2.3 23.4 1.0
CE1 A:HIS468 2.5 19.8 1.0
CD A:GLU413 2.7 18.6 1.0
NE2 A:HIS440 2.9 22.6 1.0
OE1 A:GLU413 3.0 21.9 1.0
CD2 A:HIS468 3.2 17.2 1.0
CD2 A:HIS440 3.6 22.0 1.0
NH1 A:ARG506 3.7 21.6 1.0
ND1 A:HIS468 3.8 17.1 1.0
OG A:SER438 3.9 20.0 1.0
CE1 A:HIS374 4.0 21.8 1.0
CE1 A:HIS440 4.0 22.0 1.0
CG A:GLU413 4.0 15.3 1.0
CG A:HIS468 4.1 12.9 1.0
O A:HOH650 4.2 24.7 1.0
OE1 A:GLN342 4.4 19.3 1.0
NH2 A:ARG506 4.4 16.2 1.0
CZ A:ARG506 4.4 18.0 1.0
O A:HOH940 4.4 25.8 1.0
CB A:SER438 4.6 13.7 1.0
OD2 A:ASP529 4.8 13.5 1.0
ND1 A:HIS374 4.8 20.9 1.0
CG A:HIS440 4.9 18.4 1.0
NE2 A:HIS374 4.9 20.4 1.0

Reference:

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
Page generated: Wed Dec 16 04:08:08 2020

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