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Zinc in PDB 3au6: Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp

Enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp

All present enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp, PDB code: 3au6 was solved by S.Nakane, 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 / 3.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.166, 80.166, 268.555, 90.00, 90.00, 90.00
R / Rfree (%) 25.6 / 31.9

Other elements in 3au6:

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp (pdb code 3au6). 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 Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp, PDB code: 3au6:

Zinc binding site 1 out of 1 in 3au6

Go back to Zinc Binding Sites List in 3au6
Zinc binding site 1 out of 1 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template 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 Primer/Template Dna and Ddgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn579

b:82.9
occ:0.50
 NE2 A:HIS468 2.3 66.8 1.0
OE2 A:GLU413 2.4 74.0 1.0
CD2 A:HIS468 3.1 66.8 1.0
CD A:GLU413 3.3 74.7 1.0
CE1 A:HIS468 3.4 67.3 1.0
NE2 A:HIS440 3.5 77.0 1.0
OE1 A:GLU413 3.6 76.1 1.0
OD1 A:ASP529 3.6 65.1 1.0
NH2 A:ARG506 3.9 73.4 1.0
OD2 A:ASP529 4.0 65.4 1.0
CE1 A:HIS374 4.1 83.3 1.0
CZ A:ARG506 4.1 74.5 1.0
CG A:ASP529 4.2 63.8 1.0
CG A:HIS468 4.3 67.2 1.0
NH1 A:ARG506 4.3 75.5 1.0
CE1 A:HIS440 4.4 77.2 1.0
ND1 A:HIS468 4.4 66.4 1.0
CD2 A:HIS440 4.4 76.3 1.0
CG A:GLU413 4.6 74.0 1.0
NE2 A:GLN342 4.6 64.7 1.0
OE1 A:GLN342 4.7 65.3 1.0
NE A:ARG506 4.8 74.2 1.0
ND1 A:HIS374 4.8 81.6 1.0
CD A:GLN342 5.0 65.2 1.0
OG A:SER438 5.0 67.7 1.0
NE2 A:HIS344 5.0 57.7 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: Thu Oct 24 11:16:42 2024

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