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Chlorine 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
Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp, PDB code: 3au6:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3au6

Go back to Chlorine Binding Sites List in 3au6
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl580

b:71.6
occ:1.00
 NZ A:LYS193 2.7 73.5 1.0
OD2 A:ASP194 4.0 75.1 1.0
CE A:LYS193 4.1 73.6 1.0
CG2 A:THR195 4.3 71.3 1.0
CD A:LYS193 4.5 73.7 1.0
CG A:LYS193 4.6 74.6 1.0

Chlorine binding site 2 out of 4 in 3au6

Go back to Chlorine Binding Sites List in 3au6
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl581

b:50.9
occ:1.00
 OD2 A:ASP426 3.3 73.9 1.0
CB A:ASP426 3.5 73.1 1.0
N A:TRP427 3.7 72.1 1.0
CG A:ASP426 3.9 73.6 1.0
N A:ASP426 3.9 73.3 1.0
CB A:PRO425 4.1 74.0 1.0
CA A:ASP426 4.2 73.0 1.0
CB A:TRP427 4.4 72.3 1.0
CD1 A:TRP427 4.4 74.2 1.0
C A:ASP426 4.5 72.4 1.0
CA A:TRP427 4.6 72.2 1.0
C A:PRO425 4.7 73.6 1.0
CG A:TRP427 4.8 73.2 1.0
CA A:PRO425 4.8 73.9 1.0

Chlorine binding site 3 out of 4 in 3au6

Go back to Chlorine Binding Sites List in 3au6
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl582

b:82.4
occ:1.00
 NZ A:LYS338 3.3 68.4 1.0
CG A:GLN336 3.8 64.7 1.0
CA A:GLN336 4.0 65.6 1.0
CE A:LYS338 4.3 68.3 1.0
CB A:GLN336 4.4 65.6 1.0
N A:GLN336 4.7 65.9 1.0
O A:GLN336 4.7 65.5 1.0
C A:GLN336 4.8 65.6 1.0
CD A:GLN336 4.9 63.7 1.0

Chlorine binding site 4 out of 4 in 3au6

Go back to Chlorine Binding Sites List in 3au6
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl583

b:77.0
occ:1.00
 CD A:ARG430 4.1 75.6 1.0
CG A:ARG430 4.4 73.6 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: Sat Jul 20 16:04:53 2024

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