Chlorine in PDB 5tbc: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide., PDB code: 5tbc was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.76 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.330, 79.530, 55.330, 90.00, 107.39, 90.00
R / Rfree (%) 22.8 / 27.9

Other elements in 5tbc:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. (pdb code 5tbc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide., PDB code: 5tbc:

Chlorine binding site 1 out of 1 in 5tbc

Go back to Chlorine Binding Sites List in 5tbc
Chlorine binding site 1 out of 1 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)3TC-Mp and An Another Incoming (-)3TC- Tp Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:36.7
occ:1.00
 O D:HOH108 2.6 25.9 1.0
O A:HOH663 2.8 39.8 1.0
N A:HIS34 3.0 15.7 1.0
C A:ALA32 3.2 15.5 1.0
CA A:ALA32 3.3 15.6 1.0
CB A:HIS34 3.4 17.6 1.0
N A:ILE33 3.4 15.2 1.0
CB A:ALA32 3.5 15.9 1.0
N A:LYS35 3.5 15.6 1.0
CA A:HIS34 3.6 16.3 1.0
O A:ALA32 3.6 15.0 1.0
CD2 A:HIS34 3.7 18.7 1.0
CG A:HIS34 3.8 17.9 1.0
C A:HIS34 4.0 15.7 1.0
C A:ILE33 4.0 15.5 1.0
CG A:LYS35 4.2 17.7 1.0
CA A:ILE33 4.3 15.6 1.0
O A:HOH615 4.3 23.9 1.0
CB A:LYS35 4.7 17.3 1.0
CA A:LYS35 4.7 16.4 1.0
N A:ALA32 4.7 15.7 1.0
CG2 A:ILE33 4.8 16.6 1.0
O6 D:DG1 4.9 18.4 1.0
NE2 A:HIS34 4.9 19.6 1.0
ND1 A:HIS34 5.0 19.6 1.0

Reference:

A.J.Reed, R.Vyas, A.T.Raper, Z.Suo. Structural Insights Into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed By A Dna Polymerase. J. Am. Chem. Soc. V. 139 465 2017.
ISSN: ESSN 1520-5126
PubMed: 27959534
DOI: 10.1021/JACS.6B11258
Page generated: Sat Dec 12 12:28:03 2020

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