Chlorine in PDB 5tb8: Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+., PDB code: 5tb8 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) 46.41 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.480, 81.400, 53.570, 90.00, 110.28, 90.00
R / Rfree (%) 18.2 / 23

Other elements in 5tb8:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+. also contains other interesting chemical elements:

Manganese (Mn) 6 atoms
Sodium (Na) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+. (pdb code 5tb8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+., PDB code: 5tb8:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5tb8

Go back to Chlorine Binding Sites List in 5tb8
Chlorine binding site 1 out of 2 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.


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 in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:37.7
occ:1.00
OG1 A:THR297 3.1 15.5 1.0
ND2 A:ASN294 3.3 10.4 1.0
CZ A:ARG299 3.8 32.8 1.0
NH2 A:ARG299 3.8 32.2 1.0
OD1 A:ASN294 3.8 10.8 1.0
NE A:ARG299 3.9 27.2 1.0
CB A:TYR296 3.9 15.0 1.0
CG A:ASN294 4.0 11.1 1.0
CG2 A:THR297 4.0 15.7 1.0
CD2 A:TYR296 4.0 15.6 1.0
CB A:THR297 4.2 15.8 1.0
NH1 A:ARG299 4.3 32.8 1.0
CG A:TYR296 4.4 14.9 1.0
CD A:ARG299 4.6 22.6 1.0
N A:THR297 4.7 14.3 1.0
O A:HOH561 4.7 19.9 1.0

Chlorine binding site 2 out of 2 in 5tb8

Go back to Chlorine Binding Sites List in 5tb8
Chlorine binding site 2 out of 2 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:46.1
occ:1.00
N A:HIS34 3.1 15.0 1.0
C A:ALA32 3.2 14.7 1.0
CA A:ALA32 3.3 15.1 1.0
N A:ILE33 3.4 14.7 1.0
CB A:ALA32 3.4 14.2 1.0
CB A:HIS34 3.6 15.8 1.0
CA A:HIS34 3.8 15.8 1.0
N A:LYS35 3.8 17.5 1.0
O A:ALA32 3.8 13.4 1.0
ND1 A:HIS34 3.8 18.3 1.0
O A:HOH572 4.0 24.5 1.0
CG A:HIS34 4.1 16.0 1.0
C A:ILE33 4.1 15.8 1.0
C A:HIS34 4.2 15.9 1.0
CA A:ILE33 4.3 15.5 1.0
CG A:LYS35 4.6 21.0 1.0
CG2 A:ILE33 4.6 16.8 1.0
N A:ALA32 4.7 15.8 1.0
O6 D:DG1 4.7 14.9 1.0
CE1 A:HIS34 5.0 16.2 1.0
CA A:LYS35 5.0 17.1 1.0
CB A:LYS35 5.0 18.5 1.0
O A:GLN31 5.0 17.6 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 12:28:02 2020

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