Chlorine in PDB 6dic: D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

Enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

All present enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog:
2.7.7.7;

Protein crystallography data

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dic was solved by B.D.Freudenthal, M.R.Smith, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.66 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 17.5 / 23.2

Other elements in 6dic:

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog (pdb code 6dic). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dic:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6dic

Go back to Chlorine Binding Sites List in 6dic
Chlorine binding site 1 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:33.7
occ:1.00
 O A:HOH664 2.8 40.9 1.0
N A:CYS267 3.1 16.5 1.0
O A:HOH517 3.2 24.6 1.0
N A:TYR266 3.5 20.5 1.0
C A:GLN264 3.5 17.0 1.0
CA A:GLN264 3.6 17.5 1.0
CG1 A:VAL313 3.7 25.6 1.0
CB A:TYR266 3.7 25.1 1.0
O A:GLN264 3.7 19.6 1.0
SG A:CYS267 3.8 25.7 1.0
CB A:VAL313 3.8 31.4 1.0
CB A:CYS267 3.9 21.7 1.0
CA A:TYR266 3.9 18.9 1.0
O A:ASP263 3.9 25.7 1.0
C A:TYR266 3.9 19.2 1.0
N A:TYR265 4.0 18.2 1.0
CA A:CYS267 4.1 15.7 1.0
C A:TYR265 4.4 18.5 1.0
CD2 A:TYR266 4.4 27.6 1.0
O A:TYR296 4.4 25.3 1.0
CB A:GLN264 4.5 18.6 1.0
N A:GLN264 4.5 15.3 1.0
O A:VAL313 4.6 33.5 1.0
CG A:TYR266 4.6 24.0 1.0
CG2 A:VAL313 4.6 37.3 1.0
C A:ASP263 4.6 29.3 1.0
CA A:TYR265 4.8 18.8 1.0
C A:VAL313 5.0 34.3 1.0

Chlorine binding site 2 out of 3 in 6dic

Go back to Chlorine Binding Sites List in 6dic
Chlorine binding site 2 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:40.6
occ:1.00
 O D:HOH201 3.0 36.0 1.0
N A:HIS34 3.2 25.4 1.0
CB A:HIS34 3.5 28.8 1.0
C A:ALA32 3.5 27.3 1.0
CA A:ALA32 3.6 30.4 1.0
CB A:ALA32 3.6 19.3 1.0
N A:LYS35 3.6 24.3 1.0
N A:ILE33 3.7 23.3 1.0
CA A:HIS34 3.7 32.1 1.0
CD2 A:HIS34 3.8 36.6 1.0
CG A:HIS34 3.9 38.4 1.0
O A:ALA32 3.9 29.7 1.0
C A:HIS34 4.1 25.5 1.0
C A:ILE33 4.3 29.8 1.0
CG A:LYS35 4.4 22.2 1.0
O A:HOH570 4.4 32.5 1.0
CA A:ILE33 4.6 34.8 1.0
CB A:LYS35 4.7 25.6 1.0
CA A:LYS35 4.8 19.3 1.0
O6 D:DG1 4.8 30.9 1.0

Chlorine binding site 3 out of 3 in 6dic

Go back to Chlorine Binding Sites List in 6dic
Chlorine binding site 3 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:34.7
occ:1.00
 O A:HOH747 2.9 36.9 1.0
OG1 A:THR297 3.3 25.7 1.0
ND2 A:ASN294 3.4 22.3 1.0
O A:HOH741 3.5 36.8 1.0
CG2 A:THR297 3.9 22.2 1.0
CZ A:ARG299 4.0 53.5 1.0
OD1 A:ASN294 4.0 23.0 1.0
CB A:TYR296 4.0 28.1 1.0
NE A:ARG299 4.1 36.1 1.0
NH2 A:ARG299 4.2 44.5 1.0
CG A:ASN294 4.2 18.9 1.0
CB A:THR297 4.2 23.3 1.0
CD2 A:TYR296 4.2 22.7 1.0
NH1 A:ARG299 4.3 61.5 1.0
CG A:TYR296 4.6 25.3 1.0
O A:HOH569 4.6 23.7 1.0
O T:HOH114 4.6 36.3 1.0
CD A:ARG299 4.7 32.3 1.0
N A:THR297 4.7 21.2 1.0
O A:HOH772 4.9 42.8 1.0

Reference:

M.R.Smith, D.D.Shock, W.A.Beard, M.M.Greenberg, B.D.Freudenthal, S.H.Wilson. A Guardian Residue Hinders Insertion of A Fapy•Dgtp Analog By Modulating the Open-Closed Dna Polymerase Transition. Nucleic Acids Res. V. 47 3197 2019.
ISSN: ESSN 1362-4962
PubMed: 30649431
DOI: 10.1093/NAR/GKZ002
Page generated: Sat Dec 12 12:53:04 2020

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