Chlorine in PDB 5wny: Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp

Enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny was solved by M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.65 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.480, 79.747, 55.570, 90.00, 107.23, 90.00
R / Rfree (%) 18.1 / 23.7

Other elements in 5wny:

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp (pdb code 5wny). 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 Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5wny

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Chlorine binding site 1 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:55.4
occ:1.00
O A:HOH519 2.9 29.9 1.0
N A:CYS267 3.3 21.3 1.0
CA A:GLN264 3.4 24.9 1.0
CG1 A:VAL313 3.5 33.5 1.0
C A:GLN264 3.5 25.9 1.0
N A:TYR266 3.6 24.5 1.0
O A:ASP263 3.7 33.8 1.0
SG A:CYS267 3.8 28.0 1.0
O A:GLN264 3.8 23.9 1.0
CB A:VAL313 3.8 31.4 1.0
CB A:TYR266 3.9 29.2 1.0
CB A:CYS267 4.0 20.3 1.0
CA A:TYR266 4.0 33.0 1.0
N A:TYR265 4.0 22.6 1.0
C A:TYR266 4.1 28.3 1.0
O A:TYR296 4.2 19.7 1.0
CA A:CYS267 4.3 27.2 1.0
CB A:GLN264 4.3 23.3 1.0
O A:VAL313 4.4 30.1 1.0
N A:GLN264 4.4 24.0 1.0
C A:ASP263 4.5 30.8 1.0
C A:TYR265 4.5 32.3 1.0
CD2 A:TYR266 4.5 32.6 1.0
CG A:TYR266 4.7 24.9 1.0
CG2 A:VAL313 4.7 32.5 1.0
CA A:TYR265 4.9 23.2 1.0
CG A:GLN264 4.9 26.4 1.0
C A:VAL313 5.0 30.6 1.0
CA A:VAL313 5.0 32.2 1.0

Chlorine binding site 2 out of 4 in 5wny

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Chlorine binding site 2 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:60.6
occ:1.00
C A:ALA32 3.3 31.7 1.0
CA A:ALA32 3.3 41.2 1.0
N A:HIS34 3.4 31.9 1.0
CB A:ALA32 3.4 32.8 1.0
N A:ILE33 3.6 37.5 1.0
O A:ALA32 3.6 35.6 1.0
CB A:HIS34 3.6 43.1 1.0
N A:LYS35 3.7 41.5 1.0
O D:HOH101 3.8 49.0 1.0
CA A:HIS34 3.9 39.9 1.0
ND1 A:HIS34 4.1 47.6 1.0
O A:HOH561 4.1 37.4 1.0
CG A:LYS35 4.3 35.9 1.0
C A:HIS34 4.3 37.3 1.0
CG A:HIS34 4.3 51.8 1.0
C A:ILE33 4.4 40.8 1.0
CA A:ILE33 4.6 37.2 1.0
CB A:LYS35 4.7 27.2 1.0
N A:ALA32 4.7 36.0 1.0
CA A:LYS35 4.8 34.3 1.0

Chlorine binding site 3 out of 4 in 5wny

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Chlorine binding site 3 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:64.9
occ:1.00
N A:LEU82 3.2 39.0 1.0
CB A:LYS81 3.6 52.6 1.0
CA A:LYS81 3.6 46.8 1.0
C A:LYS81 3.9 41.2 1.0
O A:LEU82 3.9 35.7 1.0
CA A:LEU82 4.1 32.2 1.0
CB A:LEU85 4.1 36.2 1.0
NH2 A:ARG89 4.1 49.5 1.0
CB A:LEU82 4.1 34.5 1.0
CD1 A:LEU85 4.3 38.2 1.0
C A:LEU82 4.4 39.9 1.0
CZ A:ARG89 4.5 48.7 1.0
CG A:GLU86 4.7 58.4 1.0
NE A:ARG89 4.7 40.3 1.0
N A:GLU86 4.8 38.8 1.0
CG A:LEU85 4.9 44.0 1.0
O A:GLY80 5.0 41.9 1.0

Chlorine binding site 4 out of 4 in 5wny

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Chlorine binding site 4 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:43.0
occ:1.00
OG1 A:THR297 3.0 29.6 1.0
NH2 A:ARG299 3.2 30.2 0.4
O A:HOH666 3.3 35.0 1.0
ND2 A:ASN294 3.3 24.2 1.0
NE A:ARG299 3.4 25.2 0.4
CZ A:ARG299 3.7 39.2 0.4
OD1 A:ASN294 3.9 26.4 1.0
CG2 A:THR297 3.9 23.0 1.0
CB A:TYR296 4.0 30.7 1.0
CZ A:ARG299 4.0 33.7 0.6
NE A:ARG299 4.0 21.0 0.6
CG A:ASN294 4.0 24.9 1.0
CB A:THR297 4.1 27.5 1.0
NH2 A:ARG299 4.1 26.1 0.6
CD2 A:TYR296 4.1 25.0 1.0
CG A:TYR296 4.5 26.1 1.0
NH1 A:ARG299 4.5 35.5 0.6
CD A:ARG299 4.6 28.7 0.4
CD A:ARG299 4.6 28.7 0.6
O T:HOH117 4.6 39.6 1.0
O A:HOH501 4.7 50.7 1.0
N A:THR297 4.7 24.2 1.0
O A:HOH557 4.7 25.8 1.0
NH1 A:ARG299 4.9 30.3 0.4
CA A:THR297 5.0 31.6 1.0

Reference:

M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal. Structures of A Dna Polymerase Inserting Therapeutic Nucleotide Analogues. Chem. Res. Toxicol. V. 30 1993 2017.
ISSN: ISSN 1520-5010
PubMed: 28862449
DOI: 10.1021/ACS.CHEMRESTOX.7B00173
Page generated: Sat Dec 12 12:37:20 2020

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