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Chlorine in PDB 3tfs: Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer

Enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer

All present enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer, PDB code: 3tfs was solved by B.T.Chamberlain, V.K.Batra, W.A.Beard, A.P.Kadina, D.D.Shock, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.56 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.770, 79.580, 55.720, 90.00, 107.75, 90.00
R / Rfree (%) 18.8 / 24.2

Other elements in 3tfs:

The structure of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer (pdb code 3tfs). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer, PDB code: 3tfs:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3tfs

Go back to Chlorine Binding Sites List in 3tfs
Chlorine binding site 1 out of 4 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:26.5
occ:1.00
 O A:HOH447 2.9 31.3 1.0
OG1 A:THR297 3.1 23.7 1.0
ND2 A:ASN294 3.3 18.8 1.0
O A:HOH431 3.3 33.1 1.0
CG2 A:THR297 3.7 21.3 1.0
CZ A:ARG299 3.8 36.7 1.0
CB A:TYR296 3.9 21.5 1.0
OD1 A:ASN294 4.0 17.6 1.0
NH1 A:ARG299 4.0 39.4 1.0
NH2 A:ARG299 4.0 32.9 1.0
CB A:THR297 4.0 22.4 1.0
CG A:ASN294 4.1 17.8 1.0
CD2 A:TYR296 4.1 21.0 1.0
NE A:ARG299 4.2 34.5 1.0
CG A:TYR296 4.5 18.6 1.0
N A:THR297 4.6 18.2 1.0
CD A:ARG299 4.7 23.9 1.0
O A:HOH358 4.7 19.1 1.0
O A:HOH584 4.8 35.7 1.0
O T:HOH416 4.9 29.5 1.0
CA A:THR297 5.0 21.3 1.0

Chlorine binding site 2 out of 4 in 3tfs

Go back to Chlorine Binding Sites List in 3tfs
Chlorine binding site 2 out of 4 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:28.2
occ:1.00
 N A:HIS34 3.2 20.5 1.0
C A:ALA32 3.5 23.8 1.0
CB A:HIS34 3.5 27.1 1.0
CB A:ALA32 3.5 22.1 1.0
CA A:ALA32 3.6 25.3 1.0
CD2 A:HIS34 3.7 30.0 1.0
N A:ILE33 3.7 20.8 1.0
N A:LYS35 3.7 19.2 1.0
CA A:HIS34 3.8 23.5 1.0
O A:ALA32 3.9 23.1 1.0
CG A:HIS34 3.9 26.9 1.0
C A:HIS34 4.2 21.4 1.0
CG A:LYS35 4.3 21.9 1.0
C A:ILE33 4.3 20.5 1.0
CA A:ILE33 4.6 23.7 1.0
O A:HOH487 4.6 26.9 1.0
CB A:LYS35 4.6 16.2 1.0
O T:HOH307 4.7 41.4 1.0
O6 D:DG1 4.7 26.7 1.0
CA A:LYS35 4.8 18.9 1.0
NE2 A:HIS34 4.9 30.4 1.0

Chlorine binding site 3 out of 4 in 3tfs

Go back to Chlorine Binding Sites List in 3tfs
Chlorine binding site 3 out of 4 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:30.8
occ:1.00
 O A:HOH378 3.1 24.3 1.0
N A:CYS267 3.2 17.3 1.0
CA A:GLN264 3.4 19.3 1.0
C A:GLN264 3.5 22.2 1.0
N A:TYR266 3.5 19.2 1.0
O A:GLN264 3.7 21.2 1.0
CG1 A:VAL313 3.7 24.2 1.0
SG A:CYS267 3.7 20.3 1.0
CB A:TYR266 3.8 24.2 1.0
O A:ASP263 3.8 25.7 1.0
CB A:CYS267 3.8 21.8 1.0
CB A:VAL313 3.8 27.2 1.0
CA A:TYR266 3.9 18.6 1.0
N A:TYR265 4.0 23.2 1.0
C A:TYR266 4.0 19.6 1.0
CA A:CYS267 4.1 15.1 1.0
O A:TYR296 4.3 17.8 1.0
CB A:GLN264 4.3 22.0 1.0
CD2 A:TYR266 4.3 30.0 1.0
C A:TYR265 4.4 19.7 1.0
N A:GLN264 4.4 22.4 1.0
C A:ASP263 4.5 22.7 1.0
CG A:TYR266 4.5 25.9 1.0
O A:VAL313 4.6 24.0 1.0
CG2 A:VAL313 4.6 22.1 1.0
CA A:TYR265 4.8 22.4 1.0
CG A:GLN264 4.8 23.1 1.0

Chlorine binding site 4 out of 4 in 3tfs

Go back to Chlorine Binding Sites List in 3tfs
Chlorine binding site 4 out of 4 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl346

b:35.9
occ:1.00
 NH2 A:ARG89 3.1 44.3 1.0
N A:LEU82 3.1 23.8 1.0
CA A:LYS81 3.6 28.9 1.0
NH1 A:ARG89 3.6 35.5 1.0
CB A:LYS81 3.7 34.3 1.0
CZ A:ARG89 3.8 40.3 1.0
C A:LYS81 3.8 28.1 1.0
CB A:LEU82 4.1 23.9 1.0
CB A:LEU85 4.1 27.2 1.0
CA A:LEU82 4.1 26.1 1.0
CD1 A:LEU85 4.2 22.8 1.0
O A:LEU82 4.3 26.6 1.0
C A:LEU82 4.6 27.6 1.0
CE1 A:PHE76 4.7 27.6 1.0
CG A:LEU85 4.8 25.1 1.0
O A:GLY80 4.8 31.0 1.0
CD1 A:PHE76 4.8 26.3 1.0
N A:LYS81 4.9 24.6 1.0
O A:LYS81 5.0 23.3 1.0
O A:HOH382 5.0 20.6 1.0
OE1 A:GLU86 5.0 52.4 1.0

Reference:

B.T.Chamberlain, V.K.Batra, W.A.Beard, A.P.Kadina, D.D.Shock, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Stereospecific Formation of A Ternary Complex of (S)-Alpha, Beta-Fluoromethylene-Datp with Dna Pol Beta. Chembiochem V. 13 528 2012.
ISSN: ISSN 1439-4227
PubMed: 22315190
DOI: 10.1002/CBIC.201100738
Page generated: Sat Dec 12 10:12:01 2020

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