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Chlorine in PDB 3tfr: Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site

Enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site

All present enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site:
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(CF2)Pp in the Active Site, PDB code: 3tfr 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) 20.69 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.890, 79.380, 55.650, 90.00, 107.64, 90.00
R / Rfree (%) 18.8 / 25.1

Other elements in 3tfr:

The structure of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site also contains other interesting chemical elements:

Fluorine (F) 2 atoms
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(CF2)Pp in the Active Site (pdb code 3tfr). 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(CF2)Pp in the Active Site, PDB code: 3tfr:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3tfr

Go back to Chlorine Binding Sites List in 3tfr
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(CF2)Pp in the Active Site


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(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl336

b:25.5
occ:1.00
 O A:HOH509 3.1 26.1 1.0
OG1 A:THR297 3.1 20.6 1.0
NH2 A:ARG299 3.3 25.8 1.0
O T:HOH454 3.3 32.3 1.0
ND2 A:ASN294 3.4 17.7 1.0
NE A:ARG299 3.6 34.4 1.0
CG2 A:THR297 3.8 20.8 1.0
OD1 A:ASN294 3.9 15.8 1.0
CZ A:ARG299 3.9 37.8 1.0
CB A:TYR296 4.0 18.8 1.0
CG A:ASN294 4.1 18.1 1.0
CB A:THR297 4.1 21.1 1.0
CD2 A:TYR296 4.1 19.4 1.0
CG A:TYR296 4.5 18.1 1.0
N A:THR297 4.6 15.2 1.0
CD A:ARG299 4.8 21.7 1.0
O A:HOH407 4.9 19.6 1.0
O T:HOH420 4.9 25.1 1.0
CA A:THR297 5.0 16.7 1.0

Chlorine binding site 2 out of 4 in 3tfr

Go back to Chlorine Binding Sites List in 3tfr
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(CF2)Pp in the Active Site


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(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl337

b:31.4
occ:1.00
 N A:CYS267 3.1 15.9 1.0
O A:HOH429 3.3 19.9 1.0
CA A:GLN264 3.4 17.2 1.0
N A:TYR266 3.4 16.6 1.0
C A:GLN264 3.4 19.1 1.0
CG1 A:VAL313 3.4 24.7 1.0
O A:GLN264 3.6 17.4 1.0
CB A:TYR266 3.6 20.3 1.0
CA A:TYR266 3.8 17.7 1.0
O A:ASP263 3.8 24.6 1.0
SG A:CYS267 3.8 23.9 1.0
CB A:VAL313 3.9 25.1 1.0
C A:TYR266 3.9 16.1 1.0
N A:TYR265 3.9 19.5 1.0
CB A:CYS267 3.9 19.0 1.0
O A:HOH682 4.0 31.8 1.0
CA A:CYS267 4.1 14.0 1.0
CB A:GLN264 4.2 15.3 1.0
C A:TYR265 4.3 19.2 1.0
O A:TYR296 4.4 14.4 1.0
CD2 A:TYR266 4.4 24.0 1.0
N A:GLN264 4.4 20.4 1.0
C A:ASP263 4.5 23.3 1.0
CG A:TYR266 4.5 21.1 1.0
O A:VAL313 4.6 22.1 1.0
CG2 A:VAL313 4.7 18.6 1.0
CA A:TYR265 4.7 21.2 1.0
CG A:GLN264 4.8 17.4 1.0

Chlorine binding site 3 out of 4 in 3tfr

Go back to Chlorine Binding Sites List in 3tfr
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(CF2)Pp in the Active Site


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(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:26.1
occ:1.00
 N A:HIS34 3.3 20.3 1.0
CB A:ALA32 3.4 22.4 1.0
C A:ALA32 3.4 23.2 1.0
CB A:HIS34 3.4 22.9 1.0
N A:LYS35 3.5 18.2 1.0
CA A:ALA32 3.6 23.2 1.0
O A:ALA32 3.6 20.4 1.0
CA A:HIS34 3.7 19.8 1.0
CD2 A:HIS34 3.8 23.6 1.0
N A:ILE33 3.8 20.2 1.0
CG A:HIS34 4.0 23.5 1.0
CG A:LYS35 4.0 19.0 1.0
C A:HIS34 4.1 19.2 1.0
O A:HOH362 4.2 29.9 1.0
C A:ILE33 4.3 15.4 1.0
O A:HOH660 4.4 26.7 1.0
CB A:LYS35 4.4 13.0 1.0
CA A:LYS35 4.6 15.9 1.0
CA A:ILE33 4.6 20.5 1.0
O6 D:DG1 4.8 23.6 1.0
CD A:LYS35 4.9 16.5 1.0
O A:HOH658 5.0 29.0 1.0

Chlorine binding site 4 out of 4 in 3tfr

Go back to Chlorine Binding Sites List in 3tfr
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(CF2)Pp in the Active Site


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(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:41.8
occ:1.00
 N A:LEU82 3.2 18.7 1.0
NH1 A:ARG89 3.2 34.7 1.0
NH2 A:ARG89 3.4 40.3 1.0
OE1 A:GLU86 3.4 43.1 1.0
CA A:LYS81 3.6 21.9 1.0
CB A:LYS81 3.7 29.8 1.0
CZ A:ARG89 3.7 35.8 1.0
C A:LYS81 3.8 21.4 1.0
CA A:LEU82 4.2 23.9 1.0
O A:LEU82 4.2 22.0 1.0
CB A:LEU82 4.3 20.3 1.0
CB A:LEU85 4.3 21.6 1.0
CD1 A:LEU85 4.4 19.2 1.0
CD A:GLU86 4.5 43.4 1.0
C A:LEU82 4.6 21.9 1.0
CG A:GLU86 4.7 27.0 1.0
O A:GLY80 4.8 23.1 1.0
N A:LYS81 4.9 19.3 1.0
CG A:LEU85 5.0 19.8 1.0
O A:LYS81 5.0 19.6 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: Sun Jul 21 05:09:07 2024

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