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Fluorine in PDB 5u2t: Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+., PDB code: 5u2t 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) 15.78 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.615, 79.395, 54.795, 90.00, 107.60, 90.00
R / Rfree (%) 20 / 24.7

Other elements in 5u2t:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. (pdb code 5u2t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+., PDB code: 5u2t:

Fluorine binding site 1 out of 1 in 5u2t

Go back to Fluorine Binding Sites List in 5u2t
Fluorine binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:48.9
occ:1.00
 FAJ A:1RY401 0.0 48.9 1.0
CAU A:1RY401 1.3 50.4 1.0
CAT A:1RY401 2.3 54.8 1.0
CAK A:1RY401 2.4 54.4 1.0
NAA A:1RY401 2.7 53.7 1.0
OAH A:1RY401 2.9 48.1 1.0
C2' P:DC10 3.3 40.9 1.0
NAN A:1RY401 3.5 57.4 1.0
NAY A:1RY401 3.6 59.6 1.0
OD2 A:ASP276 3.8 73.5 1.0
CAV A:1RY401 4.0 60.7 1.0
O3' P:DC10 4.2 41.4 1.0
PBA A:1RY401 4.3 46.8 1.0
C1' P:DC10 4.3 38.7 1.0
C3' P:DC10 4.3 39.1 1.0
CG A:ASP276 4.4 73.8 1.0
N1 P:DC10 4.6 38.4 1.0
OAR A:1RY401 4.8 46.5 1.0
CB A:ASP276 4.8 65.9 1.0
C6 P:DC10 4.8 36.5 1.0
OAO A:1RY401 4.8 57.0 1.0
CAL A:1RY401 4.8 54.7 1.0
CAX A:1RY401 4.9 59.1 1.0

Reference:

R.Vyas, A.J.Reed, A.T.Raper, W.J.Zahurancik, P.C.Wallenmeyer, Z.Suo. Structural Basis For the D-Stereoselectivity of Human Dna Polymerase Beta. Nucleic Acids Res. V. 45 6228 2017.
ISSN: ESSN 1362-4962
PubMed: 28402499
DOI: 10.1093/NAR/GKX252
Page generated: Thu Aug 1 15:31:16 2024

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