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Fluorine in PDB 4k4i: Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.

Enzymatic activity of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.

All present enzymatic activity of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp., PDB code: 4k4i 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) 45.03 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 194.440, 97.580, 105.150, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.4

Other elements in 4k4i:

The structure of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp. also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Calcium (Ca) 23 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp. (pdb code 4k4i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp., PDB code: 4k4i:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4k4i

Go back to Fluorine Binding Sites List in 4k4i
Fluorine binding site 1 out of 4 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:20.5
occ:1.00
FAJ A:1RY601 0.0 20.5 1.0
CAU A:1RY601 1.3 20.1 1.0
CAT A:1RY601 2.4 18.6 1.0
CAK A:1RY601 2.4 20.4 1.0
NAA A:1RY601 2.7 18.0 1.0
O A:HOH720 2.9 32.5 1.0
O A:HOH786 3.0 30.4 1.0
OAH A:1RY601 3.5 24.2 1.0
NAY A:1RY601 3.6 19.8 1.0
NAN A:1RY601 3.6 18.7 1.0
C6 C:DC6 3.7 22.8 1.0
C5 C:DC6 3.8 21.8 1.0
CAV A:1RY601 4.0 20.2 1.0
CB A:ALA510 4.1 20.7 1.0
O C:HOH109 4.3 32.8 1.0
N1 C:DC6 4.3 23.7 1.0
C4 C:DC6 4.5 22.7 1.0
OAO A:1RY601 4.5 22.2 1.0
C2' C:DC6 4.6 26.2 1.0
PBA A:1RY601 4.7 22.1 1.0
C3' C:DC6 4.7 27.6 1.0
CAX A:1RY601 4.8 19.8 1.0
OAP A:1RY601 4.9 20.0 1.0
C1' C:DC6 5.0 24.7 1.0

Fluorine binding site 2 out of 4 in 4k4i

Go back to Fluorine Binding Sites List in 4k4i
Fluorine binding site 2 out of 4 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F601

b:40.2
occ:1.00
FAJ E:1RY601 0.0 40.2 1.0
CAU E:1RY601 1.3 35.1 1.0
CAK E:1RY601 2.4 34.7 1.0
CAT E:1RY601 2.4 34.4 1.0
NAA E:1RY601 2.7 34.0 1.0
O E:HOH733 2.9 46.6 1.0
C6 G:DC6 3.5 31.2 1.0
NAY E:1RY601 3.6 33.0 1.0
NAN E:1RY601 3.6 30.2 1.0
OAH E:1RY601 3.6 36.8 1.0
O E:HOH761 3.7 34.1 1.0
C5 G:DC6 3.8 29.8 1.0
C2' G:DC6 3.8 32.8 1.0
CAV E:1RY601 4.0 32.3 1.0
N1 G:DC6 4.1 31.3 1.0
CB E:ALA510 4.3 36.0 1.0
OAO E:1RY601 4.4 36.3 1.0
C1' G:DC6 4.6 31.8 1.0
C4 G:DC6 4.7 31.3 1.0
PBA E:1RY601 4.8 35.9 1.0
CAX E:1RY601 4.8 30.4 1.0
OAP E:1RY601 4.9 32.4 1.0
C2 G:DC6 4.9 29.7 1.0
O5' G:DC6 5.0 29.9 1.0
C3' G:DC6 5.0 32.8 1.0

Fluorine binding site 3 out of 4 in 4k4i

Go back to Fluorine Binding Sites List in 4k4i
Fluorine binding site 3 out of 4 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F601

b:59.5
occ:1.00
FAJ I:1RY601 0.0 59.5 1.0
CAU I:1RY601 1.3 62.1 1.0
CAK I:1RY601 2.3 58.5 1.0
CAT I:1RY601 2.4 66.5 1.0
NAA I:1RY601 2.9 66.3 1.0
C5 K:DC6 3.3 26.3 1.0
NAY I:1RY601 3.6 52.8 1.0
NAN I:1RY601 3.7 65.2 1.0
C6 K:DC6 3.8 25.2 1.0
C4 K:DC6 4.0 24.7 1.0
CAV I:1RY601 4.1 58.0 1.0
N4 K:DC6 4.2 22.8 1.0
CB I:ALA510 4.4 26.6 1.0
OAD I:1RY601 4.7 48.7 1.0
CAX I:1RY601 4.7 44.7 1.0
OAP I:1RY601 4.9 41.6 1.0
N1 K:DC6 4.9 24.0 1.0

Fluorine binding site 4 out of 4 in 4k4i

Go back to Fluorine Binding Sites List in 4k4i
Fluorine binding site 4 out of 4 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:F601

b:34.2
occ:1.00
FAJ M:1RY601 0.0 34.2 1.0
CAU M:1RY601 1.3 30.5 1.0
CAK M:1RY601 2.4 27.8 1.0
CAT M:1RY601 2.4 33.2 1.0
NAA M:1RY601 2.8 32.8 1.0
C5 O:DC6 3.1 26.4 1.0
N4 O:DC6 3.4 28.7 1.0
C4 O:DC6 3.4 29.1 1.0
NAY M:1RY601 3.6 29.1 1.0
NAN M:1RY601 3.6 32.6 1.0
C6 O:DC6 4.0 27.3 1.0
CAV M:1RY601 4.0 27.6 1.0
N3 O:DC6 4.4 28.1 1.0
NH1 M:ARG514 4.6 27.1 1.0
CAX M:1RY601 4.8 29.0 1.0
N1 O:DC6 4.8 25.3 1.0
CB M:ALA510 4.8 17.7 1.0
CAM M:1RY601 5.0 30.3 1.0

Reference:

R.Vyas, W.J.Zahurancik, Z.Suo. Structural Basis For the Binding and Incorporation of Nucleotide Analogs with L-Stereochemistry By Human Dna Polymerase Lambda. Proc.Natl.Acad.Sci.Usa V. 111 E3033 2014.
ISSN: ISSN 0027-8424
PubMed: 25015085
DOI: 10.1073/PNAS.1401286111
Page generated: Thu Aug 1 03:05:31 2024

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