Atomistry » Fluorine » PDB 4jq2-4kbi » 4k4i
Atomistry »
  Fluorine »
    PDB 4jq2-4kbi »
      4k4i »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy