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Fluorine in PDB 4b3o: Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface

Enzymatic activity of Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface

All present enzymatic activity of Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13; 3.4.23.16;

Protein crystallography data

The structure of Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface, PDB code: 4b3o was solved by M.Lapkouski, L.Tian, J.T.Miller, S.F.J.Le Grice, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.73 / 3.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.598, 164.598, 129.030, 90.00, 90.00, 120.00
R / Rfree (%) 27.5 / 29.5

Other elements in 4b3o:

The structure of Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface (pdb code 4b3o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface, PDB code: 4b3o:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4b3o

Go back to Fluorine Binding Sites List in 4b3o
Fluorine binding site 1 out of 3 in the Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1557

b:69.1
occ:1.00
F1 A:EFZ1557 0.0 69.1 1.0
C13 A:EFZ1557 1.3 71.3 1.0
F2 A:EFZ1557 2.1 73.2 1.0
F3 A:EFZ1557 2.1 68.3 1.0
C7 A:EFZ1557 2.2 77.7 1.0
C6 A:EFZ1557 2.3 69.0 1.0
C5 A:EFZ1557 2.3 67.4 1.0
O2 A:EFZ1557 3.1 77.7 1.0
C8 A:EFZ1557 3.2 81.9 1.0
C1 A:EFZ1557 3.3 68.2 1.0
CG1 A:VAL106 3.3 72.4 1.0
C9 A:EFZ1557 3.4 78.1 1.0
C4 A:EFZ1557 3.4 77.4 1.0
N A:GLY190 3.8 56.2 1.0
C A:VAL189 3.9 53.2 1.0
CA A:GLY190 4.0 61.1 1.0
N A:EFZ1557 4.1 71.6 1.0
O A:VAL189 4.1 55.4 1.0
C14 A:EFZ1557 4.1 74.3 1.0
C2 A:EFZ1557 4.2 69.2 1.0
C3 A:EFZ1557 4.2 73.3 1.0
CB A:TYR188 4.2 57.5 1.0
C A:TYR188 4.3 59.1 1.0
N A:VAL189 4.4 55.5 1.0
O A:TYR188 4.4 60.8 1.0
CL A:EFZ1557 4.4 64.7 1.0
CB A:VAL106 4.5 59.1 1.0
CG2 A:VAL106 4.5 60.4 1.0
CA A:VAL189 4.6 55.5 1.0
C10 A:EFZ1557 4.7 67.4 1.0
CA A:TYR188 4.8 52.5 1.0
O A:VAL179 5.0 67.4 1.0

Fluorine binding site 2 out of 3 in 4b3o

Go back to Fluorine Binding Sites List in 4b3o
Fluorine binding site 2 out of 3 in the Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1557

b:73.2
occ:1.00
F2 A:EFZ1557 0.0 73.2 1.0
C13 A:EFZ1557 1.3 71.3 1.0
F3 A:EFZ1557 2.1 68.3 1.0
F1 A:EFZ1557 2.1 69.1 1.0
C7 A:EFZ1557 2.2 77.7 1.0
C9 A:EFZ1557 2.3 78.1 1.0
C8 A:EFZ1557 2.3 81.9 1.0
CB A:TYR188 3.0 57.5 1.0
O2 A:EFZ1557 3.1 77.7 1.0
O A:TYR188 3.2 60.8 1.0
C10 A:EFZ1557 3.2 67.4 1.0
C6 A:EFZ1557 3.3 69.0 1.0
C A:TYR188 3.4 59.1 1.0
C5 A:EFZ1557 3.5 67.4 1.0
CA A:TYR188 3.8 52.5 1.0
CB A:TYR181 3.9 67.0 1.0
CG A:TYR188 4.1 50.5 1.0
N A:VAL189 4.1 55.5 1.0
C12 A:EFZ1557 4.3 61.3 1.0
C14 A:EFZ1557 4.3 74.3 1.0
N A:TYR181 4.4 64.4 1.0
C1 A:EFZ1557 4.4 68.2 1.0
C11 A:EFZ1557 4.6 59.7 1.0
CD2 A:TYR188 4.6 59.9 1.0
CA A:VAL189 4.7 55.5 1.0
C A:VAL189 4.7 53.2 1.0
N A:GLY190 4.7 56.2 1.0
O A:VAL179 4.7 67.4 1.0
CG A:TYR181 4.8 78.9 1.0
CA A:TYR181 4.8 62.5 1.0
C4 A:EFZ1557 4.8 77.4 1.0
CD2 A:TYR181 4.9 78.6 1.0
N A:EFZ1557 4.9 71.6 1.0
N A:TYR188 4.9 54.1 1.0

Fluorine binding site 3 out of 3 in 4b3o

Go back to Fluorine Binding Sites List in 4b3o
Fluorine binding site 3 out of 3 in the Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structures of Hiv-1 Rt and Rna-Dna Complex Reveal A Unique Rt Conformation and Substrate Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1557

b:68.3
occ:1.00
F3 A:EFZ1557 0.0 68.3 1.0
C13 A:EFZ1557 1.3 71.3 1.0
F2 A:EFZ1557 2.1 73.2 1.0
F1 A:EFZ1557 2.1 69.1 1.0
C7 A:EFZ1557 2.3 77.7 1.0
O2 A:EFZ1557 2.3 77.7 1.0
O A:VAL179 3.2 67.4 1.0
C8 A:EFZ1557 3.3 81.9 1.0
N A:GLY190 3.3 56.2 1.0
C6 A:EFZ1557 3.3 69.0 1.0
C14 A:EFZ1557 3.6 74.3 1.0
O A:TYR188 3.7 60.8 1.0
CA A:GLY190 3.7 61.1 1.0
C A:VAL189 3.8 53.2 1.0
C A:VAL179 4.0 62.5 1.0
C9 A:EFZ1557 4.0 78.1 1.0
C1 A:EFZ1557 4.0 68.2 1.0
C5 A:EFZ1557 4.0 67.4 1.0
N A:EFZ1557 4.1 71.6 1.0
C A:TYR188 4.1 59.1 1.0
CG1 A:VAL179 4.2 76.2 1.0
CA A:VAL189 4.2 55.5 1.0
CB A:VAL179 4.2 69.6 1.0
O1 A:EFZ1557 4.3 69.9 1.0
N A:VAL189 4.4 55.5 1.0
O A:GLY190 4.5 68.0 1.0
O A:VAL189 4.6 55.4 1.0
C A:GLY190 4.6 66.0 1.0
CB A:TYR188 4.7 57.5 1.0
N A:TYR181 4.7 64.4 1.0
CA A:VAL179 4.7 70.2 1.0
N A:ILE180 4.8 64.0 1.0
CA A:ILE180 4.9 60.8 1.0
CB A:TYR181 4.9 67.0 1.0

Reference:

M.Lapkouski, L.Tian, J.T.Miller, S.F.J.Le Grice, W.Yang. Complexes of Hiv-1 Rt, Nnrti and Rna/Dna Hybrid Reveal A Structure Compatible with Rna Degradation Nat.Struct.Mol.Biol. V. 20 230 2013.
ISSN: ISSN 1545-9993
PubMed: 23314251
DOI: 10.1038/NSMB.2485
Page generated: Thu Aug 1 00:06:39 2024

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