Fluorine in PDB 2xzl: UPF1-Rna Complex

All present enzymatic activity of UPF1-Rna Complex:
3.6.4.13;

The structure of UPF1-Rna Complex, PDB code: 2xzl was solved by S.Chakrabarti, U.Jayachandran, F.Bonneau, F.Fiorini, C.Basquin, S.Domcke, H.Le Hir, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.882 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.135, 114.117, 65.730, 90.00, 110.24, 90.00
R / Rfree (%)	19.74 / 24.31

The structure of UPF1-Rna Complex also contains other interesting chemical elements:

Zinc	(Zn)	3 atoms
Aluminium	(Al)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Fluorine atom in the UPF1-Rna Complex (pdb code 2xzl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the UPF1-Rna Complex, PDB code: 2xzl:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the UPF1-Rna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of UPF1-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1855 b:7.8 occ:1.00 F1 A:ALF1855 0.0 7.8 1.0 AL A:ALF1855 1.8 8.6 1.0 F2 A:ALF1855 2.5 9.6 1.0 F3 A:ALF1855 2.5 10.3 1.0 NH1 A:ARG639 2.7 5.8 1.0 NH2 A:ARG801 2.8 6.3 1.0 O1B A:ADP1854 2.9 8.6 1.0 CA A:PRO432 3.0 5.5 1.0 CB A:PRO432 3.1 4.8 1.0 N A:GLY433 3.1 5.5 1.0 O A:HOH2051 3.2 4.5 1.0 NH1 A:ARG801 3.4 6.7 1.0 C A:PRO432 3.5 6.2 1.0 NH2 A:ARG639 3.5 9.1 1.0 CZ A:ARG801 3.5 6.9 1.0 CZ A:ARG639 3.6 9.8 1.0 F4 A:ALF1855 3.6 9.5 1.0 NE2 A:GLN601 3.9 5.5 1.0 OE1 A:GLN601 4.0 7.6 1.0 CG A:PRO432 4.2 4.0 1.0 CA A:GLY433 4.2 7.3 1.0 CD A:GLN601 4.3 10.0 1.0 N A:PRO432 4.3 6.8 1.0 PB A:ADP1854 4.4 6.8 1.0 O A:THR800 4.6 8.2 1.0 O A:PRO432 4.7 5.3 1.0 OG1 A:THR800 4.7 6.8 1.0 NZ A:LYS436 4.8 6.7 1.0 NE A:ARG801 4.8 5.4 1.0 NE A:ARG639 4.8 6.1 1.0 O3B A:ADP1854 4.9 9.9 1.0

Fluorine binding site 2 out of 4 in the UPF1-Rna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of UPF1-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1855 b:9.6 occ:1.00 F2 A:ALF1855 0.0 9.6 1.0 AL A:ALF1855 1.8 8.6 1.0 F1 A:ALF1855 2.5 7.8 1.0 F4 A:ALF1855 2.5 9.5 1.0 NH2 A:ARG639 2.7 9.1 1.0 O1B A:ADP1854 2.8 8.6 1.0 NH1 A:ARG801 2.9 6.7 1.0 O A:HOH2051 2.9 4.5 1.0 CA A:GLY767 3.1 8.3 1.0 C A:GLY767 3.4 10.1 1.0 O A:HOH2090 3.4 5.5 1.0 NH1 A:ARG639 3.5 5.8 1.0 CZ A:ARG639 3.5 9.8 1.0 N A:GLY767 3.5 8.4 1.0 F3 A:ALF1855 3.6 10.3 1.0 O A:GLY767 3.6 9.1 1.0 MG A:MG1856 3.7 12.6 1.0 CZ A:ARG801 3.9 6.9 1.0 NH2 A:ARG801 4.0 6.3 1.0 N A:ARG768 4.1 9.7 1.0 PB A:ADP1854 4.1 6.8 1.0 O1A A:ADP1854 4.3 6.3 1.0 O A:HOH2074 4.3 18.4 1.0 O2B A:ADP1854 4.4 10.2 1.0 O A:ARG768 4.4 11.5 1.0 NE A:ARG639 4.7 6.1 1.0 N A:GLY433 4.7 5.5 1.0 O3A A:ADP1854 4.8 14.8 1.0 O A:HOH2038 4.8 13.7 1.0 C A:GLN766 4.8 10.2 1.0 C A:ARG768 4.9 12.4 1.0 O A:HOH2073 5.0 20.9 1.0 CA A:ARG768 5.0 8.5 1.0

Fluorine binding site 3 out of 4 in the UPF1-Rna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of UPF1-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1855 b:10.3 occ:1.00 F3 A:ALF1855 0.0 10.3 1.0 AL A:ALF1855 1.8 8.6 1.0 F4 A:ALF1855 2.5 9.5 1.0 F1 A:ALF1855 2.5 7.8 1.0 NZ A:LYS436 2.7 6.7 1.0 O1B A:ADP1854 2.8 8.6 1.0 NE2 A:GLN601 2.8 5.5 1.0 O A:HOH2051 2.9 4.5 1.0 CE A:LYS436 3.4 8.3 1.0 CA A:PRO432 3.5 5.5 1.0 F2 A:ALF1855 3.6 9.6 1.0 CD A:GLN601 3.6 10.0 1.0 OE1 A:GLN601 3.6 7.6 1.0 O A:HOH2025 3.6 21.4 1.0 PB A:ADP1854 3.8 6.8 1.0 O3B A:ADP1854 3.8 9.9 1.0 N A:GLY433 3.9 5.5 1.0 O A:PRO431 4.2 5.9 1.0 N A:PRO432 4.2 6.8 1.0 C A:PRO432 4.3 6.2 1.0 O A:HOH2047 4.3 20.1 1.0 CB A:PRO432 4.3 4.8 1.0 O2B A:ADP1854 4.3 10.2 1.0 C A:PRO431 4.5 6.6 1.0 MG A:MG1856 4.5 12.6 1.0 O A:HOH2073 4.7 20.9 1.0 NH2 A:ARG801 4.7 6.3 1.0 O A:GLY430 4.8 12.3 1.0 CG A:PRO432 4.8 4.0 1.0 CD A:LYS436 4.9 6.7 1.0

Fluorine binding site 4 out of 4 in the UPF1-Rna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of UPF1-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1855 b:9.5 occ:1.00 F4 A:ALF1855 0.0 9.5 1.0 AL A:ALF1855 1.8 8.6 1.0 MG A:MG1856 2.3 12.6 1.0 O A:HOH2051 2.5 4.5 1.0 F3 A:ALF1855 2.5 10.3 1.0 F2 A:ALF1855 2.5 9.6 1.0 O1B A:ADP1854 2.8 8.6 1.0 O A:HOH2047 3.1 20.1 1.0 O A:HOH2025 3.3 21.4 1.0 O2B A:ADP1854 3.3 10.2 1.0 O A:HOH2073 3.3 20.9 1.0 O A:HOH2038 3.5 13.7 1.0 F1 A:ALF1855 3.6 7.8 1.0 PB A:ADP1854 3.6 6.8 1.0 CA A:GLY767 3.6 8.3 1.0 O A:HOH2090 3.8 5.5 1.0 N A:GLY767 4.2 8.4 1.0 NZ A:LYS436 4.3 6.7 1.0 CE A:LYS436 4.3 8.3 1.0 O3B A:ADP1854 4.3 9.9 1.0 C A:GLY767 4.5 10.1 1.0 OG1 A:THR437 4.6 18.0 1.0 O A:GLY767 4.7 9.1 1.0 OE1 A:GLN601 4.7 7.6 1.0 NH2 A:ARG639 4.8 9.1 1.0 O3A A:ADP1854 4.9 14.8 1.0 NE2 A:GLN601 4.9 5.5 1.0 O1A A:ADP1854 4.9 6.3 1.0

S.Chakrabarti, U.Jayachandran, F.Bonneau, F.Fiorini, C.Basquin, S.Domcke, H.Le Hir, E.Conti. Molecular Mechanisms For the Rna-Dependent Atpase Activity of UPF1 and Its Regulation By UPF2. Mol.Cell V. 41 693 2011.
ISSN: ISSN 1097-2765
PubMed: 21419344
DOI: 10.1016/J.MOLCEL.2011.02.010