Fluorine in PDB 2xzo: UPF1 Helicase - Rna Complex

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

The structure of UPF1 Helicase - Rna Complex, PDB code: 2xzo 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)	49.18 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.066, 101.896, 112.320, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.3

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

Aluminium	(Al)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the UPF1 Helicase - Rna Complex (pdb code 2xzo). 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 Helicase - Rna Complex, PDB code: 2xzo:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the UPF1 Helicase - 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 Helicase - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1005 b:24.1 occ:1.00 F1 A:ALF1005 0.0 24.1 1.0 AL A:ALF1005 1.8 20.2 1.0 F2 A:ALF1005 2.5 24.9 1.0 F3 A:ALF1005 2.6 22.6 1.0 O1B A:ADP1004 2.6 26.9 1.0 NH1 A:ARG703 2.8 23.7 1.0 CA A:PRO494 2.9 24.6 1.0 N A:GLY495 3.0 25.3 1.0 NH2 A:ARG865 3.0 24.4 1.0 O A:HOH1104 3.0 25.4 1.0 CB A:PRO494 3.1 22.9 1.0 C A:PRO494 3.4 24.8 1.0 F4 A:ALF1005 3.5 27.9 1.0 NH2 A:ARG703 3.6 27.4 1.0 CZ A:ARG703 3.6 30.7 1.0 NH1 A:ARG865 3.7 24.6 1.0 CZ A:ARG865 3.8 27.4 1.0 NE2 A:GLN665 3.9 24.1 1.0 OE1 A:GLN665 4.1 22.6 1.0 PB A:ADP1004 4.1 21.3 1.0 CA A:GLY495 4.1 20.1 1.0 CG A:PRO494 4.1 22.3 1.0 N A:PRO494 4.2 29.0 1.0 CD A:GLN665 4.4 24.9 1.0 O3B A:ADP1004 4.5 23.1 1.0 O A:PRO494 4.5 20.7 1.0 NZ A:LYS498 4.7 19.1 1.0 O A:THR864 4.7 30.1 1.0 O3A A:ADP1004 4.7 27.0 1.0 NE A:ARG703 4.9 25.9 1.0 O A:PRO493 4.9 20.3 1.0 CD A:PRO494 4.9 23.3 1.0 OG1 A:THR864 4.9 25.1 1.0 C A:PRO493 5.0 20.9 1.0

Fluorine binding site 2 out of 4 in the UPF1 Helicase - 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 Helicase - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1005 b:24.9 occ:1.00 F2 A:ALF1005 0.0 24.9 1.0 AL A:ALF1005 1.8 20.2 1.0 F4 A:ALF1005 2.5 27.9 1.0 F1 A:ALF1005 2.5 24.1 1.0 O1B A:ADP1004 2.6 26.9 1.0 NH2 A:ARG703 2.7 27.4 1.0 O A:HOH1104 2.8 25.4 1.0 NH1 A:ARG865 2.9 24.6 1.0 CA A:GLY831 3.2 23.9 1.0 O A:HOH1119 3.3 20.1 1.0 NH1 A:ARG703 3.4 23.7 1.0 CZ A:ARG703 3.4 30.7 1.0 C A:GLY831 3.5 29.2 1.0 O A:GLY831 3.5 26.2 1.0 F3 A:ALF1005 3.6 22.6 1.0 N A:GLY831 3.6 30.6 1.0 MG A:MG1006 3.8 23.3 1.0 CZ A:ARG865 3.8 27.4 1.0 NH2 A:ARG865 3.8 24.4 1.0 PB A:ADP1004 3.9 21.3 1.0 N A:ARG832 4.2 26.6 1.0 O1A A:ADP1004 4.4 24.4 1.0 O A:HOH1195 4.4 26.3 1.0 O2B A:ADP1004 4.4 21.6 1.0 O3A A:ADP1004 4.5 27.0 1.0 O A:ARG832 4.6 29.6 1.0 OE2 A:GLU637 4.7 36.2 1.0 N A:GLY495 4.7 25.3 1.0 NE A:ARG703 4.7 25.9 1.0 C A:GLN830 4.9 33.1 1.0

Fluorine binding site 3 out of 4 in the UPF1 Helicase - 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 Helicase - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1005 b:22.6 occ:1.00 F3 A:ALF1005 0.0 22.6 1.0 AL A:ALF1005 1.8 20.2 1.0 F4 A:ALF1005 2.5 27.9 1.0 F1 A:ALF1005 2.6 24.1 1.0 O1B A:ADP1004 2.6 26.9 1.0 O A:HOH1104 2.7 25.4 1.0 NZ A:LYS498 2.8 19.1 1.0 NE2 A:GLN665 2.8 24.1 1.0 CE A:LYS498 3.4 24.7 1.0 F2 A:ALF1005 3.6 24.9 1.0 CD A:GLN665 3.7 24.9 1.0 OE1 A:GLN665 3.7 22.6 1.0 PB A:ADP1004 3.7 21.3 1.0 O3B A:ADP1004 3.7 23.1 1.0 CA A:PRO494 3.7 24.6 1.0 MG A:MG1006 3.9 23.3 1.0 OE1 A:GLU637 4.0 47.0 1.0 N A:GLY495 4.1 25.3 1.0 O2B A:ADP1004 4.3 21.6 1.0 O A:PRO493 4.3 20.3 1.0 O A:HOH1106 4.4 30.2 1.0 OE2 A:GLU637 4.5 36.2 1.0 N A:PRO494 4.5 29.0 1.0 C A:PRO494 4.5 24.8 1.0 CB A:PRO494 4.5 22.9 1.0 CD A:GLU637 4.6 47.5 1.0 C A:PRO493 4.7 20.9 1.0 O A:GLY492 4.8 22.4 1.0 NH2 A:ARG865 4.9 24.4 1.0 CD A:LYS498 4.9 25.1 1.0 CG A:PRO494 5.0 22.3 1.0 O3A A:ADP1004 5.0 27.0 1.0

Fluorine binding site 4 out of 4 in the UPF1 Helicase - 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 Helicase - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1005 b:27.9 occ:1.00 F4 A:ALF1005 0.0 27.9 1.0 AL A:ALF1005 1.8 20.2 1.0 MG A:MG1006 2.1 23.3 1.0 O A:HOH1104 2.4 25.4 1.0 F2 A:ALF1005 2.5 24.9 1.0 F3 A:ALF1005 2.5 22.6 1.0 O1B A:ADP1004 2.6 26.9 1.0 O A:HOH1195 2.8 26.3 1.0 OE2 A:GLU637 3.0 36.2 1.0 O A:HOH1119 3.3 20.1 1.0 O A:HOH1106 3.4 30.2 1.0 CD A:GLU637 3.4 47.5 1.0 OE1 A:GLU637 3.4 47.0 1.0 CA A:GLY831 3.5 23.9 1.0 F1 A:ALF1005 3.5 24.1 1.0 O2B A:ADP1004 3.5 21.6 1.0 PB A:ADP1004 3.6 21.3 1.0 N A:GLY831 4.0 30.6 1.0 OG1 A:THR499 4.3 24.1 1.0 C A:GLY831 4.4 29.2 1.0 CG A:GLU637 4.4 36.0 1.0 O3B A:ADP1004 4.5 23.1 1.0 O A:GLY831 4.5 26.2 1.0 OE1 A:GLN665 4.6 22.6 1.0 NZ A:LYS498 4.7 19.1 1.0 CE A:LYS498 4.7 24.7 1.0 NE2 A:GLN665 4.8 24.1 1.0 NH2 A:ARG703 4.8 27.4 1.0 O3A A:ADP1004 4.8 27.0 1.0 NH1 A:ARG865 4.9 24.6 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