Fluorine in PDB 6zm2: Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna

The structure of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna, PDB code: 6zm2 was solved by F.Hamann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.78 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.66, 100.41, 140.95, 90, 90, 90
R / Rfree (%)	18.5 / 23.3

The structure of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna (pdb code 6zm2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna, PDB code: 6zm2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:32.7 occ:1.00 F1 A:BEF1101 0.0 32.7 1.0 BE A:BEF1101 1.5 30.8 1.0 F2 A:BEF1101 2.4 32.8 1.0 F3 A:BEF1101 2.5 33.9 1.0 O3B A:ADP1102 2.5 33.0 1.0 NH2 A:ARG628 2.7 30.1 1.0 NH2 A:ARG625 2.8 30.4 1.0 NH1 A:ARG625 3.1 26.1 1.0 O A:HOH1233 3.1 28.5 1.0 NH1 A:ARG628 3.2 27.0 1.0 CZ A:ARG628 3.3 30.3 1.0 CB A:THR322 3.3 33.3 1.0 CZ A:ARG625 3.4 30.9 1.0 CA A:THR322 3.4 33.5 1.0 N A:GLY323 3.5 31.9 1.0 CG2 A:THR322 3.6 29.1 1.0 C A:THR322 3.9 31.0 1.0 PB A:ADP1102 4.0 33.7 1.0 MG A:MG1103 4.5 34.2 1.0 N A:SER578 4.5 28.2 1.0 O A:GLY624 4.5 34.6 1.0 OE1 A:GLN621 4.5 30.1 1.0 NE A:ARG628 4.6 31.9 1.0 OG1 A:THR322 4.6 32.7 1.0 CA A:GLY323 4.6 28.7 1.0 O2B A:ADP1102 4.7 34.5 1.0 NE A:ARG625 4.7 33.3 1.0 CA A:SER578 4.7 26.9 1.0 O3A A:ADP1102 4.8 34.2 1.0 O A:HOH1242 4.8 29.2 1.0 N A:THR322 4.8 35.9 1.0 O A:HOH1213 4.8 29.6 1.0 O A:SER578 4.8 28.8 1.0 C A:SER578 4.8 29.2 1.0 O1B A:ADP1102 4.9 29.3 1.0 NZ A:LYS326 4.9 26.3 1.0 OE2 A:GLU419 5.0 30.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:32.8 occ:1.00 F2 A:BEF1101 0.0 32.8 1.0 BE A:BEF1101 1.5 30.8 1.0 MG A:MG1103 2.2 34.2 1.0 F1 A:BEF1101 2.4 32.7 1.0 F3 A:BEF1101 2.5 33.9 1.0 O3B A:ADP1102 2.6 33.0 1.0 O A:HOH1233 2.8 28.5 1.0 O A:HOH1255 3.0 26.8 1.0 O A:HOH1213 3.1 29.6 1.0 OE2 A:GLU419 3.1 30.9 1.0 O A:HOH1211 3.2 28.2 1.0 O2B A:ADP1102 3.2 34.5 1.0 PB A:ADP1102 3.4 33.7 1.0 CA A:SER578 3.6 26.9 1.0 N A:SER578 3.8 28.2 1.0 NH1 A:ARG628 4.1 27.0 1.0 O A:SER578 4.1 28.8 1.0 C A:SER578 4.2 29.2 1.0 O A:HOH1242 4.2 29.2 1.0 CD A:GLU419 4.2 34.6 1.0 OG1 A:THR327 4.3 29.2 1.0 NH1 A:ARG625 4.3 26.1 1.0 NH2 A:ARG625 4.4 30.4 1.0 NZ A:LYS326 4.5 26.3 1.0 O1B A:ADP1102 4.5 29.3 1.0 O2A A:ADP1102 4.5 34.5 1.0 O3A A:ADP1102 4.6 34.2 1.0 CB A:SER578 4.7 29.1 1.0 OE1 A:GLU419 4.7 30.0 1.0 NH2 A:ARG628 4.7 30.1 1.0 OG A:SER578 4.8 29.9 1.0 CZ A:ARG625 4.8 30.9 1.0 CZ A:ARG628 4.9 30.3 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Deah-Box Atpase PRP2 in Complex with Adp-BEF3 and Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:33.9 occ:1.00 F3 A:BEF1101 0.0 33.9 1.0 BE A:BEF1101 1.5 30.8 1.0 F2 A:BEF1101 2.5 32.8 1.0 F1 A:BEF1101 2.5 32.7 1.0 O3B A:ADP1102 2.6 33.0 1.0 NZ A:LYS326 2.7 26.3 1.0 O A:HOH1242 2.9 29.2 1.0 CA A:THR322 3.3 33.5 1.0 O A:HOH1233 3.4 28.5 1.0 PB A:ADP1102 3.5 33.7 1.0 O A:HOH1255 3.5 26.8 1.0 CE A:LYS326 3.6 27.2 1.0 CG2 A:THR322 3.7 29.1 1.0 CB A:THR322 3.8 33.3 1.0 O1B A:ADP1102 3.8 29.3 1.0 MG A:MG1103 3.9 34.2 1.0 CB A:ALA451 4.0 27.3 1.0 O2B A:ADP1102 4.0 34.5 1.0 N A:GLY323 4.0 31.9 1.0 N A:THR322 4.1 35.9 1.0 OE2 A:GLU419 4.1 30.9 1.0 O A:GLU321 4.1 30.6 1.0 C A:THR322 4.2 31.0 1.0 C A:GLU321 4.4 32.5 1.0 NH2 A:ARG625 4.5 30.4 1.0 OE1 A:GLN621 4.6 30.1 1.0 N A:ALA451 4.7 32.6 1.0 O A:GLY320 4.7 34.1 1.0 OE1 A:GLU419 4.8 30.0 1.0 NH2 A:ARG628 4.9 30.1 1.0 CD A:GLU419 4.9 34.6 1.0 O3A A:ADP1102 4.9 34.2 1.0 NH1 A:ARG628 5.0 27.0 1.0 CA A:ALA451 5.0 34.6 1.0

F.Hamann, L.C.Zimmerningkat, R.A.Becker, T.B.Garbers, P.Neumann, J.S.Hub, R.Ficner. The Structure of PRP2 Bound to Rna and Adp-Bef 3 - Reveals Structural Features Important For Rna Unwinding By Deah-Box Atpases. Acta Crystallogr D Struct V. 77 496 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 33825710
DOI: 10.1107/S2059798321001194