Fluorine in PDB 7oyf: Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate

The structure of Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate, PDB code: 7oyf was solved by H.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.65 / 1.88
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.334, 106.334, 107.384, 90, 90, 120
R / Rfree (%)	15.9 / 18.8

The structure of Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate (pdb code 7oyf). 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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate, PDB code: 7oyf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate


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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:F617 b:27.2 occ:1.00 F1 A:KQB617 0.0 27.2 1.0 MG A:MG601 1.9 25.6 1.0 MG1 A:KQB617 1.9 29.2 1.0 MG A:MG602 1.9 26.0 1.0 O3B A:ADP604 2.5 28.1 1.0 OE1 B:GLU71 2.6 28.5 1.0 O1 A:KQB617 2.8 31.5 1.0 OH A:TYR92 2.8 27.9 1.0 OE2 A:GLU99 2.8 22.4 1.0 O A:HOH905 2.8 28.9 1.0 OE1 A:GLU99 2.8 20.8 1.0 OD2 A:ASP94 2.9 27.9 1.0 OE1 A:GLU8 2.9 23.6 1.0 F2 A:KQB617 2.9 29.8 1.0 CD A:GLU99 3.2 26.3 1.0 CG A:ASP94 3.8 36.5 1.0 MG A:MG603 3.8 23.6 0.5 F3 A:KQB617 3.8 36.8 1.0 CD B:GLU71 3.8 29.9 1.0 O2A A:ADP604 3.9 26.2 1.0 PB A:ADP604 3.9 34.5 1.0 OE2 A:GLU10 4.0 28.1 1.0 CZ A:TYR92 4.0 27.0 1.0 O A:HOH716 4.1 32.5 1.0 CD A:GLU8 4.1 33.4 1.0 O2B A:ADP604 4.4 35.8 1.0 OD1 A:ASP94 4.4 41.8 1.0 OE2 B:GLU71 4.5 31.9 1.0 ND1 A:HIS155 4.5 24.9 1.0 CE1 A:HIS155 4.5 27.2 1.0 CB A:ASP94 4.6 27.7 1.0 O3A A:ADP604 4.7 27.3 1.0 CG A:GLU99 4.7 24.1 1.0 CE1 A:TYR92 4.8 25.1 1.0 OE2 A:GLU8 4.8 27.6 1.0 CE2 A:TYR92 4.8 31.3 1.0 CG B:GLU71 4.9 25.8 1.0 PA A:ADP604 4.9 28.2 1.0 O A:HOH702 4.9 45.2 1.0 O1B A:ADP604 5.0 36.2 1.0 CD A:GLU10 5.0 27.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate


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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:F617 b:29.8 occ:1.00 F2 A:KQB617 0.0 29.8 1.0 MG A:MG603 1.7 23.6 0.5 MG1 A:KQB617 1.9 29.2 1.0 F3 A:KQB617 2.7 36.8 1.0 ND1 A:HIS155 2.8 24.9 1.0 O2B A:ADP604 2.9 35.8 1.0 F1 A:KQB617 2.9 27.2 1.0 CE1 A:HIS155 2.9 27.2 1.0 OE1 B:GLU71 2.9 28.5 1.0 O3B A:ADP604 3.0 28.1 1.0 OE1 A:GLU8 3.1 23.6 1.0 NE2 A:HIS241 3.1 30.5 1.0 CE1 A:HIS241 3.3 25.0 1.0 O A:HOH786 3.4 37.2 1.0 OE2 B:GLU71 3.4 31.9 1.0 PB A:ADP604 3.5 34.5 1.0 CD B:GLU71 3.5 29.9 1.0 O A:HOH905 3.7 28.9 1.0 MG A:MG601 3.7 25.6 1.0 OE2 A:GLU8 3.8 27.6 1.0 CD A:GLU8 3.9 33.4 1.0 O1 A:KQB617 4.0 31.5 1.0 MG A:MG602 4.0 26.0 1.0 CG A:HIS155 4.1 25.4 1.0 NE2 A:HIS155 4.2 26.9 1.0 CD2 A:HIS241 4.4 23.4 1.0 O1B A:ADP604 4.5 36.2 1.0 ND1 A:HIS241 4.6 28.2 1.0 O3A A:ADP604 4.7 27.3 1.0 CG B:GLU71 4.8 25.8 1.0 CD2 A:HIS155 4.9 22.6 1.0 CB A:HIS155 5.0 23.8 1.0 CB B:GLU71 5.0 25.5 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate


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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:F617 b:36.8 occ:1.00 F3 A:KQB617 0.0 36.8 1.0 MG1 A:KQB617 1.9 29.2 1.0 O1 A:KQB617 2.7 31.5 1.0 F2 A:KQB617 2.7 29.8 1.0 O A:HOH786 2.8 37.2 1.0 OE2 B:GLU71 3.1 31.9 1.0 O3B A:ADP604 3.2 28.1 1.0 OE1 B:GLU71 3.4 28.5 1.0 PB A:ADP604 3.5 34.5 1.0 O2B A:ADP604 3.6 35.8 1.0 O1B A:ADP604 3.6 36.2 1.0 O A:HOH785 3.6 39.9 1.0 CD B:GLU71 3.7 29.9 1.0 F1 A:KQB617 3.8 27.2 1.0 NH1 A:ARG227 3.8 30.5 1.0 O A:HOH716 4.1 32.5 1.0 MG A:MG603 4.1 23.6 0.5 O A:HOH702 4.4 45.2 1.0 MG A:MG601 4.7 25.6 1.0 O A:HOH853 4.7 40.1 1.0 CE1 A:HIS241 4.8 25.0 1.0

H.Cui, A.U.Muller, M.Leibundgut, J.Tian, N.Ban, E.Weber-Ban. Structures of Prokaryotic Ubiquitin-Like Protein Pup in Complex with Depupylase Dop Reveal the Mechanism of Catalytic Phosphate Formation. Nat Commun V. 12 6635 2021.
ISSN: ESSN 2041-1723
PubMed: 34789727
DOI: 10.1038/S41467-021-26848-X