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

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

Resolution Low / High (Å)	47.87 / 1.75
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.827, 106.827, 107.947, 90, 90, 120
R / Rfree (%)	16.2 / 18.5

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

Magnesium

(Mg)

6 atoms

The binding sites of Fluorine atom in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate (pdb code 7oyh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate, PDB code: 7oyh:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


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/Tetrafluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:F627 b:26.3 occ:0.73 F1 A:MF4627 0.0 26.3 0.7 MG A:MF4627 1.8 24.9 0.7 O1B A:ADP605 2.4 25.3 1.0 O A:HOH719 2.7 28.5 1.0 F2 A:MF4627 2.8 37.2 0.7 F3 A:MF4627 2.9 27.0 0.7 F4 A:MF4627 3.0 23.4 0.7 NE2 A:HIS241 3.1 22.5 1.0 O A:HOH748 3.4 21.9 1.0 CE1 A:HIS241 3.4 25.1 1.0 CD2 A:HIS241 3.6 21.2 1.0 NH2 A:ARG239 3.7 29.0 1.0 PB A:ADP605 3.7 25.7 1.0 O A:HOH878 3.8 44.1 1.0 O A:HOH887 4.0 31.9 1.0 MG B:MG101 4.0 22.6 1.0 ND1 A:HIS241 4.0 24.1 1.0 OE1 A:GLU229 4.0 36.3 1.0 O2B A:ADP605 4.1 24.1 1.0 CG A:HIS241 4.2 17.8 1.0 CZ A:ARG239 4.4 27.9 1.0 NH1 A:ARG239 4.4 26.8 1.0 CD A:ARG227 4.5 22.6 1.0 O A:HOH1010 4.5 44.2 1.0 O3B A:ADP605 4.6 27.3 1.0 O3A A:ADP605 4.7 21.8 1.0 NH1 A:ARG227 4.7 25.4 1.0 OE2 A:GLU8 4.9 21.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


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/Tetrafluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:F627 b:37.2 occ:0.73 F2 A:MF4627 0.0 37.2 0.7 MG A:MF4627 1.8 24.9 0.7 O A:HOH878 2.2 44.1 1.0 NH1 A:ARG227 2.3 25.4 1.0 F1 A:MF4627 2.8 26.3 0.7 F4 A:MF4627 3.0 23.4 0.7 F3 A:MF4627 3.0 27.0 0.7 CD A:ARG227 3.2 22.6 1.0 O A:HOH1010 3.3 44.2 1.0 CZ A:ARG227 3.4 23.8 1.0 NE A:ARG227 3.7 19.9 1.0 OE1 A:GLU229 3.7 36.3 1.0 O A:HOH990 3.8 51.8 1.0 MG A:MG604 4.0 49.4 1.0 O A:HOH719 4.0 28.5 1.0 O1B A:ADP605 4.4 25.3 1.0 O B:HOH227 4.4 46.5 1.0 CG A:ARG227 4.6 17.6 1.0 NH2 A:ARG227 4.6 26.3 1.0 CD A:GLU229 4.7 34.8 1.0 MG B:MG101 4.8 22.6 1.0 OE1 B:GLU71 4.8 23.9 1.0 O A:HOH740 4.9 41.5 1.0 OE2 A:GLU229 4.9 31.4 1.0 CB A:ARG227 4.9 19.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


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/Tetrafluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:F627 b:27.0 occ:0.73 F3 A:MF4627 0.0 27.0 0.7 MG A:MF4627 1.8 24.9 0.7 OE1 B:GLU71 2.7 23.9 1.0 F4 A:MF4627 2.8 23.4 0.7 F1 A:MF4627 2.9 26.3 0.7 NE2 A:HIS241 2.9 22.5 1.0 F2 A:MF4627 3.0 37.2 0.7 O A:HOH748 3.2 21.9 1.0 CG2 A:THR217 3.3 20.5 1.0 NH1 A:ARG227 3.4 25.4 1.0 CD2 A:HIS241 3.5 21.2 1.0 MG B:MG101 3.7 22.6 1.0 CD B:GLU71 3.7 22.6 1.0 CZ A:ARG227 3.9 23.8 1.0 CD A:ARG227 3.9 22.6 1.0 CE1 A:HIS241 4.0 25.1 1.0 CE1 A:HIS155 4.1 19.2 1.0 OE2 B:GLU71 4.1 22.1 1.0 OG1 A:THR217 4.1 21.6 1.0 NE A:ARG227 4.1 19.9 1.0 CB A:THR217 4.2 20.9 1.0 ND1 A:HIS155 4.2 23.9 1.0 O B:HOH227 4.6 46.5 1.0 O1B A:ADP605 4.7 25.3 1.0 NH2 A:ARG227 4.7 26.3 1.0 CG A:HIS241 4.7 17.8 1.0 O A:HOH827 4.8 34.4 1.0 O A:HOH719 4.9 28.5 1.0 ND1 A:HIS241 4.9 24.1 1.0 O A:HOH1010 4.9 44.2 1.0 O B:HOH216 4.9 22.1 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:F627 b:23.4 occ:0.73 F4 A:MF4627 0.0 23.4 0.7 MG A:MF4627 1.8 24.9 0.7 MG B:MG101 1.9 22.6 1.0 O B:HOH216 2.5 22.1 1.0 O A:HOH1010 2.5 44.2 1.0 F3 A:MF4627 2.8 27.0 0.7 F2 A:MF4627 3.0 37.2 0.7 F1 A:MF4627 3.0 26.3 0.7 O2B A:ADP605 3.0 24.1 1.0 O A:HOH748 3.0 21.9 1.0 O1B A:ADP605 3.3 25.3 1.0 OE1 B:GLU71 3.3 23.9 1.0 OE2 B:GLU71 3.4 22.1 1.0 PB A:ADP605 3.5 25.7 1.0 O B:HOH227 3.6 46.5 1.0 CD B:GLU71 3.7 22.6 1.0 O A:HOH725 3.8 17.2 1.0 O A:HOH878 4.0 44.1 1.0 O3B A:ADP605 4.1 27.3 1.0 O A:HOH810 4.1 27.3 1.0 NH1 A:ARG227 4.2 25.4 1.0 O A:HOH990 4.3 51.8 1.0 MG A:MG604 4.4 49.4 1.0 O A:HOH740 4.6 41.5 1.0 MG A:MG601 4.7 20.3 1.0 NE2 A:HIS241 4.8 22.5 1.0 OE1 A:GLU8 4.9 21.4 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