Magnesium 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:

Fluorine

(F)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate, PDB code: 7oyh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg601 b:20.3 occ:1.00 O2A A:ADP605 1.9 18.9 1.0 O A:HOH725 1.9 17.2 1.0 OE2 A:GLU99 2.0 20.9 1.0 O2B A:ADP605 2.1 24.1 1.0 OH A:TYR92 2.1 19.3 1.0 OE1 A:GLU8 2.1 21.4 1.0 CD A:GLU99 3.0 17.2 1.0 PA A:ADP605 3.1 22.0 1.0 MG B:MG101 3.2 22.6 1.0 CD A:GLU8 3.2 25.6 1.0 PB A:ADP605 3.2 25.7 1.0 CZ A:TYR92 3.3 20.4 1.0 O3A A:ADP605 3.3 21.8 1.0 OE1 A:GLU99 3.5 18.9 1.0 O A:HOH748 3.6 21.9 1.0 MG A:MG602 3.7 19.4 1.0 CE1 A:TYR92 3.7 21.9 1.0 O A:HOH922 3.8 22.6 1.0 CG A:GLU8 3.9 18.7 1.0 OG A:SER101 4.0 22.8 1.0 O A:HOH810 4.0 27.3 1.0 O B:HOH216 4.0 22.1 1.0 O3B A:ADP605 4.1 27.3 1.0 O5' A:ADP605 4.1 22.8 1.0 OE2 A:GLU8 4.2 21.8 1.0 CB A:GLU8 4.2 19.0 1.0 O1A A:ADP605 4.3 23.2 1.0 CG A:GLU99 4.3 16.4 1.0 O1B A:ADP605 4.3 25.3 1.0 CE2 A:TYR92 4.5 25.9 1.0 OE2 B:GLU71 4.5 22.1 1.0 OD2 A:ASP94 4.5 23.6 1.0 F4 A:MF4627 4.7 23.4 0.7

Magnesium binding site 2 out of 6 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg602 b:19.4 occ:1.00 O A:HOH725 2.0 17.2 1.0 OE2 A:GLU10 2.0 21.5 1.0 OE1 A:GLU99 2.0 18.9 1.0 OD2 A:ASP94 2.1 23.6 1.0 O A:HOH922 2.1 22.6 1.0 OE2 B:GLU71 2.3 22.1 1.0 CD A:GLU99 3.0 17.2 1.0 CD A:GLU10 3.1 21.0 1.0 CG A:ASP94 3.2 32.2 1.0 MG B:MG101 3.3 22.6 1.0 CD B:GLU71 3.4 22.6 1.0 OE2 A:GLU99 3.4 20.9 1.0 CG A:GLU10 3.5 17.1 1.0 MG A:MG601 3.7 20.3 1.0 CG B:GLU71 3.8 18.3 1.0 O B:HOH216 3.8 22.1 1.0 CB A:ASP94 3.8 22.0 1.0 OH A:TYR92 4.1 19.3 1.0 O A:HOH748 4.1 21.9 1.0 OE1 A:GLU10 4.2 18.4 1.0 OD1 A:ASP94 4.2 32.8 1.0 OE1 A:GLU8 4.3 21.4 1.0 CB B:GLU71 4.3 19.2 1.0 CG A:GLU99 4.4 16.4 1.0 OE1 B:GLU71 4.5 23.9 1.0 O2B A:ADP605 4.5 24.1 1.0 ND1 A:HIS95 4.7 34.7 1.0 CE1 A:HIS155 4.8 19.2 1.0 CB A:GLU99 4.9 15.9 1.0 CZ A:TYR92 4.9 20.4 1.0 CB A:GLU10 5.0 16.4 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg603 b:31.9 occ:1.00 O A:HOH714 2.1 35.3 1.0 O A:HOH943 2.2 30.4 1.0 O A:HOH868 2.3 28.8 1.0 O A:VAL213 4.0 22.6 1.0 O1 A:SO4625 4.1 29.8 0.7 O A:HOH1016 4.3 29.7 1.0 O A:HOH896 4.3 20.6 1.0 O4 A:SO4625 4.5 19.4 0.7 O A:HOH781 4.7 25.1 1.0 S A:SO4625 5.0 31.6 0.7

Magnesium binding site 4 out of 6 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg604 b:49.4 occ:1.00 O A:HOH740 2.1 41.5 1.0 O A:HOH1010 2.2 44.2 1.0 O A:HOH996 2.2 43.8 0.7 O A:HOH878 2.3 44.1 1.0 O A:HOH980 2.4 52.4 1.0 F2 A:MF4627 4.0 37.2 0.7 O A:HOH990 4.0 51.8 1.0 O3B A:ADP605 4.3 27.3 1.0 F4 A:MF4627 4.4 23.4 0.7 O A:HOH887 4.5 31.9 1.0 C1 A:PGE624 4.5 45.4 1.0 O A:HOH810 4.6 27.3 1.0 C3 A:PGE624 4.6 57.4 1.0 C2 A:PGE624 4.6 59.3 1.0 O1 A:PGE624 4.7 57.4 1.0 OE2 A:GLU229 4.8 31.4 1.0 MG A:MF4627 4.8 24.9 0.7 OE1 A:GLU229 4.9 36.3 1.0 O1B A:ADP605 5.0 25.3 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 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:Mg627 b:24.9 occ:0.73 MG A:MF4627 0.0 24.9 0.7 F1 A:MF4627 1.8 26.3 0.7 F2 A:MF4627 1.8 37.2 0.7 F4 A:MF4627 1.8 23.4 0.7 F3 A:MF4627 1.8 27.0 0.7 MG B:MG101 3.3 22.6 1.0 NH1 A:ARG227 3.3 25.4 1.0 O1B A:ADP605 3.4 25.3 1.0 O A:HOH748 3.4 21.9 1.0 O A:HOH878 3.4 44.1 1.0 O A:HOH1010 3.5 44.2 1.0 OE1 B:GLU71 3.7 23.9 1.0 NE2 A:HIS241 3.7 22.5 1.0 O A:HOH719 4.0 28.5 1.0 CD A:ARG227 4.1 22.6 1.0 O2B A:ADP605 4.2 24.1 1.0 O B:HOH216 4.2 22.1 1.0 PB A:ADP605 4.3 25.7 1.0 CZ A:ARG227 4.3 23.8 1.0 CD2 A:HIS241 4.3 21.2 1.0 O B:HOH227 4.4 46.5 1.0 CE1 A:HIS241 4.4 25.1 1.0 OE2 B:GLU71 4.5 22.1 1.0 CD B:GLU71 4.5 22.6 1.0 NE A:ARG227 4.6 19.9 1.0 O A:HOH990 4.7 51.8 1.0 OE1 A:GLU229 4.7 36.3 1.0 MG A:MG604 4.8 49.4 1.0 O3B A:ADP605 5.0 27.3 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Tetrafluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:22.6 occ:1.00 F4 A:MF4627 1.9 23.4 0.7 O A:HOH725 2.0 17.2 1.0 O B:HOH216 2.0 22.1 1.0 O A:HOH748 2.1 21.9 1.0 O2B A:ADP605 2.2 24.1 1.0 OE2 B:GLU71 2.2 22.1 1.0 CD B:GLU71 3.1 22.6 1.0 MG A:MG601 3.2 20.3 1.0 MG A:MF4627 3.3 24.9 0.7 OE1 B:GLU71 3.3 23.9 1.0 MG A:MG602 3.3 19.4 1.0 PB A:ADP605 3.4 25.7 1.0 OE1 A:GLU8 3.6 21.4 1.0 F3 A:MF4627 3.7 27.0 0.7 O1B A:ADP605 3.7 25.3 1.0 OD2 A:ASP94 3.7 23.6 1.0 O A:HOH922 3.8 22.6 1.0 O A:HOH810 3.9 27.3 1.0 O A:HOH1010 3.9 44.2 1.0 OH A:TYR92 3.9 19.3 1.0 F1 A:MF4627 4.0 26.3 0.7 O3B A:ADP605 4.2 27.3 1.0 O B:HOH227 4.4 46.5 1.0 CG B:GLU71 4.5 18.3 1.0 ND1 A:HIS155 4.6 23.9 1.0 O3A A:ADP605 4.6 21.8 1.0 OE2 A:GLU99 4.6 20.9 1.0 CG A:ASP94 4.6 32.2 1.0 CE1 A:HIS155 4.7 19.2 1.0 CD A:GLU8 4.7 25.6 1.0 OE1 A:GLU99 4.7 18.9 1.0 F2 A:MF4627 4.8 37.2 0.7 O2A A:ADP605 4.8 18.9 1.0 OD1 A:ASP94 4.9 32.8 1.0 NE2 A:HIS241 5.0 22.5 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