Magnesium 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:

Fluorine

(F)

3 atoms

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

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


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/Trifluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:25.6 occ:1.00 F1 A:KQB617 1.9 27.2 1.0 OE2 A:GLU99 2.0 22.4 1.0 O3B A:ADP604 2.1 28.1 1.0 O2A A:ADP604 2.1 26.2 1.0 OE1 A:GLU8 2.1 23.6 1.0 OH A:TYR92 2.2 27.9 1.0 CD A:GLU99 3.0 26.3 1.0 CD A:GLU8 3.1 33.4 1.0 MG1 A:KQB617 3.1 29.2 1.0 PA A:ADP604 3.2 28.2 1.0 PB A:ADP604 3.2 34.5 1.0 CZ A:TYR92 3.3 27.0 1.0 OE1 A:GLU99 3.4 20.8 1.0 O3A A:ADP604 3.4 27.3 1.0 MG A:MG602 3.4 26.0 1.0 CE1 A:TYR92 3.7 25.1 1.0 F2 A:KQB617 3.7 29.8 1.0 O A:HOH905 3.8 28.9 1.0 CG A:GLU8 3.8 23.3 1.0 O1 A:KQB617 3.9 31.5 1.0 MG A:MG603 3.9 23.6 0.5 O2B A:ADP604 4.0 35.8 1.0 OE2 A:GLU8 4.0 27.6 1.0 OG A:SER101 4.0 27.9 1.0 CB A:GLU8 4.1 23.3 1.0 O A:HOH716 4.1 32.5 1.0 O5' A:ADP604 4.2 27.0 1.0 CG A:GLU99 4.3 24.1 1.0 O A:HOH702 4.3 45.2 1.0 O1A A:ADP604 4.4 30.8 1.0 OD2 A:ASP94 4.4 27.9 1.0 OE1 B:GLU71 4.4 28.5 1.0 O1B A:ADP604 4.4 36.2 1.0 CE2 A:TYR92 4.5 31.3 1.0 F3 A:KQB617 4.7 36.8 1.0 NH1 A:ARG90 4.9 28.2 1.0 CG A:ASP94 5.0 36.5 1.0

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


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/Trifluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:26.0 occ:1.00 F1 A:KQB617 1.9 27.2 1.0 OE1 A:GLU99 2.0 20.8 1.0 OD2 A:ASP94 2.0 27.9 1.0 OE2 A:GLU10 2.1 28.1 1.0 O A:HOH905 2.1 28.9 1.0 OE1 B:GLU71 2.3 28.5 1.0 CD A:GLU99 2.9 26.3 1.0 CD A:GLU10 3.1 27.0 1.0 CG A:ASP94 3.1 36.5 1.0 OE2 A:GLU99 3.2 22.4 1.0 MG1 A:KQB617 3.3 29.2 1.0 CD B:GLU71 3.4 29.9 1.0 MG A:MG601 3.4 25.6 1.0 CG A:GLU10 3.5 23.7 1.0 O1 A:KQB617 3.7 31.5 1.0 CB A:ASP94 3.8 27.7 1.0 CG B:GLU71 3.9 25.8 1.0 OH A:TYR92 3.9 27.9 1.0 F2 A:KQB617 4.0 29.8 1.0 OD1 A:ASP94 4.2 41.8 1.0 OE1 A:GLU8 4.2 23.6 1.0 OE1 A:GLU10 4.2 26.2 1.0 CB B:GLU71 4.2 25.5 1.0 CG A:GLU99 4.3 24.1 1.0 O3B A:ADP604 4.4 28.1 1.0 CE1 A:HIS155 4.5 27.2 1.0 OE2 B:GLU71 4.5 31.9 1.0 ND1 A:HIS95 4.7 45.5 1.0 CZ A:TYR92 4.8 27.0 1.0 CB A:GLU99 4.8 22.9 1.0 ND1 A:HIS155 4.9 24.9 1.0 MG A:MG603 5.0 23.6 0.5

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


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/Trifluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:23.6 occ:0.53 F2 A:KQB617 1.7 29.8 1.0 NE2 A:HIS241 2.1 30.5 1.0 ND1 A:HIS155 2.2 24.9 1.0 OE2 A:GLU8 2.3 27.6 1.0 OE1 A:GLU8 2.4 23.6 1.0 O2B A:ADP604 2.5 35.8 1.0 CD A:GLU8 2.7 33.4 1.0 CE1 A:HIS241 2.9 25.0 1.0 CE1 A:HIS155 3.1 27.2 1.0 CD2 A:HIS241 3.2 23.4 1.0 CG A:HIS155 3.3 25.4 1.0 MG1 A:KQB617 3.4 29.2 1.0 O3B A:ADP604 3.5 28.1 1.0 PB A:ADP604 3.5 34.5 1.0 CB A:HIS155 3.6 23.8 1.0 F1 A:KQB617 3.8 27.2 1.0 O A:HOH786 3.8 37.2 1.0 MG A:MG601 3.9 25.6 1.0 O A:HOH905 3.9 28.9 1.0 ND1 A:HIS241 4.1 28.2 1.0 F3 A:KQB617 4.1 36.8 1.0 CG A:GLU8 4.2 23.3 1.0 O3A A:ADP604 4.2 27.3 1.0 NH2 A:ARG239 4.2 29.7 1.0 NE2 A:HIS155 4.2 26.9 1.0 CG A:HIS241 4.3 23.7 1.0 CD2 A:HIS155 4.4 22.6 1.0 OE1 B:GLU71 4.4 28.5 1.0 CB A:GLU8 4.7 23.3 1.0 O1B A:ADP604 4.8 36.2 1.0 OD1 A:ASN157 4.9 23.5 1.0 MG A:MG602 5.0 26.0 1.0

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


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/Trifluoromagnesate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg617 b:29.2 occ:1.00 MG1 A:KQB617 0.0 29.2 1.0 F1 A:KQB617 1.9 27.2 1.0 F3 A:KQB617 1.9 36.8 1.0 F2 A:KQB617 1.9 29.8 1.0 O1 A:KQB617 2.0 31.5 1.0 OE1 B:GLU71 2.2 28.5 1.0 O3B A:ADP604 2.3 28.1 1.0 CD B:GLU71 3.1 29.9 1.0 MG A:MG601 3.1 25.6 1.0 OE2 B:GLU71 3.2 31.9 1.0 MG A:MG602 3.3 26.0 1.0 PB A:ADP604 3.3 34.5 1.0 MG A:MG603 3.4 23.6 0.5 O2B A:ADP604 3.6 35.8 1.0 OD2 A:ASP94 3.6 27.9 1.0 OE1 A:GLU8 3.6 23.6 1.0 O A:HOH716 3.8 32.5 1.0 OH A:TYR92 3.8 27.9 1.0 O A:HOH905 4.0 28.9 1.0 O1B A:ADP604 4.0 36.2 1.0 O A:HOH786 4.0 37.2 1.0 CE1 A:HIS155 4.4 27.2 1.0 O A:HOH702 4.5 45.2 1.0 ND1 A:HIS155 4.5 24.9 1.0 CG B:GLU71 4.5 25.8 1.0 CG A:ASP94 4.5 36.5 1.0 OE2 A:GLU99 4.6 22.4 1.0 OE1 A:GLU99 4.7 20.8 1.0 O3A A:ADP604 4.7 27.3 1.0 OD1 A:ASP94 4.7 41.8 1.0 CD A:GLU8 4.8 33.4 1.0 O2A A:ADP604 4.9 26.2 1.0 OE2 A:GLU10 5.0 28.1 1.0 NE2 A:HIS241 5.0 30.5 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