Magnesium in PDB 6k27: Pyrophosphatase with Ppi From Acinetobacter Baumannii

All present enzymatic activity of Pyrophosphatase with Ppi From Acinetobacter Baumannii:
3.6.1.1;

The structure of Pyrophosphatase with Ppi From Acinetobacter Baumannii, PDB code: 6k27 was solved by J.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 1.86
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	110.294, 110.294, 302.492, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Pyrophosphatase with Ppi From Acinetobacter Baumannii (pdb code 6k27). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Pyrophosphatase with Ppi From Acinetobacter Baumannii, PDB code: 6k27:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:49.1 occ:1.00 OD1 A:ASP70 2.2 39.1 1.0 OH A:TYR55 3.1 40.7 1.0 CG A:ASP70 3.2 39.0 1.0 O2 A:DPO201 3.3 43.9 1.0 MG A:MG204 3.6 50.6 1.0 OD2 A:ASP70 3.7 39.4 1.0 CZ A:TYR55 3.9 37.9 1.0 OE1 A:GLU20 4.0 32.5 1.0 O1 A:DPO201 4.1 48.0 1.0 CE2 A:TYR55 4.1 37.0 1.0 CB A:ASP70 4.3 35.2 1.0 P1 A:DPO201 4.3 41.8 1.0 CA A:ASP70 4.7 32.1 1.0 O A:PRO68 4.8 37.6 1.0 CE1 A:TYR55 4.9 36.0 1.0 O A:GLY56 4.9 29.5 1.0 CD A:GLU20 5.0 35.7 1.0

Magnesium binding site 2 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:49.5 occ:1.00 O3 A:DPO201 2.4 41.8 1.0 O5 A:DPO201 2.5 44.6 1.0 OD2 A:ASP97 2.7 51.1 1.0 OD2 A:ASP102 2.8 46.6 1.0 NZ A:LYS142 3.2 48.0 1.0 P1 A:DPO201 3.4 41.8 1.0 O1 A:DPO201 3.6 48.0 1.0 CG A:ASP102 3.6 50.2 1.0 P2 A:DPO201 3.6 41.8 1.0 CG A:ASP97 3.7 52.0 1.0 NZ A:LYS104 3.8 39.2 1.0 OH A:TYR141 3.8 34.9 1.0 O4 A:DPO201 4.0 40.3 1.0 O7 A:DPO201 4.1 39.2 1.0 CE A:LYS142 4.2 43.0 1.0 OD1 A:ASP102 4.3 48.6 1.0 CB A:ASP102 4.4 47.0 1.0 CB A:ASP97 4.4 49.5 1.0 OD1 A:ASP97 4.5 51.9 1.0 CE A:LYS104 4.6 40.6 1.0 O2 A:DPO201 4.8 43.9 1.0 O6 A:DPO201 4.9 42.8 1.0

Magnesium binding site 3 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:50.6 occ:1.00 OD2 A:ASP70 2.3 39.4 1.0 O1 A:DPO201 2.9 48.0 1.0 CG A:ASP70 3.0 39.0 1.0 OD2 A:ASP65 3.0 60.7 1.0 OD1 A:ASP70 3.1 39.1 1.0 OD1 A:ASP102 3.6 48.6 1.0 MG A:MG202 3.6 49.1 1.0 NZ A:LYS104 3.7 39.2 1.0 P1 A:DPO201 4.0 41.8 1.0 CG A:ASP65 4.1 60.4 1.0 O2 A:DPO201 4.2 43.9 1.0 OH A:TYR55 4.4 40.7 1.0 O3 A:DPO201 4.5 41.8 1.0 CB A:ASP70 4.5 35.2 1.0 OD1 A:ASP65 4.5 57.8 1.0 CG A:ASP102 4.5 50.2 1.0 OD2 A:ASP102 4.9 46.6 1.0 O A:PRO68 5.0 37.6 1.0

Magnesium binding site 4 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:54.8 occ:1.00 OD2 B:ASP97 2.6 55.9 1.0 O5 B:DPO201 2.6 50.5 1.0 O2 B:DPO201 2.7 45.6 1.0 OD2 B:ASP102 2.7 51.9 1.0 NZ B:LYS142 3.4 44.3 1.0 CG B:ASP102 3.6 53.3 1.0 CG B:ASP97 3.7 61.3 1.0 P1 B:DPO201 3.8 50.6 1.0 NZ B:LYS104 3.8 43.3 1.0 P2 B:DPO201 3.9 43.7 1.0 O1 B:DPO201 4.0 51.5 1.0 OH B:TYR141 4.0 35.1 1.0 OD1 B:ASP102 4.3 54.6 1.0 O4 B:DPO201 4.3 45.8 1.0 O6 B:DPO201 4.4 41.0 1.0 CE B:LYS142 4.4 38.5 1.0 CB B:ASP97 4.4 58.2 1.0 CB B:ASP102 4.4 52.9 1.0 CE B:LYS104 4.6 41.6 1.0 OD1 B:ASP97 4.7 62.2 1.0

Magnesium binding site 5 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:47.6 occ:1.00 OD2 B:ASP70 2.3 45.1 1.0 O1 B:DPO201 2.9 51.5 1.0 CG B:ASP70 3.0 41.2 1.0 OD1 B:ASP70 3.0 40.3 1.0 OD2 B:ASP65 3.0 56.7 1.0 MG B:MG204 3.5 57.4 1.0 P1 B:DPO201 3.8 50.6 1.0 NZ B:LYS104 3.8 43.3 1.0 O3 B:DPO201 3.9 46.8 1.0 OD1 B:ASP102 4.0 54.6 1.0 O2 B:DPO201 4.0 45.6 1.0 CG B:ASP65 4.1 56.9 1.0 OH B:TYR55 4.2 46.7 1.0 CB B:ASP70 4.5 37.1 1.0 OD1 B:ASP65 4.5 54.1 1.0 CG B:ASP102 4.8 53.3 1.0 OD2 B:ASP102 5.0 51.9 1.0

Magnesium binding site 6 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:57.4 occ:1.00 O3 B:DPO201 2.2 46.8 1.0 OH B:TYR55 2.8 46.7 1.0 OD1 B:ASP70 3.0 40.3 1.0 P1 B:DPO201 3.4 50.6 1.0 O1 B:DPO201 3.5 51.5 1.0 MG B:MG203 3.5 47.6 1.0 CZ B:TYR55 3.6 38.7 1.0 CE2 B:TYR55 3.6 37.5 1.0 CG B:ASP70 3.7 41.2 1.0 OD2 B:ASP70 3.9 45.1 1.0 NZ B:LYS29 3.9 40.1 1.0 OE1 B:GLU20 4.2 36.8 1.0 O2 B:DPO201 4.3 45.6 1.0 O4 B:DPO201 4.5 45.8 1.0 CB B:ASP70 4.8 37.1 1.0 CE1 B:TYR55 4.8 38.4 1.0 CD2 B:TYR55 4.9 33.9 1.0

Magnesium binding site 7 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:47.4 occ:1.00 OD2 C:ASP70 2.4 37.4 1.0 O1 C:DPO201 2.7 45.9 1.0 OD2 C:ASP65 2.9 54.1 1.0 OD1 C:ASP70 2.9 35.5 1.0 CG C:ASP70 3.0 36.7 1.0 MG C:MG204 3.3 47.2 1.0 OD1 C:ASP102 3.8 45.0 1.0 P1 C:DPO201 3.8 40.0 1.0 NZ C:LYS104 3.8 35.5 1.0 CG C:ASP65 4.0 53.7 1.0 O3 C:DPO201 4.1 38.9 1.0 O2 C:DPO201 4.2 40.4 1.0 OH C:TYR55 4.4 37.8 1.0 OD1 C:ASP65 4.5 51.2 1.0 CB C:ASP70 4.5 32.8 1.0 CG C:ASP102 4.8 46.7 1.0 CB C:ASP67 4.8 44.3 1.0 O C:PRO68 4.9 30.9 1.0 OD2 C:ASP67 4.9 55.9 1.0

Magnesium binding site 8 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:48.1 occ:1.00 O2 C:DPO201 2.4 40.4 1.0 O5 C:DPO201 2.5 43.0 1.0 OD2 C:ASP102 2.6 42.5 1.0 OD2 C:ASP97 2.7 52.0 1.0 P1 C:DPO201 3.4 40.0 1.0 CG C:ASP102 3.5 46.7 1.0 NZ C:LYS142 3.5 39.8 1.0 O1 C:DPO201 3.6 45.9 1.0 P2 C:DPO201 3.6 38.9 1.0 NZ C:LYS104 3.8 35.5 1.0 CG C:ASP97 3.9 53.9 1.0 O4 C:DPO201 3.9 37.5 1.0 OH C:TYR141 4.0 31.7 1.0 OD1 C:ASP102 4.0 45.0 1.0 O6 C:DPO201 4.1 37.5 1.0 CB C:ASP102 4.4 44.7 1.0 CE C:LYS104 4.5 36.7 1.0 CB C:ASP97 4.6 50.5 1.0 CE C:LYS142 4.6 38.1 1.0 O3 C:DPO201 4.8 38.9 1.0 OD1 C:ASP97 4.8 56.5 1.0 O7 C:DPO201 4.9 40.0 1.0

Magnesium binding site 9 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg204 b:47.2 occ:1.00 O3 C:DPO201 2.4 38.9 1.0 OD1 C:ASP70 2.8 35.5 1.0 OH C:TYR55 2.9 37.8 1.0 O1 C:DPO201 3.3 45.9 1.0 MG C:MG202 3.3 47.4 1.0 P1 C:DPO201 3.4 40.0 1.0 CG C:ASP70 3.5 36.7 1.0 CZ C:TYR55 3.7 30.6 1.0 CE2 C:TYR55 3.8 31.4 1.0 OD2 C:ASP70 3.9 37.4 1.0 NZ C:LYS29 4.1 37.6 1.0 OE1 C:GLU20 4.2 33.5 1.0 O2 C:DPO201 4.5 40.4 1.0 O4 C:DPO201 4.5 37.5 1.0 CB C:ASP70 4.6 32.8 1.0 OE2 C:GLU31 4.7 46.5 1.0 NZ C:LYS104 4.8 35.5 1.0 CE1 C:TYR55 4.9 32.1 1.0

Magnesium binding site 10 out of 24 in the Pyrophosphatase with Ppi From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pyrophosphatase with Ppi From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:50.9 occ:1.00 O7 D:DPO201 2.4 39.7 1.0 OD1 D:ASP70 2.8 36.7 1.0 OH D:TYR55 2.8 37.6 1.0 O5 D:DPO201 3.4 45.6 1.0 MG D:MG203 3.5 47.2 1.0 P2 D:DPO201 3.5 41.8 1.0 CG D:ASP70 3.5 37.4 1.0 CZ D:TYR55 3.7 31.7 1.0 CE2 D:TYR55 3.8 29.9 1.0 OD2 D:ASP70 3.9 37.5 1.0 NZ D:LYS29 4.1 38.0 1.0 OE1 D:GLU20 4.1 34.7 1.0 O6 D:DPO201 4.5 40.4 1.0 O4 D:DPO201 4.6 35.3 1.0 CB D:ASP70 4.6 31.5 1.0 NZ D:LYS104 4.8 35.7 1.0 CE1 D:TYR55 4.9 33.8 1.0

Y.Si, X.Wang, G.Yang, T.Yang, Y.Li, G.J.Ayala, X.Li, H.Wang, J.Su. Crystal Structures of Pyrophosphatase From Acinetobacter Baumannii: Snapshots of Pyrophosphate Binding and Identification of A Phosphorylated Enzyme Intermediate. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31500178
DOI: 10.3390/IJMS20184394