Magnesium in PDB 9igr: Crystal Structure of PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate

The structure of Crystal Structure of PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate, PDB code: 9igr was solved by R.Rasche, A.-M.Lawrence-Doerner, N.V.Cornelissen, D.Kuemmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.11 / 2.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.471, 88.265, 125.344, 90, 101.15, 90
R / Rfree (%)	17.6 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate (pdb code 9igr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate, PDB code: 9igr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate


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 PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:67.2 occ:1.00 O A:LEU81 2.3 64.8 1.0 O C:LYS79 2.3 65.4 1.0 O A:HOH540 2.4 69.3 1.0 O C:LEU81 2.5 53.0 1.0 O A:LYS79 2.6 70.8 1.0 HA C:LYS79 2.9 65.3 1.0 C C:LYS79 3.1 69.6 1.0 CA C:LYS79 3.4 65.0 1.0 HA A:LYS79 3.5 58.3 1.0 HB2 C:LYS79 3.5 66.4 1.0 C A:LYS79 3.5 60.2 1.0 C A:LEU81 3.5 63.7 1.0 C C:LEU81 3.6 55.8 1.0 O A:HOH554 3.8 63.0 1.0 N C:LEU81 4.0 75.5 1.0 CA A:LYS79 4.0 57.8 1.0 H C:LEU81 4.0 70.3 1.0 CB C:LYS79 4.0 64.6 1.0 HB2 C:LEU81 4.0 60.9 1.0 HB2 A:LYS79 4.0 61.6 1.0 HA A:ALA82 4.1 62.1 1.0 N C:ALA80 4.2 75.8 1.0 N A:LEU81 4.2 72.5 1.0 C C:ALA80 4.2 71.2 1.0 HB2 A:LEU81 4.2 58.5 1.0 O C:LEU78 4.2 60.5 1.0 C A:ALA80 4.3 71.2 1.0 CA C:LEU81 4.3 58.5 1.0 H A:LEU81 4.4 67.6 1.0 CA A:LEU81 4.4 58.8 1.0 HA C:ALA82 4.5 63.9 1.0 N A:ALA80 4.5 74.9 1.0 N A:ALA82 4.5 58.7 1.0 HB3 C:LYS79 4.6 66.8 1.0 CB A:LYS79 4.6 62.6 1.0 O A:ALA80 4.6 76.8 1.0 O A:LEU78 4.6 64.6 1.0 HD3 A:PRO83 4.6 67.7 1.0 CA A:ALA82 4.6 59.9 1.0 N C:LYS79 4.7 68.3 1.0 C A:ALA82 4.7 64.9 1.0 CA C:ALA80 4.7 82.5 1.0 O C:ALA80 4.7 74.5 1.0 HG3 A:PRO83 4.7 65.4 1.0 CB C:LEU81 4.7 59.8 1.0 N C:ALA82 4.7 59.9 1.0 HA C:ALA80 4.8 80.9 1.0 CB A:LEU81 4.9 57.7 1.0 CA A:ALA80 4.9 85.3 1.0 H C:ALA80 4.9 76.1 1.0 HA A:ALA80 4.9 83.8 1.0 C C:LEU78 4.9 62.6 1.0 N A:PRO83 4.9 62.4 1.0 CA C:ALA82 5.0 67.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate


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 PPK2 Class III From Erysipelotrichaceae Bacterium in Complex with Polyphosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:62.4 occ:1.00 O D:LEU81 2.3 48.6 1.0 O D:LYS79 2.5 58.5 1.0 O B:HOH534 2.5 51.6 1.0 O B:LEU81 2.7 51.2 1.0 O B:LYS79 2.8 62.4 1.0 HA D:LYS79 3.1 45.2 1.0 C D:LYS79 3.2 49.4 1.0 O D:HOH549 3.3 59.0 1.0 HA B:LYS79 3.3 53.9 1.0 C D:LEU81 3.4 42.7 1.0 C B:LYS79 3.6 57.5 1.0 CA D:LYS79 3.7 45.8 1.0 HB2 D:LEU81 3.7 53.6 1.0 N D:LEU81 3.8 57.8 1.0 C B:LEU81 3.9 41.3 1.0 HB2 B:LYS79 3.9 59.1 1.0 HB2 D:LYS79 3.9 46.9 1.0 H D:LEU81 3.9 52.3 1.0 CA B:LYS79 3.9 55.4 1.0 O D:LEU78 4.0 53.5 1.0 C D:ALA80 4.1 46.9 1.0 CA D:LEU81 4.1 47.5 1.0 O B:HOH524 4.1 58.6 1.0 N D:ALA80 4.2 63.8 1.0 HA D:ALA82 4.4 53.5 1.0 HA B:ALA82 4.4 51.0 1.0 CB D:LYS79 4.4 43.9 1.0 HB2 B:LEU81 4.4 48.1 1.0 CB D:LEU81 4.4 55.0 1.0 CB B:LYS79 4.5 55.9 1.0 N B:LEU81 4.5 55.1 1.0 N D:ALA82 4.5 48.7 1.0 O D:ALA80 4.5 63.7 1.0 CA D:ALA80 4.6 66.6 1.0 C B:ALA80 4.6 60.7 1.0 H B:LEU81 4.6 55.0 1.0 HD3 B:PRO83 4.6 48.5 1.0 O B:LEU78 4.7 58.6 1.0 N B:ALA80 4.7 56.4 1.0 CA B:LEU81 4.7 49.2 1.0 N D:LYS79 4.8 43.2 1.0 CA D:ALA82 4.8 56.0 1.0 HA D:ALA80 4.8 64.6 1.0 N B:ALA82 4.8 47.2 1.0 C D:ALA82 4.8 50.5 1.0 HB3 D:LEU81 4.8 53.8 1.0 C D:LEU78 4.8 39.2 1.0 C B:ALA82 4.8 56.3 1.0 HD3 D:PRO83 4.9 54.6 1.0 CA B:ALA82 4.9 50.5 1.0 H D:ALA80 4.9 60.0 1.0 HB3 D:LYS79 4.9 46.2 1.0 O B:ALA80 5.0 57.4 1.0 HA D:LEU81 5.0 50.1 1.0

R.M.Mitton-Fry, R.Rasche, A.M.Lawrence-Dorner, J.Eschenbach, A.Tekath, A.Rentmeister, D.Kummel, N.V.Cornelissen. Structure-Guided Engineering of A Polyphosphate Kinase 2 Class III From An Erysipelotrichaceae Bacterium to Produce Base-Modified Purine Nucleotides Rsc Chem Biol 2025.
ISSN: ESSN 2633-0679
DOI: 10.1039/D5CB00108K