Magnesium in PDB 8a0m: Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment

The structure of Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment, PDB code: 8a0m was solved by J.O.Cifuente, J.Schulze, A.Bethe, V.Didomenico, C.Litschko, I.Budde, L.Eidenberger, H.Thiesler, I.Ramon-Roth, M.Berger, H.Claus, C.Dangelo, A.Marina, R.Gerardy-Schahn, M.Schubert, M.E.Guerin, T.Fiebig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.94 / 3.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	127.911, 232.806, 129.177, 90, 118.39, 90
R / Rfree (%)	22 / 26.1

The binding sites of Magnesium atom in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment (pdb code 8a0m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment, PDB code: 8a0m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:71.7 occ:1.00 OD2 A:ASP386 2.1 77.6 1.0 OD1 A:ASP573 2.1 83.5 1.0 O A:HOH1301 2.1 82.8 1.0 O A:PHE388 2.1 70.0 1.0 O A:HOH1303 2.2 92.6 1.0 O A:HOH1302 2.3 71.5 1.0 CG A:ASP573 3.0 80.1 1.0 CG A:ASP386 3.1 82.1 1.0 OD2 A:ASP573 3.3 74.9 1.0 C A:PHE388 3.3 70.0 1.0 OD1 A:ASP386 3.5 91.2 1.0 CB A:ASP389 4.1 74.0 1.0 CA A:PHE388 4.1 70.7 1.0 CB A:PHE388 4.2 73.5 1.0 N A:PHE388 4.3 75.2 1.0 N A:ASP389 4.3 73.4 1.0 CB A:ASP386 4.3 73.8 1.0 CB A:ASP573 4.4 76.8 1.0 OG1 A:THR390 4.4 75.3 1.0 OD2 A:ASP389 4.5 88.8 1.0 CA A:ASP389 4.5 75.7 1.0 OD2 A:ASP578 4.6 66.4 1.0 C A:ASP389 4.6 81.1 1.0 N A:THR390 4.8 77.2 1.0 CG A:ASP389 4.9 81.2 1.0 N A:ASP573 4.9 79.8 1.0 C A:ILE387 5.0 78.0 1.0

Magnesium binding site 2 out of 4 in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1201 b:83.0 occ:1.00 OD2 B:ASP386 2.1 96.9 1.0 O B:HOH1303 2.1 84.4 1.0 OD1 B:ASP573 2.1 94.9 1.0 O B:PHE388 2.2 92.9 1.0 O B:HOH1302 2.2 89.9 1.0 O B:HOH1301 2.3 110.1 1.0 CG B:ASP573 3.1 88.7 1.0 CG B:ASP386 3.1 102.1 1.0 C B:PHE388 3.4 98.1 1.0 OD2 B:ASP573 3.5 89.9 1.0 OD1 B:ASP386 3.6 111.4 1.0 CA B:PHE388 4.1 98.3 1.0 CB B:PHE388 4.2 103.8 1.0 OG1 B:THR390 4.2 89.3 1.0 CB B:ASP389 4.2 98.0 1.0 N B:PHE388 4.2 100.3 1.0 CB B:ASP386 4.4 90.0 1.0 N B:ASP389 4.4 99.5 1.0 CB B:ASP573 4.4 83.5 1.0 OD2 B:ASP578 4.5 93.4 1.0 CA B:ASP389 4.7 95.1 1.0 C B:ASP389 4.7 94.6 1.0 OD2 B:ASP389 4.9 98.1 1.0 N B:ASP573 4.9 93.2 1.0 N B:THR390 4.9 97.3 1.0 C B:ILE387 5.0 99.9 1.0

Magnesium binding site 3 out of 4 in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1201 b:85.8 occ:1.00 OD2 C:ASP386 2.1 101.0 1.0 O C:HOH1303 2.1 81.1 1.0 OD1 C:ASP573 2.1 88.3 1.0 O C:HOH1302 2.3 75.4 1.0 O C:PHE388 2.4 81.2 1.0 O C:HOH1301 2.5 92.8 1.0 CG C:ASP386 3.0 104.4 1.0 CG C:ASP573 3.1 85.1 1.0 OD1 C:ASP386 3.3 106.7 1.0 OD2 C:ASP573 3.4 79.9 1.0 C C:PHE388 3.6 80.6 1.0 CB C:ASP386 4.3 94.3 1.0 OD2 C:ASP578 4.3 83.0 1.0 CA C:PHE388 4.3 83.4 1.0 CB C:PHE388 4.4 82.4 1.0 CB C:ASP389 4.4 81.7 1.0 N C:PHE388 4.4 90.2 1.0 CB C:ASP573 4.5 82.1 1.0 OG1 C:THR390 4.5 77.2 1.0 N C:ASP389 4.6 81.0 1.0 OD2 C:ASP389 4.8 101.2 1.0 N C:ASP573 4.8 87.0 1.0 CA C:ASP389 4.8 82.8 1.0 C C:ASP389 4.9 85.9 1.0

Magnesium binding site 4 out of 4 in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Capsular Polysaccharide Synthesis Multienzyme in Complex with Capsular Polymer Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1201 b:75.5 occ:1.00 O D:HOH1302 2.0 77.2 1.0 OD2 D:ASP386 2.1 81.8 1.0 OD1 D:ASP573 2.1 79.8 1.0 O D:HOH1303 2.3 81.3 1.0 O D:PHE388 2.3 77.9 1.0 O D:HOH1301 2.3 96.6 1.0 CG D:ASP573 3.0 74.1 1.0 CG D:ASP386 3.0 84.5 1.0 OD2 D:ASP573 3.3 68.9 1.0 OD1 D:ASP386 3.4 86.6 1.0 C D:PHE388 3.5 80.4 1.0 CA D:PHE388 4.2 81.7 1.0 OD2 D:ASP578 4.3 66.3 1.0 CB D:PHE388 4.3 82.4 1.0 CB D:ASP386 4.3 78.7 1.0 N D:PHE388 4.3 78.8 1.0 CB D:ASP389 4.4 80.2 1.0 CB D:ASP573 4.4 71.1 1.0 OG1 D:THR390 4.5 73.2 1.0 N D:ASP389 4.5 77.7 1.0 CA D:ASP389 4.8 77.5 1.0 OD2 D:ASP389 4.8 95.3 1.0 C D:ASP389 4.8 73.2 1.0 N D:ASP573 4.9 77.1 1.0 N D:THR390 4.9 67.2 1.0 C D:ILE387 5.0 77.5 1.0

J.O.Cifuente, J.Schulze, A.Bethe, V.Didomenico, C.Litschko, I.Budde, L.Eidenberger, H.Thiesler, I.Ramon-Roth, M.Berger, H.Claus, C.Dangelo, A.Marina, R.Gerardy-Schahn, M.Schubert, M.E.Guerin, T.Fiebig. A Multi-Enzyme Machine Polymerizes the Haemophilus Influenzae Type B Capsule Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-023-01324-3