Magnesium in PDB 7pul: Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis

All present enzymatic activity of Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis:
3.2.1.52;

The structure of Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis, PDB code: 7pul was solved by M.Garcia-Alija, J.J.Du, B.Trastoy, E.J.Sundberg, M.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.08 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.298, 57.046, 69.525, 90, 92.97, 90
R / Rfree (%)	15.8 / 18.3

The structure of Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis (pdb code 7pul). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis, PDB code: 7pul:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis


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 Endoglycosidase E GH20 Domain From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:19.3 occ:1.00 HH A:TYR710 1.8 14.5 1.0 NE2 A:HIS749 2.5 11.5 1.0 OH A:TYR710 2.6 12.1 1.0 O A:PHE720 2.7 12.1 1.0 HE2 A:TYR710 2.8 13.2 1.0 O A:HOH1218 2.8 18.1 1.0 HB3 A:LYS747 3.0 17.0 1.0 HD3 A:LYS747 3.2 24.0 1.0 H A:PHE720 3.4 13.5 1.0 CD2 A:HIS749 3.4 11.0 1.0 CE1 A:HIS749 3.4 10.7 1.0 CE2 A:TYR710 3.4 11.0 1.0 HB2 A:PHE720 3.4 12.8 1.0 CZ A:TYR710 3.5 12.5 1.0 HA A:PRO722 3.5 12.9 1.0 HD2 A:HIS749 3.5 13.2 1.0 HE1 A:HIS749 3.6 12.8 1.0 HB3 A:PRO722 3.6 14.7 1.0 C A:PHE720 3.7 11.8 1.0 CB A:LYS747 3.8 14.1 1.0 HD3 A:PRO722 3.9 13.7 1.0 N A:PHE720 3.9 11.2 1.0 HB2 A:LYS747 4.0 17.0 1.0 HB A:THR719 4.0 19.7 1.0 CD A:LYS747 4.0 20.0 1.0 HD2 A:LYS747 4.1 24.0 1.0 CA A:PRO722 4.1 10.7 1.0 N A:PRO722 4.1 10.6 1.0 CA A:PHE720 4.2 11.6 1.0 CB A:PHE720 4.2 10.7 1.0 O A:LYS747 4.2 15.6 1.0 CB A:PRO722 4.3 12.3 1.0 CD A:PRO722 4.5 11.4 1.0 C A:ASP721 4.5 12.0 1.0 CG A:LYS747 4.5 16.4 1.0 ND1 A:HIS749 4.5 9.7 1.0 CG A:HIS749 4.5 9.7 1.0 HB3 A:PHE720 4.6 12.8 1.0 O A:ASP721 4.7 10.3 1.0 HG2 A:LYS747 4.7 19.7 1.0 CD2 A:TYR710 4.8 9.5 1.0 N A:ASP721 4.8 10.6 1.0 CE1 A:TYR710 4.8 11.6 1.0 C A:LYS747 4.9 12.4 1.0 CG A:PRO722 4.9 16.0 1.0 CB A:THR719 4.9 16.4 1.0 HA A:THR719 4.9 14.5 1.0 HD1 A:PHE720 4.9 12.0 1.0 CA A:LYS747 4.9 13.2 1.0 C A:THR719 5.0 13.7 1.0 HG3 A:PRO722 5.0 19.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis


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 Endoglycosidase E GH20 Domain From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:19.1 occ:1.00 H A:GLY601 1.9 11.1 1.0 N A:GLY601 2.6 9.2 1.0 O A:ASP661 2.8 10.9 1.0 HA3 A:GLY601 2.8 11.9 1.0 OD1 A:ASN598 2.8 10.3 1.0 H A:ASP661 3.0 11.4 1.0 CA A:GLY601 3.0 9.9 1.0 H A:GLY660 3.1 11.4 1.0 HA2 A:GLY660 3.2 13.3 1.0 N A:ASP661 3.2 9.5 1.0 HD2 A:PRO600 3.3 12.1 1.0 O A:SER599 3.3 10.2 1.0 C A:SER599 3.4 9.4 1.0 C A:GLY601 3.4 9.2 1.0 O A:GLY601 3.4 9.2 1.0 C A:GLY660 3.5 10.6 1.0 N A:PRO600 3.5 9.4 1.0 N A:GLY660 3.5 9.5 1.0 CA A:GLY660 3.6 11.1 1.0 OD1 A:ASP661 3.6 12.4 1.0 CG A:ASN598 3.7 9.4 1.0 C A:ASP661 3.7 10.4 1.0 HD2 A:HIS602 3.7 12.8 1.0 HA A:SER599 3.8 11.3 1.0 C A:PRO600 3.8 9.3 1.0 CD A:PRO600 3.9 10.1 1.0 H A:SER599 3.9 12.2 1.0 HA2 A:GLY601 4.0 11.9 1.0 CA A:SER599 4.0 9.4 1.0 HD21 A:ASN598 4.0 12.8 1.0 HB2 A:HIS602 4.0 11.5 1.0 CA A:ASP661 4.0 10.3 1.0 N A:SER599 4.1 10.1 1.0 ND2 A:ASN598 4.2 10.6 1.0 CA A:PRO600 4.3 10.0 1.0 N A:HIS602 4.3 8.9 1.0 O A:GLY660 4.3 11.4 1.0 HG2 A:PRO600 4.3 10.7 1.0 CG A:ASP661 4.5 10.7 1.0 CD2 A:HIS602 4.5 10.7 1.0 HA3 A:GLY660 4.5 13.3 1.0 C A:GLY659 4.6 10.3 1.0 HD3 A:PRO600 4.6 12.1 1.0 CG A:PRO600 4.7 8.9 1.0 H A:HIS602 4.7 10.7 1.0 HA3 A:GLY659 4.7 11.2 1.0 HA A:ASP661 4.8 12.4 1.0 CB A:HIS602 4.8 9.6 1.0 HB3 A:ASN598 4.8 12.4 1.0 CB A:ASN598 4.8 10.3 1.0 C A:ASN598 4.9 10.2 1.0 CB A:ASP661 4.9 9.6 1.0 O A:PRO600 4.9 10.9 1.0 HA A:PRO600 4.9 12.0 1.0 N A:GLU662 5.0 10.6 1.0 HD22 A:ASN598 5.0 12.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Endoglycosidase E GH20 Domain From Enterococcus Faecalis


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 Endoglycosidase E GH20 Domain From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:15.7 occ:1.00 H A:ALA739 2.2 11.7 1.0 HB A:VAL738 2.7 11.7 1.0 O A:ILE709 2.7 9.9 1.0 HA A:TYR711 2.7 10.9 1.0 HA A:VAL738 2.8 12.2 1.0 O A:ASP707 2.8 10.0 1.0 O A:HOH1118 2.9 9.2 1.0 N A:ALA739 3.0 9.7 1.0 O A:ASN706 3.3 8.6 1.0 CA A:VAL738 3.4 10.2 1.0 CB A:VAL738 3.4 9.8 1.0 HB3 A:ALA739 3.5 13.8 1.0 CA A:TYR711 3.5 9.1 1.0 C A:ASP707 3.5 9.7 1.0 HA A:ASP707 3.5 10.5 1.0 O A:TYR710 3.5 10.1 1.0 N A:TYR711 3.5 9.5 1.0 HZ A:PHE744 3.6 11.7 1.0 C A:TYR710 3.6 10.3 1.0 C A:VAL738 3.7 10.7 1.0 C A:ILE709 3.7 8.9 1.0 HG12 A:VAL738 3.7 14.9 1.0 H A:ILE709 3.7 11.0 1.0 HB2 A:ALA739 3.8 13.8 1.0 HD1 A:TYR711 3.8 13.1 1.0 CB A:ALA739 3.9 11.5 1.0 H A:TYR711 3.9 11.4 1.0 N A:ILE709 4.0 9.1 1.0 CA A:ALA739 4.0 10.6 1.0 CA A:ASP707 4.0 8.8 1.0 CG1 A:VAL738 4.1 12.4 1.0 HB2 A:TYR711 4.1 12.5 1.0 C A:ASN706 4.3 7.7 1.0 N A:GLY708 4.3 8.6 1.0 HD22 A:ASN706 4.3 10.8 1.0 CB A:TYR711 4.4 10.4 1.0 C A:GLY708 4.4 9.6 1.0 CZ A:PHE744 4.4 9.7 1.0 H A:ASN712 4.4 12.8 1.0 CA A:ILE709 4.4 9.0 1.0 HG11 A:VAL738 4.5 14.9 1.0 HB2 A:TYR710 4.5 11.4 1.0 N A:TYR710 4.5 9.0 1.0 CD1 A:TYR711 4.5 10.9 1.0 HA2 A:GLY708 4.5 11.0 1.0 CA A:TYR710 4.6 9.7 1.0 C A:TYR711 4.6 10.7 1.0 HG23 A:VAL738 4.6 13.9 1.0 CG2 A:VAL738 4.7 11.6 1.0 CA A:GLY708 4.7 9.2 1.0 O A:ALA739 4.7 12.0 1.0 HE2 A:PHE744 4.7 12.4 1.0 H A:SER713 4.7 12.1 1.0 N A:ASP707 4.7 7.5 1.0 HB A:ILE709 4.7 10.1 1.0 HA A:ALA739 4.7 12.7 1.0 N A:VAL738 4.7 11.4 1.0 O A:ASP737 4.7 15.9 1.0 N A:ASN712 4.8 10.7 1.0 HB2 A:ASN706 4.8 11.0 1.0 HB1 A:ALA739 4.9 13.8 1.0 HG13 A:VAL738 4.9 14.9 1.0 C A:ALA739 4.9 10.5 1.0 O A:VAL738 4.9 13.5 1.0 CG A:TYR711 4.9 9.4 1.0 H A:GLY708 5.0 10.4 1.0 CE2 A:PHE744 5.0 10.3 1.0 HG21 A:VAL738 5.0 13.9 1.0

M.Garcia-Alija, J.J.Du, I.Ordonez, A.Diz-Vallenilla, A.Moraleda-Montoya, N.Sultana, C.G.Huynh, C.Li, T.C.Donahue, L.X.Wang, B.Trastoy, E.J.Sundberg, M.E.Guerin. Mechanism of Cooperative N-Glycan Processing By the Multi-Modular Endoglycosidase Endoe. Nat Commun V. 13 1137 2022.
ISSN: ESSN 2041-1723
PubMed: 35241669
DOI: 10.1038/S41467-022-28722-W