Magnesium in PDB 6z9k: Cap Domain of Enterococcal Prga

The structure of Cap Domain of Enterococcal Prga, PDB code: 6z9k was solved by R.P.A.Berntsson, A.Schmitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.70 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.874, 35.998, 84.854, 90.00, 114.47, 90.00
R / Rfree (%)	16.3 / 20.1

The binding sites of Magnesium atom in the Cap Domain of Enterococcal Prga (pdb code 6z9k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cap Domain of Enterococcal Prga, PDB code: 6z9k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cap Domain of Enterococcal Prga


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cap Domain of Enterococcal Prga within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:28.3 occ:1.00 NE2 A:HIS477 2.7 25.6 1.0 O A:HOH946 2.7 30.8 1.0 N A:LEU438 2.9 15.2 1.0 CE1 A:HIS412 3.2 17.2 1.0 O A:LEU438 3.2 19.4 1.0 NE2 A:HIS412 3.3 18.4 1.0 CD2 A:HIS477 3.3 22.8 1.0 O A:HOH794 3.4 33.0 1.0 CB A:LEU438 3.6 18.2 1.0 CA A:LEU438 3.6 17.1 1.0 O A:HOH918 3.6 41.1 1.0 CE1 A:HIS477 3.8 24.9 1.0 C A:LEU438 3.8 17.6 1.0 C A:ASN437 3.9 14.8 1.0 CA A:ASN437 4.0 15.4 1.0 ND1 A:HIS412 4.3 17.0 1.0 CD2 A:HIS412 4.5 18.7 1.0 CE A:MET466 4.5 21.2 1.0 CG A:HIS477 4.6 21.4 1.0 O A:GLU436 4.7 14.8 1.0 ND1 A:HIS477 4.8 23.9 1.0 CB A:ASN437 4.9 16.2 1.0 CG A:LEU438 4.9 20.5 1.0 OD1 A:ASN437 4.9 19.8 1.0 O A:HOH813 5.0 31.4 1.0

Magnesium binding site 2 out of 2 in the Cap Domain of Enterococcal Prga


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cap Domain of Enterococcal Prga within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:32.0 occ:1.00 NE2 B:HIS477 2.7 27.7 1.0 O B:HOH896 2.9 36.5 1.0 N B:LEU438 2.9 13.9 1.0 O B:HOH982 3.0 32.1 1.0 CE1 B:HIS412 3.1 17.8 1.0 CD2 B:HIS477 3.2 24.1 1.0 O B:LEU438 3.3 17.5 1.0 O B:HOH753 3.3 34.3 1.0 NE2 B:HIS412 3.3 19.4 1.0 CB B:LEU438 3.7 15.8 1.0 CA B:LEU438 3.7 14.9 1.0 O B:HOH1004 3.8 42.3 1.0 C B:ASN437 3.9 13.6 1.0 C B:LEU438 3.9 15.8 1.0 CE1 B:HIS477 3.9 27.1 1.0 CA B:ASN437 3.9 14.1 1.0 CE B:MET466 4.3 19.8 1.0 ND1 B:HIS412 4.3 17.7 1.0 CG B:HIS477 4.4 21.0 1.0 CD2 B:HIS412 4.5 21.1 1.0 O B:GLU436 4.6 14.6 1.0 OD1 B:ASN437 4.7 16.7 1.0 ND1 B:HIS477 4.8 22.7 1.0 CB B:ASN437 4.8 14.5 1.0 CG B:HIS412 5.0 18.1 1.0

A.Schmitt, H.Hirt, M.A.Jarva, W.S.Sun, J.Ter Beek, G.M.Dunny, R.P.Berntsson. Enterococcal Prga Extends Far Outside the Cell and Provides Surface Exclusion to Protect Against Unwanted Conjugation. J.Mol.Biol. V. 432 5681 2020.
ISSN: ESSN 1089-8638
PubMed: 32860774
DOI: 10.1016/J.JMB.2020.08.018