Magnesium in PDB 8dx0: Vansc Ca Domain

All present enzymatic activity of Vansc Ca Domain:
2.7.13.3;

The structure of Vansc Ca Domain, PDB code: 8dx0 was solved by P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.16 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.7, 40.23, 64.71, 90, 91.64, 90
R / Rfree (%)	18.5 / 20

The binding sites of Magnesium atom in the Vansc Ca Domain (pdb code 8dx0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Vansc Ca Domain, PDB code: 8dx0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Vansc Ca Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vansc Ca Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:29.7 occ:1.00 O A:HOH503 2.1 44.9 1.0 O A:HOH564 2.2 43.0 1.0 OE2 A:GLU252 2.5 44.4 1.0 O A:HOH579 2.6 41.1 1.0 OE1 A:GLU252 2.6 44.4 1.0 CD A:GLU252 2.8 45.2 1.0 CG A:GLU252 4.1 36.2 1.0 O A:HOH504 4.2 43.9 1.0 NH1 A:ARG256 4.3 25.5 1.0 NE A:ARG256 4.7 27.0 1.0 O A:HOH529 4.7 44.7 1.0 CB A:GLU252 4.9 28.0 1.0 CZ A:ARG256 5.0 23.9 1.0

Magnesium binding site 2 out of 3 in the Vansc Ca Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vansc Ca Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:35.8 occ:1.00 O B:HOH589 1.9 42.5 1.0 O B:HOH516 1.9 43.6 1.0 O B:HOH553 2.2 41.0 1.0 O B:HOH503 2.2 38.9 1.0 OE2 B:GLU231 2.5 58.6 1.0 OE1 B:GLU231 2.7 56.2 1.0 CD B:GLU231 2.9 54.3 1.0 OD1 B:ASN234 3.1 35.4 1.0 CG B:ASN234 4.2 31.0 1.0 CG B:GLU231 4.4 37.9 1.0 CA B:ASN234 4.5 25.1 1.0 O B:HOH562 4.7 47.8 1.0 CB B:ASN234 4.8 29.7 1.0 CA B:GLU231 4.8 26.5 1.0 O B:HOH511 4.8 28.5 1.0 O B:HOH521 4.8 29.5 1.0 O B:LEU235 4.9 27.6 1.0

Magnesium binding site 3 out of 3 in the Vansc Ca Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Vansc Ca Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:49.0 occ:1.00 O B:HOH544 2.0 51.7 1.0 O B:HOH533 2.1 43.2 1.0 OD1 B:ASP250 2.4 48.1 1.0 OE1 B:GLU211 2.9 59.6 1.0 OD2 B:ASP250 3.0 42.3 1.0 CG B:ASP250 3.1 40.9 1.0 OE2 B:GLU252 3.1 52.2 1.0 OE2 B:GLU211 3.6 49.6 1.0 CD B:GLU211 3.6 55.0 1.0 CD B:GLU252 3.9 49.1 1.0 CG B:GLU252 4.0 41.3 1.0 CB B:GLU252 4.5 33.1 1.0 N B:GLU252 4.5 27.0 1.0 CB B:ASP250 4.5 29.5 1.0 N B:THR251 4.7 25.6 1.0 OE1 B:GLU252 4.9 41.0 1.0 CG B:GLU211 5.0 47.8 1.0

K.C.Grasty, C.Guzik, E.J.D'lauro, S.B.Padrick, J.Beld, P.J.Loll. Structure of Vans From Vancomycin-Resistant Enterococci: A Sensor Kinase with Weak Atp Binding. J.Biol.Chem. V. 299 03001 2023.
ISSN: ESSN 1083-351X
PubMed: 36764524
DOI: 10.1016/J.JBC.2023.103001