Magnesium in PDB 4f5d: Eris/Sting in Complex with Ligand

The structure of Eris/Sting in Complex with Ligand, PDB code: 4f5d was solved by Y.H.Huang, X.Y.Liu, X.D.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 3.00
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	111.850, 111.850, 35.020, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.2

The binding sites of Magnesium atom in the Eris/Sting in Complex with Ligand (pdb code 4f5d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Eris/Sting in Complex with Ligand, PDB code: 4f5d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Eris/Sting in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Eris/Sting in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:55.5 occ:1.00 OH A:TYR240 2.9 48.7 1.0 O A:GLY166 2.9 30.9 1.0 O2P A:C2E401 2.9 23.0 1.0 NH2 A:ARG232 2.9 38.5 1.0 NE A:ARG232 3.0 42.7 1.0 NH1 A:ARG238 3.4 28.7 1.0 CZ A:ARG232 3.4 36.3 1.0 C A:GLY166 3.8 25.6 1.0 CA A:GLY166 3.8 25.5 1.0 CZ A:ARG238 3.8 34.8 1.0 CZ A:TYR240 4.0 36.8 1.0 NH2 A:ARG238 4.0 41.2 1.0 O1P A:C2E401 4.0 64.9 1.0 P1 A:C2E401 4.1 52.2 1.0 CD A:ARG232 4.2 38.4 1.0 CD2 A:LEU170 4.2 44.1 1.0 CE2 A:TYR240 4.2 26.5 1.0 CG2 B:THR263 4.3 49.3 1.0 CG A:ARG232 4.5 38.5 1.0 O5' A:C2E401 4.5 18.8 1.0 NH1 A:ARG232 4.7 27.0 1.0 NE A:ARG238 4.7 33.5 1.0 CB A:ARG232 4.7 40.3 1.0

Magnesium binding site 2 out of 2 in the Eris/Sting in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Eris/Sting in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:59.7 occ:1.00 O21 A:C2E401 2.7 14.3 1.0 O B:GLY166 3.1 29.9 1.0 OH B:TYR240 3.1 48.6 1.0 NH1 B:ARG238 3.1 27.3 1.0 NH2 B:ARG232 3.2 36.9 1.0 NE B:ARG232 3.4 41.2 1.0 CZ B:ARG238 3.6 34.7 1.0 O11 A:C2E401 3.6 21.8 1.0 CZ B:ARG232 3.7 35.8 1.0 P11 A:C2E401 3.7 33.2 1.0 NH2 B:ARG238 3.7 39.8 1.0 C B:GLY166 3.9 23.5 1.0 CA B:GLY166 3.9 26.0 1.0 CG2 A:THR263 4.1 48.6 1.0 CZ B:TYR240 4.2 37.5 1.0 O5A A:C2E401 4.3 36.6 1.0 CE2 B:TYR240 4.4 26.1 1.0 CD B:ARG232 4.5 36.4 1.0 NE B:ARG238 4.5 33.2 1.0 CD2 B:LEU170 4.6 43.6 1.0 O3' A:C2E401 4.7 39.0 1.0 CG B:ARG232 4.7 40.9 1.0 CB B:ARG232 4.9 40.9 1.0 NH1 B:ARG232 4.9 26.6 1.0 OG1 A:THR263 5.0 34.1 1.0

Y.H.Huang, X.Y.Liu, X.X.Du, Z.F.Jiang, X.D.Su. The Structural Basis For the Sensing and Binding of Cyclic Di-Gmp By Sting Nat.Struct.Mol.Biol. V. 19 728 2012.
ISSN: ISSN 1545-9993
PubMed: 22728659
DOI: 10.1038/NSMB.2333