Magnesium in PDB 3rlh: Crystal Structure of A Class II Phospholipase D From Loxosceles Intermedia Venom

All present enzymatic activity of Crystal Structure of A Class II Phospholipase D From Loxosceles Intermedia Venom:
3.1.4.41;

The structure of Crystal Structure of A Class II Phospholipase D From Loxosceles Intermedia Venom, PDB code: 3rlh was solved by P.O.Giuseppe, A.Ullah, S.S.Veiga, M.T.Murakami, R.K.Arni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.16 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.810, 49.300, 56.300, 90.00, 105.83, 90.00
R / Rfree (%)	17.2 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of A Class II Phospholipase D From Loxosceles Intermedia Venom (pdb code 3rlh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of A Class II Phospholipase D From Loxosceles Intermedia Venom, PDB code: 3rlh:

Magnesium binding site 1 out of 1 in the Crystal Structure of A Class II Phospholipase D From Loxosceles Intermedia Venom


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 A Class II Phospholipase D From Loxosceles Intermedia Venom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg286 b:14.3 occ:1.00 OE2 A:GLU32 2.0 12.5 1.0 OD1 A:ASP34 2.1 10.9 1.0 O A:HOH294 2.2 11.1 1.0 OD2 A:ASP91 2.2 11.8 1.0 O2 A:PEG289 2.2 2.0 0.5 O1 A:PEG289 2.2 3.9 0.5 C1 A:PEG291 2.8 5.6 0.5 CD A:GLU32 3.0 9.2 1.0 CG A:ASP34 3.1 15.9 1.0 CG A:ASP91 3.2 10.8 1.0 C1 A:PEG289 3.2 11.8 0.5 C3 A:PEG289 3.2 2.0 0.5 C2 A:PEG289 3.2 8.6 0.5 OE1 A:GLU32 3.3 11.9 1.0 CB A:ASP91 3.5 9.8 1.0 OD2 A:ASP34 3.5 14.4 1.0 O1 A:PEG291 3.7 2.0 0.5 C2 A:PEG291 3.8 2.0 0.5 O4 A:PEG289 3.9 5.7 0.5 CE A:LYS93 4.0 13.3 1.0 NZ A:LYS93 4.0 14.9 1.0 C3 A:PEG291 4.0 11.7 0.5 C4 A:PEG289 4.0 7.7 0.5 CD2 A:HIS47 4.1 20.3 1.0 CG A:GLU32 4.3 9.9 1.0 OD1 A:ASP91 4.3 13.3 1.0 CB A:ASP34 4.4 12.5 1.0 NE2 A:HIS12 4.5 15.8 1.0 O2 A:PEG291 4.5 11.6 0.5 NE2 A:HIS47 4.6 18.3 1.0 CD2 A:HIS12 4.7 13.5 1.0 CA A:ASP34 4.8 12.0 1.0 N A:ASP34 4.9 10.0 1.0 CA A:ASP91 5.0 10.3 1.0

P.O.De Giuseppe, A.Ullah, D.T.Silva, L.H.Gremski, A.C.Wille, D.Chaves Moreira, A.S.Ribeiro, O.M.Chaim, M.T.Murakami, S.S.Veiga, R.K.Arni. Structure of A Novel Class II Phospholipase D: Catalytic Cleft Is Modified By A Disulphide Bridge. Biochem.Biophys.Res.Commun. V. 409 622 2011.
ISSN: ISSN 0006-291X
PubMed: 21616057
DOI: 10.1016/J.BBRC.2011.05.053