Magnesium in PDB 4knv: The Crystal Structure of Apo Human HDHD4 From Se-Mad

All present enzymatic activity of The Crystal Structure of Apo Human HDHD4 From Se-Mad:
3.1.3.29;

The structure of The Crystal Structure of Apo Human HDHD4 From Se-Mad, PDB code: 4knv was solved by H.E.Klei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.36 / 1.99
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.340, 53.436, 63.958, 65.50, 74.99, 85.17
R / Rfree (%)	20 / 24.6

The binding sites of Magnesium atom in the The Crystal Structure of Apo Human HDHD4 From Se-Mad (pdb code 4knv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of Apo Human HDHD4 From Se-Mad, PDB code: 4knv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of Apo Human HDHD4 From Se-Mad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Apo Human HDHD4 From Se-Mad within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:13.5 occ:1.00 O A:ASP14 2.3 10.7 1.0 O A:HOH412 2.4 12.2 1.0 O3 A:PO4301 2.5 10.9 1.0 OD1 A:ASP189 2.5 12.6 1.0 O A:HOH402 2.5 17.6 1.0 OD2 A:ASP12 2.5 13.9 1.0 CG A:ASP12 3.3 14.0 1.0 OD1 A:ASP12 3.3 14.0 1.0 C A:ASP14 3.4 11.9 1.0 CG A:ASP189 3.6 16.5 1.0 OG1 A:THR190 3.8 13.4 1.0 P A:PO4301 3.9 11.4 1.0 CB A:ASP14 4.0 10.4 1.0 OD2 A:ASP189 4.1 19.1 1.0 CA A:ASP14 4.1 9.3 1.0 O A:HOH486 4.1 20.9 1.0 N A:ASP14 4.2 9.5 1.0 OD2 A:ASP194 4.2 14.1 1.0 CB A:ASN15 4.3 9.9 1.0 OG1 A:THR16 4.3 12.7 1.0 O A:HOH401 4.4 14.4 1.0 N A:ASN15 4.5 9.5 1.0 O4 A:PO4301 4.6 8.8 1.0 O1 A:PO4301 4.6 14.2 1.0 N A:THR16 4.6 15.8 1.0 ND2 A:ASN15 4.6 10.2 1.0 O A:HOH434 4.7 24.0 1.0 CB A:ASP12 4.7 12.3 1.0 CA A:ASN15 4.8 10.6 1.0 N A:ASP189 4.8 12.8 1.0 CB A:ASP189 4.8 12.4 1.0 O2 A:PO4301 4.8 11.2 1.0 C A:ASN15 4.9 16.6 1.0 C A:LEU13 4.9 11.6 1.0 CB A:THR190 4.9 16.1 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of Apo Human HDHD4 From Se-Mad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Apo Human HDHD4 From Se-Mad within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:16.6 occ:1.00 O B:ASP14 2.3 11.7 1.0 OD1 B:ASP189 2.4 15.2 1.0 O B:HOH448 2.4 13.4 1.0 OD2 B:ASP12 2.5 13.6 1.0 O4 B:PO4301 2.5 10.6 1.0 O B:HOH402 2.7 15.4 1.0 CG B:ASP12 3.3 13.1 1.0 OD1 B:ASP12 3.3 11.2 1.0 C B:ASP14 3.5 13.2 1.0 CG B:ASP189 3.6 17.7 1.0 O B:HOH476 3.6 23.1 1.0 OG1 B:THR190 3.8 14.3 1.0 P B:PO4301 4.0 10.9 1.0 CB B:ASP14 4.1 10.4 1.0 CA B:ASP14 4.1 11.5 1.0 OD2 B:ASP189 4.1 18.8 1.0 OD2 B:ASP194 4.2 13.2 1.0 N B:ASP14 4.2 12.4 1.0 OG1 B:THR16 4.3 14.1 1.0 CB B:ASN15 4.4 12.1 1.0 O B:HOH401 4.4 12.6 1.0 N B:ASN15 4.5 12.0 1.0 N B:ASP189 4.6 14.4 1.0 O2 B:PO4301 4.7 12.4 1.0 CB B:ASP189 4.7 15.1 1.0 O3 B:PO4301 4.7 12.1 1.0 CB B:ASP12 4.7 12.3 1.0 O B:HOH437 4.7 25.8 1.0 ND2 B:ASN15 4.7 10.5 1.0 N B:THR16 4.8 14.4 1.0 O1 B:PO4301 4.8 13.3 1.0 CA B:ASN15 4.8 12.6 1.0 CB B:THR190 4.9 13.3 1.0 C B:ASN15 4.9 17.2 1.0 N B:THR190 4.9 13.4 1.0 C B:LEU13 4.9 12.8 1.0

S.H.Kim, K.L.Constantine, G.J.Duke, V.Goldfarb, J.T.Hunt, S.Johnson, K.Kish, H.E.Klei, P.A.Mcdonnell, W.J.Metzler, L.Mueller, M.A.Poss, C.R.Fairchild, R.S.Bhide. Design, Synthesis, Functional and Structural Characterization of An Inhibitor of N-Acetylneuraminate-9-Phosphate Phosphatase: Observation of Extensive Dynamics in An Enzyme/Inhibitor Complex. Bioorg.Med.Chem.Lett. V. 23 4107 2013.
ISSN: ISSN 0960-894X
PubMed: 23747226
DOI: 10.1016/J.BMCL.2013.05.052