Magnesium in PDB 5d9b: Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Native Data)

The structure of Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Native Data), PDB code: 5d9b was solved by K.Yamashita, D.Pan, T.Okuda, T.Murai, A.Kodan, T.Yamaguchi, K.Gomi, N.Kajiyama, H.Kato, H.Ago, M.Yamamoto, T.Nakatsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.210, 77.590, 84.760, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.2

The binding sites of Magnesium atom in the Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Native Data) (pdb code 5d9b). 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 Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Native Data), PDB code: 5d9b:

Magnesium binding site 1 out of 1 in the Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Native Data)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Native Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:16.2 occ:1.00 OD1 A:ASP212 2.0 19.0 1.0 O A:HOH549 2.0 18.5 1.0 OE1 A:GLU18 2.0 16.7 1.0 OD1 A:ASN160 2.1 19.8 1.0 O A:HOH515 2.2 17.4 1.0 O A:HOH611 2.2 18.2 1.0 CD A:GLU18 3.0 18.3 1.0 CG A:ASN160 3.0 18.4 1.0 CG A:ASP212 3.1 17.3 1.0 OE2 A:GLU18 3.4 18.7 1.0 ND2 A:ASN160 3.5 17.5 1.0 OD2 A:ASP212 3.7 21.0 1.0 O A:HOH520 3.7 25.5 1.0 O4 A:MPD402 4.0 24.6 1.0 ND2 A:ASN110 4.1 20.9 1.0 O A:THR255 4.2 15.8 1.0 CG A:GLU18 4.3 15.0 1.0 OD2 A:ASP111 4.3 21.1 1.0 N A:GLY213 4.3 14.8 1.0 CB A:ASN160 4.3 16.2 1.0 CB A:ASP212 4.3 15.1 1.0 C A:ASP212 4.4 16.9 1.0 O A:HOH543 4.5 22.2 1.0 CG A:ASP111 4.6 19.0 1.0 CA A:ASP212 4.6 15.0 1.0 CB A:ASP111 4.6 14.8 1.0 OD1 A:ASN110 4.7 22.5 1.0 CG A:ASN110 4.8 21.4 1.0 CA A:ASN160 4.8 17.5 1.0 CA A:GLY213 4.8 17.3 1.0 O A:ASP212 4.9 18.1 1.0

K.Yamashita, D.Pan, T.Okuda, M.Sugahara, A.Kodan, T.Yamaguchi, T.Murai, K.Gomi, N.Kajiyama, E.Mizohata, M.Suzuki, E.Nango, K.Tono, Y.Joti, T.Kameshima, J.Park, C.Song, T.Hatsui, M.Yabashi, S.Iwata, H.Kato, H.Ago, M.Yamamoto, T.Nakatsu. An Isomorphous Replacement Method For Efficient De Novo Phasing For Serial Femtosecond Crystallography. Sci Rep V. 5 14017 2015.
ISSN: ESSN 2045-2322
PubMed: 26360462
DOI: 10.1038/SREP14017