Magnesium in PDB 5xfe: Luciferin-Regenerating Enzyme Solved By Sad Using Xfel (Refined Against 11,000 Patterns)

Protein crystallography data

The structure of Luciferin-Regenerating Enzyme Solved By Sad Using Xfel (Refined Against 11,000 Patterns), PDB code: 5xfe 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) 24.57 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.900, 77.030, 84.530, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.3

Other elements in 5xfe:

The structure of Luciferin-Regenerating Enzyme Solved By Sad Using Xfel (Refined Against 11,000 Patterns) also contains other interesting chemical elements:

Mercury (Hg) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Luciferin-Regenerating Enzyme Solved By Sad Using Xfel (Refined Against 11,000 Patterns) (pdb code 5xfe). 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 Sad Using Xfel (Refined Against 11,000 Patterns), PDB code: 5xfe:

Magnesium binding site 1 out of 1 in 5xfe

Go back to Magnesium Binding Sites List in 5xfe
Magnesium binding site 1 out of 1 in the Luciferin-Regenerating Enzyme Solved By Sad Using Xfel (Refined Against 11,000 Patterns)


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 Sad Using Xfel (Refined Against 11,000 Patterns) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:14.7
occ:1.00
OD1 A:ASP212 2.0 13.9 1.0
OE1 A:GLU18 2.0 16.2 1.0
OD1 A:ASN160 2.0 17.1 1.0
O A:HOH549 2.1 16.4 1.0
O A:HOH518 2.1 16.3 1.0
O A:HOH629 2.2 18.4 1.0
CD A:GLU18 2.9 16.9 1.0
CG A:ASN160 3.0 18.2 1.0
CG A:ASP212 3.1 15.3 1.0
OE2 A:GLU18 3.3 17.3 1.0
ND2 A:ASN160 3.5 18.2 1.0
OD2 A:ASP212 3.7 17.8 1.0
O A:HOH519 3.7 21.9 1.0
O4 A:MPD404 3.9 22.6 1.0
ND2 A:ASN110 4.0 17.5 1.0
O A:THR255 4.2 14.7 1.0
CG A:GLU18 4.2 14.0 1.0
OD2 A:ASP111 4.3 18.1 1.0
N A:GLY213 4.3 16.6 1.0
CB A:ASN160 4.3 17.3 1.0
C A:ASP212 4.4 15.8 1.0
CB A:ASP212 4.4 13.7 1.0
O A:HOH539 4.5 30.8 1.0
O A:HOH527 4.5 20.9 1.0
CG A:ASP111 4.5 17.3 1.0
CB A:ASP111 4.5 15.0 1.0
CA A:ASP212 4.6 14.2 1.0
OD1 A:ASN110 4.7 20.9 1.0
CG A:ASN110 4.7 18.3 1.0
CA A:ASN160 4.8 16.8 1.0
O A:ASP212 4.8 16.3 1.0
CA A:GLY213 4.8 14.8 1.0

Reference:

K.Yamashita, N.Kuwabara, T.Nakane, T.Murai, E.Mizohata, M.Sugahara, D.Pan, T.Masuda, M.Suzuki, T.Sato, A.Kodan, T.Yamaguchi, E.Nango, T.Tanaka, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, H.Manya, T.Endo, R.Kato, T.Senda, H.Kato, S.Iwata, H.Ago, M.Yamamoto, F.Yumoto, T.Nakatsu. Experimental Phase Determination with Selenomethionine or Mercury-Derivatization in Serial Femtosecond Crystallography Iucrj V. 4 639 2017.
ISSN: ESSN 2052-2525
PubMed: 28989719
DOI: 10.1107/S2052252517008557
Page generated: Mon Dec 14 22:08:43 2020

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