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

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

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

Magnesium

(Mg)

1 atom

The binding sites of Mercury 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 Mercury atom.
In total 2 binding sites of Mercury where determined in the Luciferin-Regenerating Enzyme Solved By Sad Using Xfel (Refined Against 11,000 Patterns), PDB code: 5xfe:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 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 Mercury with other atoms in the Hg 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:Hg401 b:19.5 occ:0.65 O A:HOH660 2.3 13.1 1.0 SG A:CYS52 2.3 25.3 1.0 HG A:HG402 2.7 19.4 0.1 CB A:CYS52 3.1 21.4 1.0 CD2 A:TRP84 3.3 19.3 1.0 CG A:TRP84 3.4 19.7 1.0 CE3 A:TRP84 3.6 19.3 1.0 CD2 A:PHE39 3.7 15.7 1.0 CB A:TRP84 3.7 19.0 1.0 CE2 A:TRP84 3.9 19.8 1.0 CD1 A:TRP84 4.0 20.4 1.0 CD2 A:LEU82 4.0 25.9 1.0 CG A:PHE39 4.2 16.3 1.0 CB A:PHE39 4.2 16.5 1.0 NE1 A:TRP84 4.2 18.0 1.0 CE2 A:PHE39 4.3 18.1 1.0 CZ3 A:TRP84 4.4 21.4 1.0 CB A:PRO91 4.5 25.3 1.0 CA A:CYS52 4.5 17.2 1.0 CZ2 A:TRP84 4.7 21.6 1.0 CD A:PRO91 4.8 22.9 1.0 CG A:PRO91 4.8 27.7 1.0 CH2 A:TRP84 4.8 19.7 1.0 CA A:PRO91 4.8 20.7 1.0 CB A:LEU82 4.8 23.8 1.0 N A:PRO91 4.9 21.2 1.0 CG A:LEU82 4.9 29.7 1.0 C A:CYS52 4.9 18.2 1.0

Mercury binding site 2 out of 2 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 Mercury with other atoms in the Hg binding site number 2 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:Hg402 b:19.4 occ:0.14 CB A:CYS52 2.5 21.4 1.0 CZ3 A:TRP84 2.5 21.4 1.0 CH2 A:TRP84 2.5 19.7 1.0 HG A:HG401 2.7 19.5 0.7 CE3 A:TRP84 2.7 19.3 1.0 CZ2 A:TRP84 2.7 21.6 1.0 CE2 A:TRP84 2.9 19.8 1.0 CD2 A:TRP84 2.9 19.3 1.0 CB A:PHE39 3.2 16.5 1.0 SG A:CYS52 3.3 25.3 1.0 CA A:CYS52 3.7 17.2 1.0 N A:CYS52 3.8 16.5 1.0 NE1 A:TRP84 3.8 18.0 1.0 O A:HOH660 3.9 13.1 1.0 CG A:TRP84 3.9 19.7 1.0 O A:PHE39 4.0 17.2 1.0 C A:PHE39 4.1 15.7 1.0 CG A:PHE39 4.1 16.3 1.0 CA A:PHE39 4.2 14.7 1.0 C A:PHE51 4.3 20.6 1.0 CD2 A:PHE39 4.4 15.7 1.0 CD1 A:TRP84 4.4 20.4 1.0 N A:HIS40 4.6 14.4 1.0 C A:CYS52 4.6 18.2 1.0 O A:CYS52 4.7 18.4 1.0 O A:PHE51 4.8 19.8 1.0 CD1 A:ILE61 4.8 17.1 1.0 N A:PHE39 4.8 13.8 1.0 CB A:TRP84 4.9 19.0 1.0 CA A:PHE51 4.9 20.3 1.0

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