Mercury in PDB 5d9d: Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature

The structure of Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature, PDB code: 5d9d 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)	41.86 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.107, 77.177, 84.916, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 17.8

The structure of Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature 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 Synchrotron Radiation at Room Temperature (pdb code 5d9d). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 3 binding sites of Mercury where determined in the Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature, PDB code: 5d9d:
Jump to Mercury binding site number: 1; 2; 3;

Mercury binding site 1 out of 3 in the Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature


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 Synchrotron Radiation at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg402 b:16.4 occ:0.51 SG A:CYS52 2.2 25.4 1.0 O A:HOH657 2.3 14.4 1.0 HG A:HG403 2.7 17.8 0.2 CD2 A:LEU82 2.7 15.7 0.5 CB A:CYS52 3.1 20.6 1.0 CD2 A:TRP84 3.3 17.4 1.0 CG A:TRP84 3.5 15.1 1.0 CE3 A:TRP84 3.6 18.9 1.0 HG A:HG404 3.6 31.2 0.1 CD2 A:PHE39 3.7 12.7 1.0 CG A:LEU82 3.8 20.9 0.5 CB A:TRP84 3.8 17.0 1.0 CD1 A:LEU82 3.8 22.0 0.5 CE2 A:TRP84 4.0 19.9 1.0 CD1 A:TRP84 4.0 15.5 1.0 CD2 A:LEU82 4.2 15.3 0.5 CG A:PHE39 4.2 10.3 1.0 CB A:PHE39 4.2 11.9 1.0 NE1 A:TRP84 4.3 13.6 1.0 CZ3 A:TRP84 4.3 19.3 1.0 CE2 A:PHE39 4.3 12.9 1.0 CG A:PRO91 4.5 22.7 1.0 CA A:CYS52 4.5 13.7 1.0 CB A:PRO91 4.6 22.1 1.0 CZ2 A:TRP84 4.6 20.5 1.0 CH2 A:TRP84 4.8 20.6 1.0 CA A:PRO91 4.9 16.8 1.0 CB A:LEU82 4.9 20.9 0.5 C A:CYS52 4.9 11.8 1.0 N A:PRO91 4.9 18.8 1.0 CB A:LEU82 5.0 20.3 0.5 CG A:LEU82 5.0 21.5 0.5

Mercury binding site 2 out of 3 in the Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature


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 Synchrotron Radiation at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg403 b:17.8 occ:0.20 CZ3 A:TRP84 2.4 19.3 1.0 CH2 A:TRP84 2.4 20.6 1.0 CB A:CYS52 2.5 20.6 1.0 CE3 A:TRP84 2.6 18.9 1.0 CZ2 A:TRP84 2.7 20.5 1.0 HG A:HG402 2.7 16.4 0.5 CD2 A:TRP84 2.9 17.4 1.0 CE2 A:TRP84 2.9 19.9 1.0 SG A:CYS52 3.2 25.4 1.0 CB A:PHE39 3.3 11.9 1.0 CA A:CYS52 3.8 13.7 1.0 N A:CYS52 3.8 11.8 1.0 NE1 A:TRP84 3.9 13.6 1.0 O A:HOH657 3.9 14.4 1.0 O A:PHE39 3.9 13.0 1.0 CG A:TRP84 4.0 15.1 1.0 C A:PHE39 4.1 11.9 1.0 CG A:PHE39 4.2 10.3 1.0 C A:PHE51 4.3 15.1 1.0 CA A:PHE39 4.3 8.7 1.0 CD2 A:PHE39 4.4 12.7 1.0 CD1 A:TRP84 4.4 15.5 1.0 N A:HIS40 4.6 9.9 1.0 C A:CYS52 4.7 11.8 1.0 HG A:HG404 4.7 31.2 0.1 O A:CYS52 4.7 16.4 1.0 CD1 A:ILE61 4.8 16.0 1.0 O A:PHE51 4.8 14.7 1.0 CA A:PHE51 4.9 14.3 1.0 CB A:TRP84 4.9 17.0 1.0 N A:PHE39 4.9 8.9 1.0

Mercury binding site 3 out of 3 in the Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Luciferin-Regenerating Enzyme Solved By Sad Using Synchrotron Radiation at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg404 b:31.2 occ:0.12 C A:ALA90 2.2 22.7 1.0 SG A:CYS52 2.2 25.4 1.0 N A:PRO91 2.4 18.8 1.0 O A:ALA90 2.6 18.0 1.0 CA A:ALA90 2.7 22.2 1.0 N A:ALA90 3.1 21.2 1.0 CB A:CYS52 3.1 20.6 1.0 CA A:PRO91 3.1 16.8 1.0 CD A:PRO91 3.1 24.1 1.0 CD1 A:TRP84 3.2 15.5 1.0 NE1 A:TRP84 3.3 13.6 1.0 C A:ALA89 3.5 18.3 1.0 O A:SER88 3.5 14.8 1.0 HG A:HG402 3.6 16.4 0.5 CG A:PRO91 3.7 22.7 1.0 O A:ALA89 3.8 18.5 1.0 CA A:CYS52 3.8 13.7 1.0 CB A:PRO91 3.9 22.1 1.0 CG A:TRP84 4.0 15.1 1.0 CE2 A:TRP84 4.1 19.9 1.0 CB A:ALA90 4.2 23.1 1.0 C A:PRO91 4.3 20.1 1.0 C A:SER88 4.4 14.7 1.0 N A:LYS53 4.4 10.2 1.0 CD2 A:TRP84 4.4 17.4 1.0 C A:CYS52 4.5 11.8 1.0 CA A:ALA89 4.5 12.9 1.0 HG A:HG403 4.7 17.8 0.2 CB A:TRP84 4.7 17.0 1.0 O A:HOH554 4.8 21.1 1.0 N A:ALA89 4.8 13.6 1.0 O A:LYS53 4.9 13.9 1.0 O A:PRO91 4.9 21.2 1.0 CZ2 A:TRP84 5.0 20.5 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