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

Protein crystallography data

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

Other elements in 5d9d:

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

Mercury Binding Sites:

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 5d9d

Go back to Mercury Binding Sites List in 5d9d
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 5d9d

Go back to Mercury Binding Sites List in 5d9d
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 5d9d

Go back to Mercury Binding Sites List in 5d9d
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

Reference:

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
Page generated: Sun Dec 13 19:12:31 2020

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