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Mercury in PDB 5d9c: Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Hg Derivative Data)

Protein crystallography data

The structure of Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Hg Derivative Data), PDB code: 5d9c 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) 24.71 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.100, 77.500, 84.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.5

Other elements in 5d9c:

The structure of Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Hg Derivative Data) 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 Siras Using Xfel (Refined Against Hg Derivative Data) (pdb code 5d9c). 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 Siras Using Xfel (Refined Against Hg Derivative Data), PDB code: 5d9c:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 5d9c

Go back to Mercury Binding Sites List in 5d9c
Mercury binding site 1 out of 2 in the Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Hg Derivative Data)


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 Siras Using Xfel (Refined Against Hg Derivative Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg403

b:23.2
occ:0.66
SG A:CYS52 1.9 23.4 0.5
O A:HOH662 2.3 18.6 1.0
SG A:CYS52 2.6 23.9 0.5
HG A:HG404 2.7 29.2 0.2
CD2 A:LEU82 2.8 33.8 0.4
CB A:CYS52 3.0 19.8 0.5
CD2 A:TRP84 3.3 22.5 1.0
CB A:CYS52 3.4 21.4 0.5
CG A:TRP84 3.4 22.5 1.0
CE3 A:TRP84 3.6 22.8 1.0
CD1 A:LEU82 3.6 33.0 0.4
CG A:LEU82 3.7 35.5 0.4
CD2 A:PHE39 3.7 19.7 1.0
CB A:TRP84 3.8 22.3 1.0
CE2 A:TRP84 3.9 25.0 1.0
CD1 A:TRP84 4.0 26.4 1.0
CG A:PHE39 4.2 17.6 1.0
CD2 A:LEU82 4.2 33.8 0.6
CB A:PHE39 4.2 17.1 1.0
NE1 A:TRP84 4.3 21.3 1.0
CZ3 A:TRP84 4.3 27.0 1.0
CE2 A:PHE39 4.4 19.6 1.0
CG A:PRO91 4.4 30.4 1.0
CA A:CYS52 4.5 21.1 0.5
CA A:CYS52 4.6 21.1 0.5
CB A:PRO91 4.6 27.8 1.0
CZ2 A:TRP84 4.7 21.4 1.0
O A:CYS52 4.7 17.8 0.5
C A:CYS52 4.8 19.7 0.5
CH2 A:TRP84 4.8 25.3 1.0
CA A:PRO91 4.9 24.9 1.0
N A:PRO91 4.9 23.8 1.0
CB A:LEU82 4.9 23.3 0.6
CB A:LEU82 5.0 23.3 0.4
CG A:LEU82 5.0 35.5 0.6

Mercury binding site 2 out of 2 in 5d9c

Go back to Mercury Binding Sites List in 5d9c
Mercury binding site 2 out of 2 in the Luciferin-Regenerating Enzyme Solved By Siras Using Xfel (Refined Against Hg Derivative Data)


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 Siras Using Xfel (Refined Against Hg Derivative Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg404

b:29.2
occ:0.16
CZ3 A:TRP84 2.5 27.0 1.0
CH2 A:TRP84 2.5 25.3 1.0
CB A:CYS52 2.6 19.8 0.5
HG A:HG403 2.7 23.2 0.7
CE3 A:TRP84 2.7 22.8 1.0
CZ2 A:TRP84 2.8 21.4 1.0
CB A:CYS52 2.9 21.4 0.5
SG A:CYS52 2.9 23.4 0.5
CD2 A:TRP84 2.9 22.5 1.0
CE2 A:TRP84 2.9 25.0 1.0
CB A:PHE39 3.2 17.1 1.0
N A:CYS52 3.7 20.7 0.5
SG A:CYS52 3.7 23.9 0.5
N A:CYS52 3.7 20.7 0.5
CA A:CYS52 3.7 21.1 0.5
CA A:CYS52 3.8 21.1 0.5
O A:HOH662 3.9 18.6 1.0
NE1 A:TRP84 3.9 21.3 1.0
CG A:TRP84 4.0 22.5 1.0
O A:PHE39 4.0 18.8 1.0
C A:PHE39 4.0 20.6 1.0
CG A:PHE39 4.1 17.6 1.0
CA A:PHE39 4.2 16.2 1.0
C A:PHE51 4.3 21.5 1.0
CD2 A:PHE39 4.4 19.7 1.0
O A:CYS52 4.4 17.8 0.5
CD1 A:TRP84 4.4 26.4 1.0
C A:CYS52 4.5 19.7 0.5
N A:HIS40 4.6 17.4 1.0
C A:CYS52 4.7 20.0 0.5
O A:PHE51 4.8 20.5 1.0
N A:PHE39 4.8 16.8 1.0
CD1 A:ILE61 4.9 22.7 1.0
CA A:PHE51 4.9 20.1 1.0
O A:CYS52 5.0 16.0 0.5
CB A:TRP84 5.0 22.3 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 Aug 11 06:17:24 2024

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