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Mercury in PDB 5gx3: Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement)

Protein crystallography data

The structure of Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement), PDB code: 5gx3 was solved by K.Hasegawa, K.Yamashita, T.Murai, N.Nuemket, K.Hirata, G.Ueno, H.Ago, T.Nakatsu, T.Kumasaka, M.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.16 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.469, 76.859, 84.326, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.2

Other elements in 5gx3:

The structure of Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement) (pdb code 5gx3). 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 Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement), PDB code: 5gx3:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 5gx3

Go back to Mercury Binding Sites List in 5gx3
Mercury binding site 1 out of 2 in the Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement)


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 Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg401

b:20.6
occ:0.55
HG A:HG402 2.0 15.6 0.2
SG A:CYS52 2.7 14.7 1.0
CB A:CYS52 3.2 13.5 1.0
CD2 A:TRP84 3.3 11.4 1.0
CG A:TRP84 3.4 11.9 1.0
CE3 A:TRP84 3.5 12.8 1.0
CD2 A:PHE39 3.5 11.2 1.0
CB A:TRP84 3.6 12.2 1.0
CD2 A:LEU82 3.9 17.6 1.0
CE2 A:TRP84 4.0 11.7 1.0
CG A:PHE39 4.0 9.7 1.0
CD1 A:TRP84 4.0 11.5 1.0
CB A:PHE39 4.1 10.5 1.0
CE2 A:PHE39 4.2 11.7 1.0
CZ3 A:TRP84 4.3 12.9 1.0
NE1 A:TRP84 4.3 11.6 1.0
CG A:PRO91 4.4 15.7 1.0
CZ2 A:TRP84 4.7 11.9 1.0
CB A:LEU82 4.7 14.8 1.0
CA A:CYS52 4.7 11.2 1.0
CB A:PRO91 4.8 16.0 1.0
CG A:LEU82 4.8 17.6 1.0
CH2 A:TRP84 4.8 12.5 1.0
CD1 A:PHE39 4.9 11.0 1.0
CA A:PRO91 5.0 14.2 1.0

Mercury binding site 2 out of 2 in 5gx3

Go back to Mercury Binding Sites List in 5gx3
Mercury binding site 2 out of 2 in the Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement)


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 Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 6.9 Mgy (6TH Measurement) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg402

b:15.6
occ:0.20
HG A:HG401 2.0 20.6 0.6
CD1 A:ILE61 3.6 12.0 1.0
CE3 A:TRP84 3.6 12.8 1.0
CD2 A:LEU82 3.6 17.6 1.0
CD2 A:PHE39 3.8 11.2 1.0
CB A:LEU82 3.9 14.8 1.0
CG A:PHE39 3.9 9.7 1.0
CB A:TRP84 3.9 12.2 1.0
CD2 A:TRP84 4.0 11.4 1.0
CD1 A:PHE71 4.2 11.8 1.0
CG A:TRP84 4.2 11.9 1.0
CE2 A:PHE39 4.2 11.7 1.0
CB A:PHE39 4.3 10.5 1.0
CD1 A:PHE39 4.3 11.0 1.0
CG1 A:VAL73 4.3 11.1 1.0
CG A:LEU82 4.4 17.6 1.0
CZ3 A:TRP84 4.4 12.9 1.0
CG A:PHE71 4.4 10.8 1.0
CB A:PHE71 4.5 11.4 1.0
CG1 A:ILE61 4.6 11.4 1.0
CZ A:PHE39 4.6 11.5 1.0
CE1 A:PHE39 4.6 11.4 1.0
SG A:CYS52 4.7 14.7 1.0
CE1 A:PHE71 4.8 13.3 1.0

Reference:

K.Hasegawa, K.Yamashita, T.Murai, N.Nuemket, K.Hirata, G.Ueno, H.Ago, T.Nakatsu, T.Kumasaka, M.Yamamoto. Development of A Dose-Limiting Data Collection Strategy For Serial Synchrotron Rotation Crystallography J Synchrotron Radiat V. 24 29 2017.
ISSN: ESSN 1600-5775
PubMed: 28009544
DOI: 10.1107/S1600577516016362
Page generated: Sun Dec 13 19:12:45 2020

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