Atomistry » Mercury » PDB 5ca2-5l9w » 5gx1
Atomistry »
  Mercury »
    PDB 5ca2-5l9w »
      5gx1 »

Mercury in PDB 5gx1: Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 1.1 Mgy (1ST Measurement)

Protein crystallography data

The structure of Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 1.1 Mgy (1ST Measurement), PDB code: 5gx1 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) 42.10 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.415, 76.724, 84.206, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.3

Other elements in 5gx1:

The structure of Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 1.1 Mgy (1ST 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 1.1 Mgy (1ST Measurement) (pdb code 5gx1). 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 1.1 Mgy (1ST Measurement), PDB code: 5gx1:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 5gx1

Go back to Mercury Binding Sites List in 5gx1
Mercury binding site 1 out of 2 in the Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 1.1 Mgy (1ST 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 1.1 Mgy (1ST Measurement) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg401

b:10.0
occ:0.67
HG A:HG402 2.3 15.2 0.2
SG A:CYS52 2.5 12.3 1.0
CB A:CYS52 3.2 11.1 1.0
CD2 A:TRP84 3.3 9.0 1.0
CG A:TRP84 3.3 9.5 1.0
CD2 A:PHE39 3.5 8.8 1.0
CE3 A:TRP84 3.5 10.4 1.0
CB A:TRP84 3.7 9.8 1.0
CE2 A:TRP84 3.8 9.2 1.0
CD1 A:TRP84 3.9 9.1 1.0
CG A:PHE39 4.0 7.3 1.0
CD2 A:LEU82 4.0 15.2 1.0
CB A:PHE39 4.1 8.1 1.0
NE1 A:TRP84 4.1 9.2 1.0
CE2 A:PHE39 4.2 9.2 1.0
CG A:PRO91 4.3 13.3 1.0
CZ3 A:TRP84 4.3 10.5 1.0
CZ2 A:TRP84 4.6 9.4 1.0
CA A:CYS52 4.6 8.8 1.0
CB A:PRO91 4.7 13.6 1.0
CH2 A:TRP84 4.7 10.0 1.0
CB A:LEU82 4.8 12.3 1.0
CD A:PRO91 4.8 13.0 1.0
N A:PRO91 4.8 12.3 1.0
CA A:PRO91 4.9 11.8 1.0
CG A:LEU82 4.9 15.2 1.0
CD1 A:PHE39 5.0 8.6 1.0

Mercury binding site 2 out of 2 in 5gx1

Go back to Mercury Binding Sites List in 5gx1
Mercury binding site 2 out of 2 in the Luciferin-Regenerating Enzyme Collected with Serial Synchrotron Rotational Crystallography with Accumulated Dose of 1.1 Mgy (1ST 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 1.1 Mgy (1ST Measurement) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg402

b:15.2
occ:0.18
HG A:HG401 2.3 10.0 0.7
CE3 A:TRP84 3.6 10.4 1.0
CB A:LEU82 3.7 12.3 1.0
CB A:TRP84 3.7 9.8 1.0
CD2 A:LEU82 3.7 15.2 1.0
CD1 A:ILE61 3.7 9.6 1.0
CD1 A:PHE71 3.9 9.4 1.0
CD2 A:TRP84 4.0 9.0 1.0
CG A:TRP84 4.0 9.5 1.0
CD2 A:PHE39 4.1 8.8 1.0
CG A:PHE39 4.2 7.3 1.0
CG A:PHE71 4.2 8.3 1.0
CB A:PHE71 4.2 9.0 1.0
CG A:LEU82 4.3 15.2 1.0
CG1 A:VAL73 4.3 8.7 1.0
CE2 A:PHE39 4.4 9.2 1.0
CZ3 A:TRP84 4.5 10.5 1.0
CD1 A:PHE39 4.5 8.6 1.0
CB A:PHE39 4.6 8.1 1.0
CE1 A:PHE71 4.6 10.9 1.0
CG1 A:ILE61 4.7 8.9 1.0
SG A:CYS52 4.7 12.3 1.0
CZ A:PHE39 4.8 9.0 1.0
O A:LEU82 4.8 9.9 1.0
CE1 A:PHE39 4.8 8.9 1.0
CA A:LEU82 4.9 9.9 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 Aug 11 06:23:11 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy