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Mercury in PDB 5cv3: C. Remanei Pgl-1 Dimerization Domain - Hg

Protein crystallography data

The structure of C. Remanei Pgl-1 Dimerization Domain - Hg, PDB code: 5cv3 was solved by S.T.Aoki, C.A.Bingman, M.Wickens, J.E.Kimble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.71 / 3.17
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.312, 87.312, 45.059, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 26.7

Mercury Binding Sites:

The binding sites of Mercury atom in the C. Remanei Pgl-1 Dimerization Domain - Hg (pdb code 5cv3). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the C. Remanei Pgl-1 Dimerization Domain - Hg, PDB code: 5cv3:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 5cv3

Go back to Mercury Binding Sites List in 5cv3
Mercury binding site 1 out of 2 in the C. Remanei Pgl-1 Dimerization Domain - Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of C. Remanei Pgl-1 Dimerization Domain - Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg501

b:0.8
occ:1.00
HG A:EMC501 0.0 0.8 1.0
C1 A:EMC501 2.0 92.6 1.0
SG A:CYS354 2.3 46.0 1.0
C2 A:EMC501 2.9 93.0 1.0
CD1 A:TRP356 3.5 41.6 1.0
CB A:CYS354 4.1 36.2 1.0
NE1 A:TRP356 4.3 41.3 1.0
CG A:TRP356 4.6 37.6 1.0
CA A:CYS354 4.9 34.3 1.0
CB A:TRP356 4.9 25.8 1.0

Mercury binding site 2 out of 2 in 5cv3

Go back to Mercury Binding Sites List in 5cv3
Mercury binding site 2 out of 2 in the C. Remanei Pgl-1 Dimerization Domain - Hg


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of C. Remanei Pgl-1 Dimerization Domain - Hg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:94.2
occ:1.00
HG A:EMC502 0.0 94.2 1.0
C1 A:EMC502 2.0 99.4 1.0
SG A:CYS262 2.3 10.6 1.0
O A:SER258 2.3 40.3 1.0
C2 A:EMC502 2.9 78.1 1.0
CB A:CYS262 3.0 23.2 1.0
N A:CYS262 3.2 30.0 1.0
C A:SER258 3.5 37.3 1.0
CA A:CYS262 3.6 26.7 1.0
OG A:SER258 3.8 27.8 1.0
C A:GLY261 3.9 26.7 1.0
CA A:SER258 4.2 20.8 1.0
CA A:GLY261 4.3 18.7 1.0
N A:GLN259 4.6 39.4 1.0
CB A:SER258 4.6 21.2 1.0
N A:GLY261 4.7 23.2 1.0
O A:GLY261 4.7 27.1 1.0
CA A:GLN259 4.8 30.0 1.0
O A:GLN259 4.9 25.1 1.0

Reference:

S.T.Aoki, A.M.Kershner, C.A.Bingman, M.Wickens, J.Kimble. Pgl Germ Granule Assembly Protein Is A Base-Specific, Single-Stranded Rnase. Proc.Natl.Acad.Sci.Usa V. 113 1279 2016.
ISSN: ESSN 1091-6490
PubMed: 26787882
DOI: 10.1073/PNAS.1524400113
Page generated: Sun Dec 13 19:12:28 2020

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