Mercury in PDB 6kr6: Crystal Structure of Drosophila Piwi

The structure of Crystal Structure of Drosophila Piwi, PDB code: 6kr6 was solved by S.Yamaguchi, A.Oe, K.Yamashita, S.Hirano, N.Mastumoto, R.Ishitani, H.Nishimasu, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.090, 115.640, 119.890, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 25.9

The structure of Crystal Structure of Drosophila Piwi also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Mercury atom in the Crystal Structure of Drosophila Piwi (pdb code 6kr6). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 7 binding sites of Mercury where determined in the Crystal Structure of Drosophila Piwi, PDB code: 6kr6:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7;

Mercury binding site 1 out of 7 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg904 b:0.6 occ:0.32 CB A:CYS317 3.1 0.0 1.0 CB A:ARG320 3.3 1.0 1.0 SG A:CYS317 3.4 0.9 1.0 N A:ARG320 3.9 0.8 1.0 CA A:ARG320 4.1 0.8 1.0 O A:ARG320 4.5 0.9 1.0 CA A:CYS317 4.5 0.7 1.0 N A:LYS318 4.7 0.7 1.0 C A:ARG320 4.7 0.6 1.0 N A:GLY319 4.8 0.9 1.0

Mercury binding site 2 out of 7 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg905 b:71.7 occ:0.72 SG A:CYS814 2.7 71.2 1.0 OD2 A:ASP685 2.8 0.3 1.0 CB A:CYS814 3.1 61.9 1.0 O A:CYS814 3.1 66.5 1.0 C A:CYS814 3.3 69.9 1.0 CG A:ASP685 3.7 92.5 1.0 CA A:CYS814 3.7 67.3 1.0 CB A:ASP685 3.8 83.8 1.0 CG2 A:VAL810 3.9 61.3 1.0 N A:GLN815 4.0 66.4 1.0 OD2 A:ASP614 4.1 87.8 1.0 CB A:VAL810 4.2 67.4 1.0 CG1 A:VAL810 4.3 72.3 1.0 CB A:LYS818 4.5 74.7 1.0 CA A:GLN815 4.5 59.0 1.0 CG A:ASP614 4.7 95.1 1.0 OD1 A:ASP685 4.8 94.6 1.0 CB A:ASP614 4.8 71.9 1.0 CA A:ASP685 5.0 85.2 1.0

Mercury binding site 3 out of 7 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg906 b:0.2 occ:0.70 OE1 A:GLN512 2.7 0.5 1.0 SG A:CYS531 2.7 0.4 1.0 OG A:SER534 2.8 98.9 1.0 O A:CYS531 3.2 0.9 1.0 CB A:ALA479 3.3 91.0 1.0 CB A:PRO536 3.5 88.5 1.0 CG A:PRO536 3.6 92.7 1.0 CB A:CYS531 3.8 0.6 1.0 C A:CYS531 3.9 0.1 1.0 CD A:GLN512 3.9 0.2 1.0 CB A:SER534 4.1 0.2 1.0 CD A:PRO536 4.2 89.8 1.0 CA A:CYS531 4.2 0.7 1.0 CA A:ALA479 4.4 94.2 1.0 CB A:GLN512 4.5 0.1 1.0 N A:ALA479 4.6 83.7 1.0 CA A:PRO536 4.6 90.5 1.0 N A:PRO536 4.6 91.5 1.0 C A:TRP478 4.7 84.0 1.0 O A:TRP478 4.8 88.9 1.0 CG A:GLN512 4.8 0.3 1.0 NE2 A:GLN512 4.8 0.9 1.0 N A:VAL532 4.9 0.5 1.0

Mercury binding site 4 out of 7 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg907 b:0.2 occ:0.56 HG A:HG907 0.0 0.2 0.6 SG A:CYS648 2.8 0.9 0.6 OG1 A:THR657 3.2 0.1 1.0 HG A:HG907 3.3 0.8 0.4 CB A:CYS648 4.0 0.6 0.6 CA A:CYS648 4.1 0.3 0.6 CA A:GLY627 4.1 71.7 1.0 N A:GLY627 4.1 73.3 1.0 CA A:CYS648 4.2 0.5 0.4 CG2 A:ILE615 4.3 85.2 1.0 N A:CYS648 4.4 0.4 0.6 CZ A:PHE613 4.4 82.6 1.0 N A:CYS648 4.5 0.7 0.4 SG A:CYS648 4.6 0.2 0.4 O A:GLU647 4.6 0.3 1.0 CB A:THR657 4.6 0.2 1.0 C A:GLU647 4.7 0.9 1.0 O A:THR646 4.7 93.5 1.0 CG2 A:THR646 4.8 92.0 1.0 C A:TYR626 5.0 76.8 1.0 CB A:CYS648 5.0 0.4 0.4 O A:ALA625 5.0 0.3 1.0

Mercury binding site 5 out of 7 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg907 b:0.8 occ:0.44 HG A:HG907 0.0 0.8 0.4 SG A:CYS648 1.9 0.9 0.6 SG A:CYS648 2.7 0.2 0.4 CB A:CYS648 3.3 0.6 0.6 HG A:HG907 3.3 0.2 0.6 CG2 A:ILE615 4.0 85.2 1.0 CB A:ALA625 4.0 0.9 1.0 CB A:CYS648 4.2 0.4 0.4 CA A:CYS648 4.5 0.3 0.6 CA A:CYS648 4.6 0.5 0.4 O A:ALA625 4.8 0.3 1.0 CB A:ILE615 4.9 86.6 1.0 C A:ALA625 5.0 0.7 1.0

Mercury binding site 6 out of 7 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg908 b:0.2 occ:0.59 NE2 A:GLN243 2.7 0.6 1.0 SG A:CYS188 2.7 1.0 1.0 OE1 A:GLN243 2.8 0.4 1.0 CB A:CYS188 2.8 0.3 1.0 CD A:GLN243 2.9 0.7 1.0 O A:CYS188 2.9 0.4 1.0 C A:CYS188 3.2 0.4 1.0 CA A:CYS188 3.6 0.2 1.0 CG A:GLN243 4.0 0.5 1.0 N A:ALA189 4.1 0.8 1.0 CA A:ALA189 4.6 0.3 1.0 N A:CYS188 4.9 0.1 1.0

Mercury binding site 7 out of 7 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg909 b:0.5 occ:0.49 SG A:CYS271 2.7 0.8 1.0 CB A:CYS271 3.1 0.7 1.0 CA A:CYS271 3.8 0.3 1.0 CB A:GLU281 3.9 0.7 1.0 O A:GLU281 4.3 0.8 1.0 O A:CYS271 4.4 0.5 1.0 C A:CYS271 4.5 0.6 1.0 C A:GLU281 4.5 0.2 1.0 CA A:GLU281 4.8 0.6 1.0 N A:CYS271 5.0 0.6 1.0 CB A:ASN285 5.0 0.9 1.0

S.Yamaguchi, A.Oe, K.Nishida, K.Yamashita, A.Kajiya, S.Hirano, N.Matsumoto, N.Dohmae, R.Ishitani, K.Saito, H.Siomi, H.Nishimasu, M.Siomi, O.Nureki. Crystal Structure of Drosophila Piwi. Nat Commun V. 11 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-14687-1