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Mercury in PDB 6kr6: Crystal Structure of Drosophila Piwi

Protein crystallography data

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

Other elements in 6kr6:

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

Zinc (Zn) 8 atoms

Mercury Binding Sites:

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 6kr6

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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 6kr6

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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 6kr6

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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 6kr6

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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 6kr6

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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 6kr6

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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 6kr6

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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

Reference:

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
Page generated: Sun Dec 13 19:15:22 2020

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