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:
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
Go back to
Mercury Binding Sites List in 6kr6
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
Go back to
Mercury Binding Sites List in 6kr6
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
Go back to
Mercury Binding Sites List in 6kr6
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
Go back to
Mercury Binding Sites List in 6kr6
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
Go back to
Mercury Binding Sites List in 6kr6
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
Go back to
Mercury Binding Sites List in 6kr6
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
Go back to
Mercury Binding Sites List in 6kr6
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 Aug 11 07:27:33 2024
|