Mercury in PDB 1wsp: Crystal Structure of Axin Dix Domain
Protein crystallography data
The structure of Crystal Structure of Axin Dix Domain, PDB code: 1wsp
was solved by
N.Shibata,
T.Hanamura,
R.Yamamoto,
Y.Ueda,
H.Yamamoto,
A.Kikuchi,
Y.Higuchi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.17 /
2.90
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.130,
92.130,
85.540,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
24.6 /
31.1
|
Mercury Binding Sites:
The binding sites of Mercury atom in the Crystal Structure of Axin Dix Domain
(pdb code 1wsp). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the
Crystal Structure of Axin Dix Domain, PDB code: 1wsp:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Mercury binding site 1 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 1 out
of 9 in the Crystal Structure of Axin Dix Domain
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 Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1094
b:0.4
occ:0.68
|
O
|
A:HOH184
|
2.9
|
73.6
|
1.0
|
SG
|
A:CYS750
|
2.9
|
89.1
|
1.0
|
OG
|
A:SER752
|
3.4
|
52.2
|
1.0
|
O
|
A:SER752
|
3.9
|
66.1
|
1.0
|
CB
|
A:CYS750
|
3.9
|
82.3
|
1.0
|
CA
|
A:CYS750
|
4.3
|
78.8
|
1.0
|
CB
|
A:SER752
|
4.5
|
49.1
|
1.0
|
C
|
A:SER752
|
4.6
|
61.8
|
1.0
|
N
|
A:SER752
|
4.8
|
67.6
|
1.0
|
CA
|
A:SER752
|
4.9
|
64.8
|
1.0
|
NH1
|
A:ARG773
|
4.9
|
0.8
|
1.0
|
C
|
A:CYS750
|
4.9
|
78.0
|
1.0
|
N
|
A:ASP751
|
5.0
|
71.5
|
1.0
|
NH2
|
A:ARG773
|
5.0
|
98.8
|
1.0
|
|
Mercury binding site 2 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 2 out
of 9 in the Crystal Structure of Axin Dix Domain
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 Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1095
b:64.2
occ:1.00
|
C4
|
A:BEZ501
|
2.2
|
81.1
|
1.0
|
SG
|
A:CYS760
|
2.3
|
51.6
|
1.0
|
C5
|
A:BEZ501
|
2.6
|
69.2
|
1.0
|
CB
|
A:CYS760
|
2.8
|
23.3
|
1.0
|
CE1
|
A:PHE759
|
3.3
|
24.9
|
1.0
|
C3
|
A:BEZ501
|
3.4
|
77.0
|
1.0
|
CZ
|
A:PHE759
|
3.8
|
26.7
|
1.0
|
OH
|
A:TYR790
|
4.0
|
75.6
|
1.0
|
C6
|
A:BEZ501
|
4.0
|
76.8
|
1.0
|
CE1
|
A:TYR790
|
4.0
|
33.9
|
1.0
|
CD1
|
A:PHE759
|
4.1
|
20.8
|
1.0
|
CA
|
A:CYS760
|
4.3
|
34.0
|
1.0
|
CB
|
A:LYS830
|
4.3
|
35.4
|
1.0
|
O
|
A:HOH105
|
4.5
|
53.6
|
1.0
|
CZ
|
A:TYR790
|
4.5
|
45.0
|
1.0
|
CD
|
A:LYS830
|
4.5
|
35.2
|
1.0
|
C2
|
A:BEZ501
|
4.6
|
71.0
|
1.0
|
CE2
|
A:PHE759
|
4.8
|
31.6
|
1.0
|
C1
|
A:BEZ501
|
4.8
|
81.7
|
1.0
|
N
|
A:CYS760
|
4.8
|
39.6
|
1.0
|
CG
|
A:LYS830
|
4.9
|
51.4
|
1.0
|
|
Mercury binding site 3 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 3 out
of 9 in the Crystal Structure of Axin Dix Domain
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 Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1096
b:91.3
occ:0.45
|
SG
|
A:CYS803
|
2.5
|
0.6
|
1.0
|
CB
|
A:CYS803
|
3.4
|
87.9
|
1.0
|
N
|
A:CYS803
|
3.6
|
74.5
|
1.0
|
CB
|
A:ASP802
|
3.8
|
68.2
|
1.0
|
CA
|
A:CYS803
|
4.0
|
67.0
|
1.0
|
C
|
A:ASP802
|
4.0
|
74.6
|
1.0
|
CA
|
A:ASP802
|
4.5
|
69.5
|
1.0
|
O
|
A:ASP802
|
4.6
|
85.9
|
1.0
|
O
|
A:HOH197
|
4.6
|
53.6
|
1.0
|
OD2
|
A:ASP802
|
4.9
|
80.1
|
1.0
|
CG
|
A:ASP802
|
4.9
|
81.1
|
1.0
|
|
Mercury binding site 4 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 4 out
of 9 in the Crystal Structure of Axin Dix Domain
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 Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg1194
b:82.0
occ:0.64
|
SG
|
B:CYS750
|
3.0
|
98.9
|
1.0
|
O
|
B:SER752
|
3.1
|
52.3
|
1.0
|
O
|
B:HOH53
|
3.6
|
64.1
|
1.0
|
CB
|
B:CYS750
|
4.0
|
90.7
|
1.0
|
N
|
B:ASP751
|
4.0
|
71.7
|
1.0
|
CA
|
B:CYS750
|
4.1
|
84.7
|
1.0
|
N
|
B:SER752
|
4.2
|
50.6
|
1.0
|
OG
|
B:SER752
|
4.2
|
55.9
|
1.0
|
C
|
B:SER752
|
4.2
|
52.7
|
1.0
|
OD2
|
B:ASP751
|
4.3
|
65.0
|
1.0
|
C
|
B:CYS750
|
4.5
|
77.8
|
1.0
|
CA
|
B:SER752
|
4.7
|
52.2
|
1.0
|
|
Mercury binding site 5 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 5 out
of 9 in the Crystal Structure of Axin Dix Domain
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 Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg1195
b:82.7
occ:0.80
|
SG
|
B:CYS760
|
2.6
|
54.5
|
1.0
|
CE1
|
B:PHE759
|
3.4
|
12.5
|
1.0
|
OH
|
B:TYR790
|
3.4
|
37.8
|
1.0
|
CB
|
B:CYS760
|
3.6
|
52.0
|
1.0
|
CZ
|
B:PHE759
|
3.7
|
26.4
|
1.0
|
CE2
|
B:TYR790
|
3.9
|
25.7
|
1.0
|
O
|
B:HOH60
|
4.0
|
37.1
|
1.0
|
CZ
|
B:TYR790
|
4.1
|
44.9
|
1.0
|
CD1
|
B:PHE759
|
4.2
|
24.3
|
1.0
|
CB
|
B:LYS830
|
4.2
|
63.0
|
1.0
|
O
|
B:HOH63
|
4.3
|
48.2
|
1.0
|
CE2
|
B:PHE759
|
4.7
|
35.0
|
1.0
|
CG
|
B:LYS830
|
4.9
|
50.0
|
1.0
|
CA
|
B:CYS760
|
5.0
|
54.8
|
1.0
|
|
Mercury binding site 6 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 6 out
of 9 in the Crystal Structure of Axin Dix Domain
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 Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg1196
b:87.5
occ:0.63
|
SG
|
B:CYS803
|
4.2
|
84.4
|
1.0
|
O
|
B:HOH64
|
4.5
|
38.3
|
1.0
|
|
Mercury binding site 7 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 7 out
of 9 in the Crystal Structure of Axin Dix Domain
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 Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg295
b:71.8
occ:0.80
|
SG
|
C:CYS760
|
2.4
|
48.0
|
1.0
|
OH
|
C:TYR790
|
3.3
|
44.6
|
1.0
|
CZ
|
C:PHE759
|
3.4
|
17.4
|
1.0
|
CB
|
C:CYS760
|
3.5
|
39.8
|
1.0
|
CE1
|
C:PHE759
|
3.6
|
30.4
|
1.0
|
O
|
C:HOH24
|
3.8
|
39.5
|
1.0
|
CE2
|
C:TYR790
|
3.9
|
20.7
|
1.0
|
CZ
|
C:TYR790
|
4.0
|
51.0
|
1.0
|
CE2
|
C:PHE759
|
4.2
|
30.0
|
1.0
|
CB
|
C:LYS830
|
4.2
|
52.6
|
1.0
|
CD1
|
C:PHE759
|
4.4
|
43.1
|
1.0
|
O
|
C:HOH66
|
4.4
|
56.8
|
1.0
|
CG
|
C:LYS830
|
4.6
|
52.8
|
1.0
|
O
|
C:HOH146
|
4.6
|
67.1
|
1.0
|
CA
|
C:CYS760
|
4.9
|
37.3
|
1.0
|
CD2
|
C:PHE759
|
4.9
|
44.2
|
1.0
|
|
Mercury binding site 8 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 8 out
of 9 in the Crystal Structure of Axin Dix Domain
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 8 of Crystal Structure of Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg296
b:84.7
occ:0.62
|
SG
|
C:CYS750
|
2.7
|
90.8
|
1.0
|
O
|
C:SER752
|
3.5
|
55.1
|
1.0
|
O
|
C:HOH43
|
3.6
|
40.1
|
1.0
|
O
|
C:CYS750
|
3.7
|
87.1
|
1.0
|
C
|
C:CYS750
|
3.8
|
91.9
|
1.0
|
CA
|
C:CYS750
|
3.9
|
95.5
|
1.0
|
CB
|
C:CYS750
|
3.9
|
89.6
|
1.0
|
N
|
C:SER752
|
4.1
|
65.2
|
1.0
|
C
|
C:SER752
|
4.3
|
60.4
|
1.0
|
N
|
C:ASP751
|
4.5
|
84.2
|
1.0
|
CA
|
C:SER752
|
4.6
|
54.4
|
1.0
|
CB
|
C:SER752
|
4.7
|
50.6
|
1.0
|
|
Mercury binding site 9 out
of 9 in 1wsp
Go back to
Mercury Binding Sites List in 1wsp
Mercury binding site 9 out
of 9 in the Crystal Structure of Axin Dix Domain
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 9 of Crystal Structure of Axin Dix Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg297
b:74.1
occ:0.58
|
O
|
C:HOH186
|
3.9
|
63.8
|
1.0
|
O
|
C:HOH111
|
3.9
|
48.5
|
1.0
|
|
Reference:
N.Shibata,
T.Hanamura,
R.Yamamoto,
Y.Ueda,
H.Yamamoto,
A.Kikuchi,
Y.Higuchi.
Crystal Structure of Axin Dix Domain To Be Published.
Page generated: Sun Aug 11 01:44:48 2024
|