Mercury in PDB 5td8: Crystal Structure of An Extended Dwarf NDC80 Complex
Protein crystallography data
The structure of Crystal Structure of An Extended Dwarf NDC80 Complex, PDB code: 5td8
was solved by
R.Valverde,
J.Ingram,
S.C.Harrison,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
113.41 /
7.53
|
|
Space group
|
I 41 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
226.825,
226.825,
237.270,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
31.2 /
32.8
|
Mercury Binding Sites:
The binding sites of Mercury atom in the Crystal Structure of An Extended Dwarf NDC80 Complex
(pdb code 5td8). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the
Crystal Structure of An Extended Dwarf NDC80 Complex, PDB code: 5td8:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
Mercury binding site 1 out
of 6 in 5td8
Go back to
Mercury Binding Sites List in 5td8
Mercury binding site 1 out
of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex
 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 An Extended Dwarf NDC80 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg701
b:81.5
occ:0.85
|
HD11
|
A:LEU304
|
2.4
|
14.5
|
1.0
|
|
HG
|
B:CYS140
|
2.4
|
14.5
|
1.0
|
|
HD13
|
A:LEU304
|
2.4
|
14.5
|
1.0
|
|
HH
|
A:TYR282
|
2.5
|
14.5
|
1.0
|
|
OH
|
A:TYR282
|
2.6
|
0.1
|
1.0
|
|
CZ
|
A:TYR282
|
2.7
|
98.9
|
1.0
|
|
SG
|
B:CYS140
|
2.8
|
78.2
|
1.0
|
|
CD1
|
A:LEU304
|
2.8
|
98.6
|
1.0
|
|
HE2
|
A:TYR282
|
2.9
|
14.5
|
1.0
|
|
CE2
|
A:TYR282
|
2.9
|
97.4
|
1.0
|
|
HD21
|
A:LEU304
|
3.1
|
14.5
|
1.0
|
|
HD22
|
A:LEU304
|
3.2
|
14.5
|
1.0
|
|
CD2
|
A:LEU304
|
3.5
|
0.1
|
1.0
|
|
HD12
|
A:LEU304
|
3.6
|
14.5
|
1.0
|
|
CE1
|
A:TYR282
|
3.6
|
99.2
|
1.0
|
|
CG
|
A:LEU304
|
3.8
|
0.5
|
1.0
|
|
CD2
|
A:TYR282
|
3.9
|
96.3
|
1.0
|
|
HE1
|
A:TYR282
|
3.9
|
14.5
|
1.0
|
|
HB3
|
B:CYS140
|
4.1
|
14.5
|
1.0
|
|
CB
|
B:CYS140
|
4.2
|
75.0
|
1.0
|
|
HG
|
A:LEU304
|
4.3
|
14.5
|
1.0
|
|
HD2
|
A:TYR282
|
4.4
|
14.5
|
1.0
|
|
HD23
|
A:LEU304
|
4.4
|
14.5
|
1.0
|
|
CD1
|
A:TYR282
|
4.4
|
98.1
|
1.0
|
|
CG
|
A:TYR282
|
4.5
|
96.6
|
1.0
|
|
HB2
|
A:LEU304
|
4.7
|
14.5
|
1.0
|
|
HB2
|
B:CYS140
|
4.8
|
14.5
|
1.0
|
|
CB
|
A:LEU304
|
4.8
|
0.2
|
1.0
|
|
HA
|
B:CYS140
|
5.0
|
14.5
|
1.0
|
|
Mercury binding site 2 out
of 6 in 5td8
Go back to
Mercury Binding Sites List in 5td8
Mercury binding site 2 out
of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex
 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 An Extended Dwarf NDC80 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg702
b:0.9
occ:0.71
|
HG
|
B:SER64
|
2.0
|
14.5
|
1.0
|
|
HA
|
A:CYS235
|
2.1
|
14.5
|
1.0
|
|
HA
|
B:SER64
|
2.4
|
14.5
|
1.0
|
|
SG
|
A:CYS235
|
2.4
|
0.5
|
1.0
|
|
O
|
A:CYS235
|
2.6
|
0.7
|
1.0
|
|
CA
|
A:CYS235
|
2.6
|
0.2
|
1.0
|
|
OG
|
B:SER64
|
2.7
|
0.9
|
1.0
|
|
O
|
B:SER64
|
2.8
|
0.3
|
1.0
|
|
CB
|
A:CYS235
|
2.8
|
0.7
|
1.0
|
|
C
|
A:CYS235
|
2.9
|
0.5
|
1.0
|
|
CA
|
B:SER64
|
3.0
|
0.1
|
1.0
|
|
HB2
|
A:CYS235
|
3.0
|
14.5
|
1.0
|
|
CB
|
B:SER64
|
3.1
|
0.0
|
1.0
|
|
HB2
|
B:SER64
|
3.2
|
14.5
|
1.0
|
|
C
|
B:SER64
|
3.3
|
0.8
|
1.0
|
|
HG23
|
A:VAL239
|
3.4
|
14.5
|
1.0
|
|
HB3
|
A:CYS235
|
3.7
|
14.5
|
1.0
|
|
N
|
A:CYS235
|
4.0
|
0.6
|
1.0
|
|
HB3
|
B:SER64
|
4.1
|
14.5
|
1.0
|
|
HB2
|
A:LYS238
|
4.1
|
14.5
|
1.0
|
|
N
|
A:LEU236
|
4.1
|
0.5
|
1.0
|
|
CG2
|
A:VAL239
|
4.2
|
0.9
|
1.0
|
|
HG21
|
A:VAL239
|
4.3
|
14.5
|
1.0
|
|
N
|
B:SER64
|
4.3
|
0.8
|
1.0
|
|
H
|
A:CYS235
|
4.4
|
14.5
|
1.0
|
|
HD2
|
A:LYS238
|
4.5
|
14.5
|
1.0
|
|
O
|
B:SER63
|
4.6
|
90.5
|
1.0
|
|
N
|
B:ASN65
|
4.6
|
0.2
|
1.0
|
|
HG22
|
A:VAL239
|
4.6
|
14.5
|
1.0
|
|
H
|
A:LEU236
|
4.6
|
14.5
|
1.0
|
|
HA
|
A:LEU236
|
4.7
|
14.5
|
1.0
|
|
H
|
A:VAL239
|
4.7
|
14.5
|
1.0
|
|
O
|
A:MET234
|
4.7
|
0.2
|
1.0
|
|
C
|
A:MET234
|
4.8
|
0.8
|
1.0
|
|
H
|
B:SER64
|
4.9
|
14.5
|
1.0
|
|
C
|
B:SER63
|
4.9
|
92.3
|
1.0
|
|
CA
|
A:LEU236
|
5.0
|
0.7
|
1.0
|
|
Mercury binding site 3 out
of 6 in 5td8
Go back to
Mercury Binding Sites List in 5td8
Mercury binding site 3 out
of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex
 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 An Extended Dwarf NDC80 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg501
b:0.1
occ:1.00
|
HG13
|
B:VAL127
|
2.5
|
14.5
|
1.0
|
|
SG
|
B:CYS23
|
2.7
|
44.9
|
1.0
|
|
HZ
|
B:PHE52
|
2.9
|
14.5
|
1.0
|
|
HB3
|
B:ALA130
|
2.9
|
14.5
|
1.0
|
|
HG3
|
B:ARG131
|
3.0
|
14.5
|
1.0
|
|
CG1
|
B:VAL127
|
3.5
|
0.6
|
1.0
|
|
HB3
|
B:CYS23
|
3.5
|
14.5
|
1.0
|
|
HA
|
B:VAL127
|
3.5
|
14.5
|
1.0
|
|
CZ
|
B:PHE52
|
3.6
|
0.4
|
1.0
|
|
HG2
|
B:ARG131
|
3.7
|
14.5
|
1.0
|
|
HG
|
B:CYS23
|
3.7
|
14.5
|
1.0
|
|
HE1
|
B:PHE52
|
3.7
|
14.5
|
1.0
|
|
HB1
|
B:ALA130
|
3.7
|
14.5
|
1.0
|
|
CB
|
B:ALA130
|
3.7
|
0.5
|
1.0
|
|
CG
|
B:ARG131
|
3.7
|
0.3
|
1.0
|
|
O
|
B:VAL127
|
3.8
|
0.7
|
1.0
|
|
HG22
|
B:VAL127
|
3.8
|
14.5
|
1.0
|
|
CB
|
B:CYS23
|
3.8
|
44.5
|
1.0
|
|
HG12
|
B:VAL127
|
3.8
|
14.5
|
1.0
|
|
HE
|
B:ARG131
|
3.8
|
14.5
|
1.0
|
|
HG11
|
B:VAL127
|
4.0
|
14.5
|
1.0
|
|
H
|
B:ARG131
|
4.0
|
14.5
|
1.0
|
|
CE1
|
B:PHE52
|
4.0
|
0.4
|
1.0
|
|
HA
|
B:CYS23
|
4.1
|
14.5
|
1.0
|
|
CA
|
B:VAL127
|
4.2
|
0.1
|
1.0
|
|
NE
|
B:ARG131
|
4.2
|
0.9
|
1.0
|
|
CB
|
B:VAL127
|
4.2
|
0.5
|
1.0
|
|
N
|
B:ARG131
|
4.3
|
0.9
|
1.0
|
|
HB2
|
B:ALA130
|
4.3
|
14.5
|
1.0
|
|
C
|
B:VAL127
|
4.3
|
0.9
|
1.0
|
|
CD
|
B:ARG131
|
4.4
|
0.5
|
1.0
|
|
CG2
|
B:VAL127
|
4.5
|
0.8
|
1.0
|
|
HB2
|
B:CYS23
|
4.5
|
14.5
|
1.0
|
|
HD2
|
B:ARG131
|
4.5
|
14.5
|
1.0
|
|
CA
|
B:CYS23
|
4.6
|
44.6
|
1.0
|
|
C
|
B:ALA130
|
4.6
|
0.6
|
1.0
|
|
HA
|
B:ARG131
|
4.7
|
14.5
|
1.0
|
|
CE2
|
B:PHE52
|
4.7
|
0.4
|
1.0
|
|
CA
|
B:ALA130
|
4.7
|
0.4
|
1.0
|
|
HE2
|
B:PHE25
|
4.7
|
14.5
|
1.0
|
|
HE2
|
B:PHE52
|
4.8
|
14.5
|
1.0
|
|
HG21
|
B:VAL127
|
4.9
|
14.5
|
1.0
|
|
CB
|
B:ARG131
|
4.9
|
0.2
|
1.0
|
|
CA
|
B:ARG131
|
4.9
|
0.4
|
1.0
|
|
CZ
|
B:ARG131
|
5.0
|
0.7
|
1.0
|
|
HH21
|
B:ARG131
|
5.0
|
14.5
|
1.0
|
|
Mercury binding site 4 out
of 6 in 5td8
Go back to
Mercury Binding Sites List in 5td8
Mercury binding site 4 out
of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex
 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 An Extended Dwarf NDC80 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg502
b:0.3
occ:0.83
|
HD11
|
B:ILE49
|
2.1
|
14.5
|
1.0
|
|
CD1
|
B:ILE49
|
2.9
|
97.1
|
1.0
|
|
HD12
|
B:ILE49
|
3.0
|
14.5
|
1.0
|
|
HE2
|
B:PHE98
|
3.0
|
14.5
|
1.0
|
|
SG
|
B:CYS94
|
3.1
|
0.6
|
1.0
|
|
HD1
|
B:TYR45
|
3.1
|
14.5
|
1.0
|
|
HG13
|
B:ILE49
|
3.2
|
14.5
|
1.0
|
|
HB3
|
B:TYR45
|
3.2
|
14.5
|
1.0
|
|
CD2
|
B:PHE97
|
3.2
|
0.9
|
1.0
|
|
CB
|
B:CYS94
|
3.4
|
0.7
|
1.0
|
|
CD1
|
B:TYR45
|
3.4
|
0.8
|
1.0
|
|
CG1
|
B:ILE49
|
3.5
|
96.7
|
1.0
|
|
CA
|
B:CYS94
|
3.5
|
0.9
|
1.0
|
|
CE2
|
B:PHE97
|
3.6
|
0.5
|
1.0
|
|
CE2
|
B:PHE98
|
3.6
|
0.6
|
1.0
|
|
HD13
|
B:ILE49
|
3.7
|
14.5
|
1.0
|
|
CG
|
B:TYR45
|
3.8
|
0.6
|
1.0
|
|
HG12
|
B:ILE49
|
3.8
|
14.5
|
1.0
|
|
CB
|
B:TYR45
|
3.9
|
0.6
|
1.0
|
|
CG
|
B:PHE97
|
4.0
|
0.3
|
1.0
|
|
HA
|
B:TYR45
|
4.1
|
14.5
|
1.0
|
|
CE1
|
B:TYR45
|
4.2
|
0.8
|
1.0
|
|
HZ
|
B:PHE98
|
4.2
|
14.5
|
1.0
|
|
CZ
|
B:PHE98
|
4.2
|
1.0
|
1.0
|
|
HD21
|
B:LEU123
|
4.3
|
14.5
|
1.0
|
|
CD2
|
B:PHE98
|
4.3
|
0.8
|
1.0
|
|
HD2
|
B:PHE98
|
4.3
|
14.5
|
1.0
|
|
HE1
|
B:TYR45
|
4.4
|
14.5
|
1.0
|
|
CB
|
B:PHE97
|
4.4
|
0.7
|
1.0
|
|
N
|
B:CYS94
|
4.4
|
0.6
|
1.0
|
|
CA
|
B:TYR45
|
4.4
|
0.6
|
1.0
|
|
O
|
B:TYR45
|
4.6
|
0.5
|
1.0
|
|
HE1
|
B:PHE106
|
4.6
|
14.5
|
1.0
|
|
C
|
B:CYS94
|
4.6
|
0.3
|
1.0
|
|
O
|
B:CYS94
|
4.6
|
0.3
|
1.0
|
|
CZ
|
B:PHE97
|
4.6
|
0.4
|
1.0
|
|
HB2
|
B:TYR45
|
4.7
|
14.5
|
1.0
|
|
CD2
|
B:TYR45
|
4.7
|
0.3
|
1.0
|
|
C
|
B:TYR45
|
4.8
|
0.3
|
1.0
|
|
H
|
B:ILE49
|
4.8
|
14.5
|
1.0
|
|
HB
|
B:ILE48
|
4.9
|
14.5
|
1.0
|
|
CB
|
B:ILE49
|
4.9
|
96.1
|
1.0
|
|
CD1
|
B:PHE97
|
4.9
|
0.2
|
1.0
|
|
CD2
|
B:LEU123
|
5.0
|
0.7
|
1.0
|
|
Mercury binding site 5 out
of 6 in 5td8
Go back to
Mercury Binding Sites List in 5td8
Mercury binding site 5 out
of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex
 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 An Extended Dwarf NDC80 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Hg301
b:68.2
occ:0.77
|
HB3
|
D:CYS169
|
1.9
|
14.5
|
1.0
|
|
HB2
|
D:LEU217
|
2.2
|
14.5
|
1.0
|
|
HD12
|
D:LEU217
|
2.3
|
14.5
|
1.0
|
|
HD2
|
D:PHE163
|
2.4
|
14.5
|
1.0
|
|
HD13
|
D:LEU217
|
2.5
|
14.5
|
1.0
|
|
CD1
|
D:LEU217
|
2.8
|
73.5
|
1.0
|
|
CB
|
D:CYS169
|
2.8
|
64.8
|
1.0
|
|
CD2
|
D:PHE163
|
2.8
|
68.4
|
1.0
|
|
HB3
|
D:LEU217
|
2.8
|
14.5
|
1.0
|
|
HB2
|
D:PHE163
|
2.8
|
14.5
|
1.0
|
|
CB
|
D:LEU217
|
2.8
|
73.5
|
1.0
|
|
HB2
|
D:CYS169
|
2.9
|
14.5
|
1.0
|
|
HA
|
D:ARG214
|
3.0
|
14.5
|
1.0
|
|
CG
|
D:PHE163
|
3.3
|
68.0
|
1.0
|
|
CG
|
D:LEU217
|
3.4
|
73.5
|
1.0
|
|
HG
|
D:CYS169
|
3.4
|
14.5
|
1.0
|
|
CB
|
D:PHE163
|
3.5
|
67.5
|
1.0
|
|
CE2
|
D:PHE163
|
3.5
|
69.0
|
1.0
|
|
HD11
|
D:LEU217
|
3.6
|
14.5
|
1.0
|
|
SG
|
D:CYS169
|
3.7
|
65.1
|
1.0
|
|
HE2
|
D:PHE163
|
3.7
|
14.5
|
1.0
|
|
HG
|
D:LEU217
|
3.9
|
14.5
|
1.0
|
|
CA
|
D:CYS169
|
3.9
|
64.5
|
1.0
|
|
HB3
|
D:PHE163
|
3.9
|
14.5
|
1.0
|
|
CA
|
D:ARG214
|
4.0
|
67.2
|
1.0
|
|
C
|
D:CYS169
|
4.0
|
64.5
|
1.0
|
|
HG
|
D:LEU218
|
4.1
|
14.5
|
1.0
|
|
O
|
D:ALA213
|
4.1
|
67.1
|
1.0
|
|
HG3
|
D:ARG214
|
4.1
|
14.5
|
1.0
|
|
CA
|
D:LEU217
|
4.2
|
73.5
|
1.0
|
|
H
|
D:LEU218
|
4.2
|
14.5
|
1.0
|
|
O
|
D:ARG214
|
4.2
|
67.1
|
1.0
|
|
HA
|
D:CYS169
|
4.2
|
14.5
|
1.0
|
|
H
|
D:PHE163
|
4.3
|
14.5
|
1.0
|
|
CD1
|
D:PHE163
|
4.3
|
68.3
|
1.0
|
|
O
|
D:CYS169
|
4.4
|
64.1
|
1.0
|
|
H
|
D:LEU217
|
4.4
|
14.5
|
1.0
|
|
N
|
D:TRP170
|
4.4
|
66.2
|
1.0
|
|
N
|
D:LEU218
|
4.5
|
75.1
|
1.0
|
|
HD22
|
D:LEU217
|
4.5
|
14.5
|
1.0
|
|
CZ
|
D:PHE163
|
4.5
|
69.3
|
1.0
|
|
C
|
D:LEU217
|
4.5
|
73.5
|
1.0
|
|
HA
|
D:TRP170
|
4.6
|
14.5
|
1.0
|
|
CD2
|
D:LEU217
|
4.6
|
73.5
|
1.0
|
|
C
|
D:ARG214
|
4.6
|
67.2
|
1.0
|
|
H
|
D:TRP170
|
4.6
|
14.5
|
1.0
|
|
N
|
D:ARG214
|
4.7
|
67.2
|
1.0
|
|
C
|
D:ALA213
|
4.7
|
67.2
|
1.0
|
|
CA
|
D:PHE163
|
4.7
|
66.8
|
1.0
|
|
N
|
D:LEU217
|
4.8
|
73.7
|
1.0
|
|
N
|
D:PHE163
|
4.8
|
66.8
|
1.0
|
|
CB
|
D:ARG214
|
4.8
|
67.2
|
1.0
|
|
CE1
|
D:PHE163
|
4.8
|
69.0
|
1.0
|
|
HB2
|
D:ARG214
|
4.8
|
14.5
|
1.0
|
|
HA
|
D:LEU217
|
4.9
|
14.5
|
1.0
|
|
CG
|
D:ARG214
|
4.9
|
67.2
|
1.0
|
|
HD23
|
D:LEU218
|
4.9
|
14.5
|
1.0
|
|
HD1
|
D:PHE163
|
4.9
|
14.5
|
1.0
|
|
CG
|
D:LEU218
|
5.0
|
75.2
|
1.0
|
|
CA
|
D:TRP170
|
5.0
|
66.5
|
1.0
|
|
Mercury binding site 6 out
of 6 in 5td8
Go back to
Mercury Binding Sites List in 5td8
Mercury binding site 6 out
of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex
 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 An Extended Dwarf NDC80 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Hg302
b:77.6
occ:0.68
|
HA
|
D:MET175
|
2.3
|
14.5
|
1.0
|
|
O
|
D:MET175
|
2.8
|
74.6
|
1.0
|
|
CA
|
D:MET175
|
3.1
|
73.1
|
1.0
|
|
SD
|
D:MET175
|
3.1
|
70.6
|
1.0
|
|
O
|
D:ALA174
|
3.2
|
74.1
|
1.0
|
|
C
|
D:MET175
|
3.3
|
74.5
|
1.0
|
|
HG3
|
D:MET175
|
3.5
|
14.5
|
1.0
|
|
CG
|
D:MET175
|
3.7
|
72.2
|
1.0
|
|
CB
|
D:MET175
|
4.0
|
72.8
|
1.0
|
|
C
|
D:ALA174
|
4.1
|
74.5
|
1.0
|
|
N
|
D:MET175
|
4.1
|
73.0
|
1.0
|
|
HB2
|
D:MET175
|
4.5
|
14.5
|
1.0
|
|
HG23
|
D:VAL173
|
4.6
|
14.5
|
1.0
|
|
N
|
D:HIS176
|
4.6
|
82.2
|
1.0
|
|
HG2
|
D:MET175
|
4.6
|
14.5
|
1.0
|
|
HB3
|
D:MET175
|
4.7
|
14.5
|
1.0
|
|
HG21
|
D:VAL159
|
4.8
|
14.5
|
1.0
|
|
CE
|
D:MET175
|
4.8
|
69.5
|
1.0
|
|
H
|
D:MET175
|
4.9
|
14.5
|
1.0
|
|
Reference:
R.Valverde,
J.Ingram,
S.C.Harrison.
Conserved Tetramer Junction in the Kinetochore NDC80 Complex. Cell Rep V. 17 1915 2016.
ISSN: ESSN 2211-1247
PubMed: 27851957
DOI: 10.1016/J.CELREP.2016.10.065
Page generated: Sun Aug 11 06:53:58 2024
|
