Yttrium in PDB 3k39: Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
Enzymatic activity of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
All present enzymatic activity of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir:
3.2.1.18;
Protein crystallography data
The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir, PDB code: 3k39
was solved by
A.J.Oakley,
J.L.Mckimm-Breschkin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.90 /
2.54
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.964,
124.874,
125.245,
90.03,
92.11,
91.27
|
R / Rfree (%)
|
19.8 /
21.4
|
Other elements in 3k39:
The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir also contains other interesting chemical elements:
Yttrium Binding Sites:
The binding sites of Yttrium atom in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
(pdb code 3k39). This binding sites where shown within
5.0 Angstroms radius around Yttrium atom.
In total 4 binding sites of Yttrium where determined in the
Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir, PDB code: 3k39:
Jump to Yttrium binding site number:
1;
2;
3;
4;
Yttrium binding site 1 out
of 4 in 3k39
Go back to
Yttrium Binding Sites List in 3k39
Yttrium binding site 1 out
of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
A full contact list of Yttrium with other atoms in the Y binding
site number 1 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Y1
b:28.9
occ:1.00
|
OE1
|
A:GLU168
|
2.1
|
23.1
|
1.0
|
O
|
C:HOH2017
|
2.1
|
13.7
|
0.2
|
O
|
C:HOH2007
|
2.2
|
13.7
|
0.2
|
OE1
|
D:GLU168
|
2.2
|
23.3
|
1.0
|
OE1
|
C:GLU168
|
2.2
|
23.1
|
1.0
|
O
|
C:HOH2013
|
2.2
|
13.7
|
0.2
|
OE1
|
B:GLU168
|
2.2
|
23.3
|
1.0
|
O
|
C:HOH2014
|
2.3
|
13.7
|
0.2
|
CD
|
A:GLU168
|
3.3
|
22.7
|
1.0
|
CD
|
D:GLU168
|
3.3
|
22.6
|
1.0
|
CD
|
C:GLU168
|
3.4
|
22.5
|
1.0
|
CD
|
B:GLU168
|
3.4
|
22.7
|
1.0
|
OE2
|
D:GLU168
|
3.9
|
24.2
|
1.0
|
OE2
|
A:GLU168
|
3.9
|
24.4
|
1.0
|
OE2
|
C:GLU168
|
4.0
|
24.1
|
1.0
|
OE2
|
B:GLU168
|
4.0
|
24.4
|
1.0
|
CG
|
A:GLU168
|
4.5
|
19.6
|
1.0
|
CG
|
D:GLU168
|
4.5
|
19.8
|
1.0
|
CG
|
B:GLU168
|
4.5
|
19.7
|
1.0
|
CG
|
C:GLU168
|
4.5
|
19.8
|
1.0
|
CB
|
A:GLU168
|
4.7
|
18.2
|
1.0
|
CB
|
D:GLU168
|
4.7
|
18.4
|
1.0
|
CB
|
B:GLU168
|
4.7
|
18.2
|
1.0
|
CB
|
C:GLU168
|
4.7
|
18.4
|
1.0
|
|
Yttrium binding site 2 out
of 4 in 3k39
Go back to
Yttrium Binding Sites List in 3k39
Yttrium binding site 2 out
of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
A full contact list of Yttrium with other atoms in the Y binding
site number 2 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Y2
b:28.1
occ:1.00
|
OE1
|
E:GLU168
|
2.2
|
23.1
|
1.0
|
OE1
|
H:GLU168
|
2.2
|
23.6
|
1.0
|
OE1
|
G:GLU168
|
2.2
|
23.6
|
1.0
|
O
|
E:HOH2070
|
2.3
|
13.5
|
0.2
|
OE1
|
F:GLU168
|
2.3
|
23.7
|
1.0
|
O
|
E:HOH2069
|
2.3
|
13.5
|
0.2
|
O
|
E:HOH2068
|
2.3
|
13.5
|
0.2
|
O
|
E:HOH2007
|
2.5
|
13.5
|
0.2
|
CD
|
E:GLU168
|
3.4
|
22.5
|
1.0
|
CD
|
G:GLU168
|
3.4
|
22.4
|
1.0
|
CD
|
H:GLU168
|
3.4
|
22.8
|
1.0
|
CD
|
F:GLU168
|
3.5
|
22.9
|
1.0
|
OE2
|
E:GLU168
|
3.9
|
24.2
|
1.0
|
OE2
|
G:GLU168
|
4.0
|
24.2
|
1.0
|
OE2
|
H:GLU168
|
4.0
|
24.0
|
1.0
|
OE2
|
F:GLU168
|
4.1
|
24.5
|
1.0
|
CG
|
G:GLU168
|
4.5
|
20.0
|
1.0
|
CG
|
E:GLU168
|
4.6
|
20.0
|
1.0
|
CG
|
H:GLU168
|
4.6
|
19.7
|
1.0
|
CG
|
F:GLU168
|
4.6
|
19.8
|
1.0
|
CB
|
H:GLU168
|
4.7
|
18.4
|
1.0
|
CB
|
G:GLU168
|
4.8
|
18.5
|
1.0
|
CB
|
F:GLU168
|
4.8
|
18.5
|
1.0
|
CB
|
E:GLU168
|
4.8
|
18.5
|
1.0
|
|
Yttrium binding site 3 out
of 4 in 3k39
Go back to
Yttrium Binding Sites List in 3k39
Yttrium binding site 3 out
of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
A full contact list of Yttrium with other atoms in the Y binding
site number 3 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Y3
b:29.6
occ:1.00
|
OE1
|
J:GLU168
|
2.2
|
23.0
|
1.0
|
OE1
|
I:GLU168
|
2.2
|
23.4
|
1.0
|
O
|
L:HOH2007
|
2.2
|
13.6
|
0.2
|
OE1
|
L:GLU168
|
2.2
|
23.1
|
1.0
|
O
|
L:HOH2014
|
2.2
|
13.6
|
0.2
|
O
|
L:HOH2013
|
2.2
|
13.6
|
0.2
|
OE1
|
K:GLU168
|
2.2
|
23.3
|
1.0
|
O
|
J:HOH2007
|
2.4
|
13.6
|
0.2
|
CD
|
I:GLU168
|
3.3
|
22.6
|
1.0
|
CD
|
J:GLU168
|
3.4
|
22.7
|
1.0
|
CD
|
K:GLU168
|
3.4
|
22.5
|
1.0
|
CD
|
L:GLU168
|
3.4
|
22.7
|
1.0
|
OE2
|
I:GLU168
|
3.9
|
24.1
|
1.0
|
OE2
|
K:GLU168
|
3.9
|
24.2
|
1.0
|
OE2
|
J:GLU168
|
4.0
|
24.4
|
1.0
|
OE2
|
L:GLU168
|
4.0
|
24.2
|
1.0
|
CG
|
I:GLU168
|
4.5
|
19.7
|
1.0
|
CG
|
J:GLU168
|
4.5
|
19.7
|
1.0
|
CG
|
K:GLU168
|
4.6
|
19.8
|
1.0
|
CG
|
L:GLU168
|
4.6
|
19.6
|
1.0
|
CB
|
I:GLU168
|
4.7
|
18.2
|
1.0
|
CB
|
J:GLU168
|
4.7
|
18.4
|
1.0
|
CB
|
K:GLU168
|
4.7
|
18.3
|
1.0
|
CB
|
L:GLU168
|
4.8
|
18.3
|
1.0
|
|
Yttrium binding site 4 out
of 4 in 3k39
Go back to
Yttrium Binding Sites List in 3k39
Yttrium binding site 4 out
of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
A full contact list of Yttrium with other atoms in the Y binding
site number 4 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Y4
b:30.9
occ:1.00
|
OE1
|
O:GLU168
|
2.2
|
23.5
|
1.0
|
OE1
|
M:GLU168
|
2.2
|
23.8
|
1.0
|
OE1
|
P:GLU168
|
2.2
|
23.5
|
1.0
|
O
|
O:HOH2017
|
2.3
|
13.6
|
0.2
|
O
|
O:HOH2013
|
2.3
|
13.7
|
0.2
|
OE1
|
N:GLU168
|
2.3
|
23.3
|
1.0
|
O
|
O:HOH2007
|
2.3
|
13.7
|
0.2
|
O
|
O:HOH2014
|
2.4
|
13.7
|
0.2
|
CD
|
M:GLU168
|
3.4
|
22.7
|
1.0
|
CD
|
O:GLU168
|
3.4
|
22.8
|
1.0
|
CD
|
P:GLU168
|
3.4
|
22.5
|
1.0
|
CD
|
N:GLU168
|
3.4
|
22.6
|
1.0
|
OE2
|
M:GLU168
|
4.0
|
24.2
|
1.0
|
OE2
|
O:GLU168
|
4.0
|
24.2
|
1.0
|
OE2
|
P:GLU168
|
4.0
|
24.1
|
1.0
|
OE2
|
N:GLU168
|
4.0
|
24.8
|
1.0
|
CG
|
M:GLU168
|
4.6
|
19.9
|
1.0
|
CG
|
P:GLU168
|
4.6
|
19.8
|
1.0
|
CG
|
O:GLU168
|
4.6
|
19.8
|
1.0
|
CG
|
N:GLU168
|
4.6
|
19.8
|
1.0
|
CB
|
P:GLU168
|
4.7
|
18.4
|
1.0
|
CB
|
M:GLU168
|
4.7
|
18.3
|
1.0
|
CB
|
N:GLU168
|
4.8
|
18.6
|
1.0
|
CB
|
O:GLU168
|
4.8
|
18.2
|
1.0
|
|
Reference:
A.J.Oakley,
S.Barrett,
T.S.Peat,
J.Newman,
V.A.Streltsov,
L.Waddington,
T.Saito,
M.Tashiro,
J.L.Mckimm-Breschkin.
Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses. J.Med.Chem. 2010.
ISSN: ISSN 0022-2623
PubMed: 20695427
DOI: 10.1021/JM100621S
Page generated: Sat Oct 12 20:33:32 2024
|