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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:

Calcium (Ca) 16 atoms

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: Wed Dec 16 02:41:01 2020

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