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Yttrium in PDB 3k3a: Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir

Enzymatic activity of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir

All present enzymatic activity of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir:
3.2.1.18;

Protein crystallography data

The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir, PDB code: 3k3a 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) 49.69 / 2.59
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 111.802, 123.836, 123.967, 90.04, 90.17, 90.10
R / Rfree (%) 20.7 / 22.9

Other elements in 3k3a:

The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir 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 Oseltamivir (pdb code 3k3a). 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 Oseltamivir, PDB code: 3k3a:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in 3k3a

Go back to Yttrium Binding Sites List in 3k3a
Yttrium binding site 1 out of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir


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 Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y467

b:50.2
occ:1.00
 OE1 D:GLU168 2.2 43.0 1.0
OE1 A:GLU168 2.3 42.5 1.0
OE1 C:GLU168 2.4 42.7 1.0
OE1 B:GLU168 2.5 43.1 1.0
O A:HOH2014 2.6 12.7 0.2
O A:HOH2002 2.6 12.7 0.2
O A:HOH2007 2.6 12.7 0.2
O B:HOH2007 2.6 12.7 0.2
O A:HOH2013 3.1 27.9 0.2
O C:HOH2046 3.1 27.9 0.2
O A:HOH2046 3.1 27.9 0.2
O C:HOH2049 3.1 27.9 0.2
CD D:GLU168 3.5 40.8 1.0
CD A:GLU168 3.5 40.8 1.0
CD C:GLU168 3.6 40.8 1.0
CD B:GLU168 3.7 40.9 1.0
OE2 D:GLU168 4.1 41.1 1.0
OE2 A:GLU168 4.2 41.3 1.0
OE2 C:GLU168 4.3 41.5 1.0
OE2 B:GLU168 4.4 41.2 1.0
CG A:GLU168 4.6 39.4 1.0
CG D:GLU168 4.6 39.4 1.0
CG C:GLU168 4.7 39.5 1.0
CG B:GLU168 4.8 39.4 1.0
CB D:GLU168 4.8 39.3 1.0
CB A:GLU168 4.8 39.4 1.0
CB B:GLU168 5.0 39.1 1.0
CB C:GLU168 5.0 39.3 1.0

Yttrium binding site 2 out of 4 in 3k3a

Go back to Yttrium Binding Sites List in 3k3a
Yttrium binding site 2 out of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir


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 Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Y2

b:46.4
occ:1.00
 OE1 G:GLU168 2.3 43.1 1.0
OE1 F:GLU168 2.3 42.9 1.0
OE1 E:GLU168 2.3 43.1 1.0
OE1 H:GLU168 2.5 43.2 1.0
O E:HOH2014 2.6 12.6 0.2
O G:HOH2007 2.7 12.6 0.2
O E:HOH2007 2.7 12.6 0.2
O E:HOH2002 2.7 12.6 0.2
O E:HOH2013 3.0 28.0 0.2
O G:HOH2046 3.1 28.0 0.2
O E:HOH2046 3.1 28.0 0.2
O G:HOH468 3.1 28.0 0.2
CD F:GLU168 3.5 40.8 1.0
CD G:GLU168 3.5 41.0 1.0
CD E:GLU168 3.5 41.0 1.0
CD H:GLU168 3.7 40.7 1.0
OE2 F:GLU168 4.1 41.3 1.0
OE2 E:GLU168 4.2 41.5 1.0
OE2 G:GLU168 4.2 41.2 1.0
OE2 H:GLU168 4.3 41.2 1.0
CG G:GLU168 4.6 39.4 1.0
CG F:GLU168 4.6 39.5 1.0
CG E:GLU168 4.7 39.3 1.0
CG H:GLU168 4.8 39.5 1.0
CB G:GLU168 4.9 39.5 1.0
CB E:GLU168 5.0 39.5 1.0
CB F:GLU168 5.0 39.4 1.0

Yttrium binding site 3 out of 4 in 3k3a

Go back to Yttrium Binding Sites List in 3k3a
Yttrium binding site 3 out of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir


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 Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Y3

b:50.2
occ:1.00
 OE1 K:GLU168 2.2 43.0 1.0
OE1 J:GLU168 2.2 43.1 1.0
OE1 I:GLU168 2.4 42.9 1.0
OE1 L:GLU168 2.4 43.0 1.0
O I:HOH470 2.6 12.7 0.2
O I:HOH467 2.6 12.6 0.2
O I:HOH2007 2.6 12.6 0.2
O I:HOH468 2.7 12.6 0.2
O K:HOH2048 3.0 27.9 0.2
O I:HOH469 3.0 27.9 0.2
O K:HOH2046 3.1 27.9 0.2
O K:HOH467 3.1 27.9 0.2
CD J:GLU168 3.5 40.8 1.0
CD K:GLU168 3.5 41.0 1.0
CD I:GLU168 3.6 40.9 1.0
CD L:GLU168 3.7 40.8 1.0
OE2 J:GLU168 4.1 40.9 1.0
OE2 K:GLU168 4.2 41.4 1.0
OE2 I:GLU168 4.3 41.4 1.0
OE2 L:GLU168 4.4 40.7 1.0
CG K:GLU168 4.5 39.4 1.0
CG J:GLU168 4.6 39.4 1.0
CG I:GLU168 4.7 39.3 1.0
CG L:GLU168 4.7 39.3 1.0
CB K:GLU168 4.8 39.3 1.0
CB J:GLU168 4.9 39.0 1.0

Yttrium binding site 4 out of 4 in 3k3a

Go back to Yttrium Binding Sites List in 3k3a
Yttrium binding site 4 out of 4 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Oseltamivir


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 Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Y4

b:51.6
occ:1.00
 OE1 P:GLU168 2.2 42.8 1.0
OE1 M:GLU168 2.3 43.0 1.0
OE1 O:GLU168 2.4 42.8 1.0
OE1 N:GLU168 2.5 43.0 1.0
O N:HOH469 2.6 12.6 0.2
O N:HOH467 2.6 12.6 0.2
O M:HOH2007 2.7 12.6 0.2
O N:HOH2007 2.7 12.7 0.2
O M:HOH2002 3.0 28.1 0.2
O O:HOH2046 3.0 28.1 0.2
O M:HOH2046 3.0 28.1 0.2
O O:HOH467 3.1 28.1 0.2
CD P:GLU168 3.4 40.9 1.0
CD M:GLU168 3.6 40.8 1.0
CD O:GLU168 3.6 40.9 1.0
CD N:GLU168 3.8 40.8 1.0
OE2 P:GLU168 4.1 41.0 1.0
OE2 O:GLU168 4.2 41.4 1.0
OE2 M:GLU168 4.3 41.2 1.0
OE2 N:GLU168 4.4 41.0 1.0
CG P:GLU168 4.5 39.2 1.0
CG M:GLU168 4.6 39.4 1.0
CG O:GLU168 4.7 39.5 1.0
CB M:GLU168 4.9 39.5 1.0
CG N:GLU168 4.9 39.3 1.0
CB P:GLU168 4.9 39.1 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 02:41:03 2020

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