Atomistry » Yttrium » PDB 1dde-3ph5 » 3k39
Atomistry »
  Yttrium »
    PDB 1dde-3ph5 »
      3k39 »

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

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy