Yttrium in PDB 3k38: Crystal Structure of B/Perth Neuraminidase D197E Mutant

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

The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant, PDB code: 3k38 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)	61.78 / 2.19
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	111.155, 123.683, 123.789, 90.04, 90.19, 90.19
R / Rfree (%)	19.1 / 22

The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant also contains other interesting chemical elements:

Calcium

(Ca)

16 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Yttrium atom in the Crystal Structure of B/Perth Neuraminidase D197E Mutant (pdb code 3k38). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 20 binding sites of Yttrium where determined in the Crystal Structure of B/Perth Neuraminidase D197E Mutant, PDB code: 3k38:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Yttrium binding site 1 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y1002 b:13.7 occ:0.70 OD2 A:ASP149 2.3 25.1 1.0 O2 A:SO41001 2.3 14.8 1.0 O A:HOH563 2.4 14.0 1.0 CG A:ASP149 3.3 23.7 1.0 S A:SO41001 3.8 15.9 1.0 O A:HOH590 3.8 17.2 1.0 CB A:ASP149 3.9 22.7 1.0 O A:HOH940 4.1 13.1 1.0 OH A:TYR409 4.2 21.3 1.0 OD1 A:ASP149 4.3 21.1 1.0 O3 A:SO41001 4.4 14.7 1.0 O4 A:SO41001 4.4 14.7 1.0 O1 A:SO41001 4.6 14.8 1.0 OE2 A:GLU117 4.7 23.2 1.0 O A:HOH663 4.9 12.9 1.0 O A:HOH902 4.9 9.5 1.0 OE1 A:GLU276 5.0 17.5 1.0

Yttrium binding site 2 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y1 b:18.0 occ:1.00 OE1 B:GLU168 2.1 15.5 1.0 OE1 C:GLU168 2.2 16.4 1.0 OE1 D:GLU168 2.2 19.2 1.0 O A:HOH864 2.3 8.1 1.0 OE1 A:GLU168 2.3 17.9 1.0 CD B:GLU168 3.3 18.4 1.0 CD C:GLU168 3.3 18.7 1.0 CD D:GLU168 3.4 19.9 1.0 CD A:GLU168 3.5 18.2 1.0 OE2 B:GLU168 3.9 21.7 1.0 OE2 C:GLU168 3.9 20.5 1.0 OE2 D:GLU168 3.9 23.9 1.0 OE2 A:GLU168 4.0 18.6 1.0 CG B:GLU168 4.4 17.0 1.0 CG C:GLU168 4.5 17.0 1.0 CG D:GLU168 4.5 18.7 1.0 CB C:GLU168 4.6 16.3 1.0 CB B:GLU168 4.6 18.0 1.0 CG A:GLU168 4.6 16.5 1.0 CB D:GLU168 4.7 17.9 1.0 O A:HOH1258 4.7 11.1 1.0 CB A:GLU168 4.7 16.5 1.0

Yttrium binding site 3 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Y1002 b:15.4 occ:0.70 OD2 B:ASP149 2.2 25.2 1.0 O2 B:SO41001 2.3 15.5 1.0 O B:HOH1264 2.5 5.3 1.0 CG B:ASP149 3.3 21.7 1.0 S B:SO41001 3.7 17.2 1.0 CB B:ASP149 3.9 22.1 1.0 OH B:TYR409 4.2 20.4 1.0 O3 B:SO41001 4.2 12.6 1.0 OD1 B:ASP149 4.3 19.5 1.0 O4 B:SO41001 4.4 15.8 1.0 OE2 B:GLU117 4.5 19.6 1.0 O1 B:SO41001 4.6 18.5 1.0 OE1 B:GLU276 5.0 18.4 1.0

Yttrium binding site 4 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Y1002 b:15.3 occ:0.70 O2 C:SO41001 2.3 16.7 1.0 OD2 C:ASP149 2.3 23.2 1.0 O C:HOH942 3.4 18.3 1.0 CG C:ASP149 3.4 23.1 1.0 S C:SO41001 3.7 15.7 1.0 O C:HOH1004 3.9 11.0 1.0 CB C:ASP149 3.9 21.9 1.0 OH C:TYR409 4.3 20.8 1.0 O3 C:SO41001 4.3 16.1 1.0 O4 C:SO41001 4.4 15.7 1.0 OD1 C:ASP149 4.4 23.3 1.0 O1 C:SO41001 4.6 16.0 1.0 OE2 C:GLU117 4.7 20.2 1.0 OE1 C:GLU276 5.0 21.8 1.0

Yttrium binding site 5 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Crystal Structure of B/Perth Neuraminidase D197E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Y1002 b:14.8 occ:0.70 OD2 D:ASP149 2.2 24.1 1.0 O2 D:SO41001 2.3 19.7 1.0 CG D:ASP149 3.3 20.6 1.0 S D:SO41001 3.7 15.5 1.0 CB D:ASP149 3.9 21.1 1.0 OH D:TYR409 4.3 17.1 1.0 O3 D:SO41001 4.3 14.5 1.0 OD1 D:ASP149 4.3 21.5 1.0 O4 D:SO41001 4.4 15.6 1.0 OE2 D:GLU117 4.5 20.7 1.0 O1 D:SO41001 4.6 16.5 1.0

Yttrium binding site 6 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Crystal Structure of B/Perth Neuraminidase D197E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Y2 b:21.6 occ:1.00 OE1 G:GLU168 2.1 21.3 1.0 OE1 H:GLU168 2.1 20.4 1.0 OE1 E:GLU168 2.1 19.0 1.0 O G:HOH1232 2.2 13.6 1.0 OE1 F:GLU168 2.4 23.6 1.0 CD H:GLU168 3.3 22.7 1.0 CD G:GLU168 3.3 21.2 1.0 CD E:GLU168 3.3 21.0 1.0 CD F:GLU168 3.5 22.1 1.0 OE2 G:GLU168 3.8 21.5 1.0 OE2 H:GLU168 3.8 20.9 1.0 OE2 E:GLU168 3.9 22.3 1.0 OE2 F:GLU168 4.0 20.6 1.0 CG H:GLU168 4.5 19.5 1.0 CG G:GLU168 4.5 17.8 1.0 CG E:GLU168 4.5 17.7 1.0 CB H:GLU168 4.7 19.2 1.0 CG F:GLU168 4.7 19.9 1.0 CB G:GLU168 4.7 18.0 1.0 CB E:GLU168 4.7 17.2 1.0 CB F:GLU168 4.8 18.8 1.0 O G:HOH490 4.9 12.5 1.0

Yttrium binding site 7 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 7 of Crystal Structure of B/Perth Neuraminidase D197E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Y1002 b:15.8 occ:0.70 OD2 E:ASP149 2.2 23.9 1.0 O2 E:SO41001 2.3 14.7 1.0 O E:HOH838 2.4 7.8 1.0 O E:HOH905 2.5 11.8 1.0 CG E:ASP149 3.3 23.1 1.0 S E:SO41001 3.7 16.7 1.0 CB E:ASP149 3.9 22.0 1.0 O3 E:SO41001 4.1 14.2 1.0 OD1 E:ASP149 4.2 20.7 1.0 OH E:TYR409 4.3 20.5 1.0 O4 E:SO41001 4.5 15.1 1.0 OE2 E:GLU117 4.5 24.4 1.0 O1 E:SO41001 4.6 15.1 1.0 O E:HOH1284 4.8 7.6 1.0 O E:HOH1023 4.9 10.3 1.0 OE1 E:GLU276 5.0 20.9 1.0

Yttrium binding site 8 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 8 of Crystal Structure of B/Perth Neuraminidase D197E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Y1002 b:16.9 occ:0.70 O2 F:SO41001 2.3 13.6 1.0 OD2 F:ASP149 2.3 26.2 1.0 CG F:ASP149 3.3 24.9 1.0 S F:SO41001 3.7 16.9 1.0 CB F:ASP149 3.9 23.2 1.0 OH F:TYR409 4.2 18.9 1.0 OD1 F:ASP149 4.2 24.9 1.0 O3 F:SO41001 4.3 17.0 1.0 OE2 F:GLU117 4.4 24.4 1.0 O4 F:SO41001 4.4 16.6 1.0 O1 F:SO41001 4.5 15.8 1.0 O F:HOH634 4.8 4.7 1.0

Yttrium binding site 9 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 9 of Crystal Structure of B/Perth Neuraminidase D197E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ G:Y1002 b:15.2 occ:0.70 OD2 G:ASP149 2.2 22.9 1.0 O2 G:SO41001 2.3 14.1 1.0 O G:HOH480 2.3 9.7 1.0 CG G:ASP149 3.3 22.5 1.0 O G:HOH1122 3.4 17.6 1.0 S G:SO41001 3.7 15.7 1.0 CB G:ASP149 3.9 21.8 1.0 O3 G:SO41001 4.1 13.2 1.0 OH G:TYR409 4.3 17.8 1.0 OD1 G:ASP149 4.3 24.1 1.0 O4 G:SO41001 4.5 15.6 1.0 O1 G:SO41001 4.5 15.2 1.0 OE2 G:GLU117 4.5 24.5 1.0 O G:HOH740 4.9 10.2 1.0 OE1 G:GLU276 5.0 21.9 1.0 O G:HOH489 5.0 8.2 1.0

Yttrium binding site 10 out of 20 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 10 of Crystal Structure of B/Perth Neuraminidase D197E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ H:Y1002 b:17.0 occ:0.70 O2 H:SO41001 2.3 14.0 1.0 OD2 H:ASP149 2.3 26.9 1.0 O H:HOH986 2.7 8.7 1.0 CG H:ASP149 3.4 24.8 1.0 O H:HOH1209 3.4 14.1 1.0 S H:SO41001 3.7 16.8 1.0 CB H:ASP149 3.9 23.9 1.0 OH H:TYR409 4.2 21.2 1.0 O3 H:SO41001 4.3 14.7 1.0 OD1 H:ASP149 4.3 25.6 1.0 OE2 H:GLU117 4.3 22.0 1.0 O1 H:SO41001 4.5 15.7 1.0 O4 H:SO41001 4.5 14.5 1.0 O H:HOH558 4.8 9.8 1.0 OE1 H:GLU276 4.9 21.4 1.0

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