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Calcium in PDB 3cye: Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects

Enzymatic activity of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects

All present enzymatic activity of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects:
3.2.1.18;

Protein crystallography data

The structure of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects, PDB code: 3cye was solved by X.Zhu, X.Xu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.86 / 1.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 117.728, 138.472, 117.860, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects (pdb code 3cye). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects, PDB code: 3cye:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3cye

Go back to Calcium Binding Sites List in 3cye
Calcium binding site 1 out of 5 in the Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:11.2
occ:0.77
 OD2 A:ASP324 2.3 10.3 0.8
O A:GLY345 2.4 13.1 0.8
O A:ASP293 2.4 10.2 0.8
O A:ASN347 2.4 12.2 0.8
O A:HOH3044 2.4 11.2 0.8
O A:GLY297 2.4 11.0 0.8
CG A:ASP324 3.4 10.1 0.8
C A:GLY345 3.5 13.3 0.8
C A:GLY297 3.5 11.0 0.8
C A:ASN347 3.6 12.2 0.8
C A:ASP293 3.6 10.0 0.8
CA A:GLY348 4.0 10.6 0.8
O A:HOH3007 4.0 9.1 0.8
O A:ALA346 4.1 13.7 0.8
CA A:GLY345 4.2 12.9 0.8
C A:ALA346 4.2 12.7 0.8
CB A:ASP324 4.2 11.3 0.8
N A:GLY348 4.3 12.0 0.8
N A:GLY297 4.3 11.2 0.8
CA A:ASN294 4.3 10.4 0.8
OD1 A:ASP324 4.3 11.7 0.8
N A:SER298 4.4 10.7 0.8
CA A:SER298 4.4 11.2 0.8
N A:ASN347 4.4 13.4 0.8
N A:ASN294 4.4 10.8 0.8
CA A:GLY297 4.5 10.6 0.8
N A:ALA346 4.5 12.9 0.8
CA A:ASP293 4.6 10.1 0.8
O A:ASN344 4.6 13.0 0.8
CA A:ASN347 4.6 13.6 0.8
C A:ASN294 4.7 10.9 0.8
CA A:ALA346 4.7 13.3 0.8
N A:ASP293 4.7 10.9 0.8
OD1 A:ASP293 4.8 10.2 0.8
CB A:ASP293 4.8 10.7 0.8
O A:PRO326 4.9 13.6 0.8

Calcium binding site 2 out of 5 in 3cye

Go back to Calcium Binding Sites List in 3cye
Calcium binding site 2 out of 5 in the Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:12.7
occ:0.77
 OD1 A:ASN381 2.3 10.1 0.8
OD1 A:ASP379 2.4 12.3 0.8
OD1 A:ASP387 2.4 14.6 0.8
O A:HOH3043 2.4 15.9 0.8
O A:SER389 2.4 14.0 0.8
O A:HOH3108 2.5 20.4 0.8
OD2 A:ASP379 2.7 12.4 0.8
CG A:ASP379 2.8 11.4 0.8
CG A:ASP387 3.3 15.1 0.8
CG A:ASN381 3.4 11.0 0.8
C A:SER389 3.5 15.3 0.8
OD2 A:ASP387 3.6 18.6 0.8
O A:ASP387 3.9 12.9 0.8
ND2 A:ASN381 4.0 11.3 0.8
N A:SER389 4.1 15.8 0.8
CA A:SER389 4.2 15.7 0.8
CB A:ASP379 4.3 11.2 0.8
CB A:SER389 4.4 16.5 0.8
N A:GLY382 4.4 9.6 0.8
C A:ASP387 4.4 13.9 0.8
C A:ASN381 4.5 10.4 0.8
N A:ASN381 4.5 10.0 0.8
CA A:GLY382 4.5 10.3 0.8
N A:PHE390 4.6 14.6 0.8
CB A:ASP387 4.6 13.4 0.8
CB A:ASN381 4.6 9.8 0.8
O A:HOH3073 4.7 17.2 0.8
CA A:ASN381 4.7 9.6 0.8
OG A:SER319 4.7 10.7 0.8
CA A:PHE390 4.8 14.3 0.8
C A:SER388 4.8 15.9 0.8
O A:ASN381 4.9 10.8 0.8
CA A:ASP387 4.9 13.7 0.8
CA A:ASP379 4.9 10.2 0.8
O A:HOH3371 4.9 40.9 0.8

Calcium binding site 3 out of 5 in 3cye

Go back to Calcium Binding Sites List in 3cye
Calcium binding site 3 out of 5 in the Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:53.9
occ:0.38
 O A:HOH3186 2.6 33.6 0.8
O B:HOH3262 2.6 33.5 0.8
O B:HOH3278 3.1 33.3 0.4
OD2 B:ASP113 4.3 14.3 0.8
OD2 A:ASP113 4.4 14.1 0.8
OD1 B:ASP113 4.5 15.4 0.8
OD1 A:ASP113 4.6 16.2 0.8
O B:HOH3341 4.6 42.1 0.8
CG B:ASP113 4.8 14.4 0.8
CG A:ASP113 4.9 13.5 0.8

Calcium binding site 4 out of 5 in 3cye

Go back to Calcium Binding Sites List in 3cye
Calcium binding site 4 out of 5 in the Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:12.7
occ:0.77
 OD1 B:ASN381 2.2 10.6 0.8
O B:HOH3092 2.3 19.0 0.8
OD1 B:ASP379 2.4 11.7 0.8
O B:SER389 2.4 14.1 0.8
OD1 B:ASP387 2.4 13.4 0.8
O B:HOH3023 2.4 14.6 0.8
OD2 B:ASP379 2.6 12.2 0.8
CG B:ASP379 2.8 13.2 0.8
CG B:ASP387 3.3 14.8 0.8
CG B:ASN381 3.3 10.5 0.8
C B:SER389 3.5 14.9 0.8
OD2 B:ASP387 3.5 19.8 0.8
O B:ASP387 3.8 15.2 0.8
ND2 B:ASN381 3.8 11.8 0.8
N B:SER389 4.0 14.8 0.8
CA B:SER389 4.1 15.3 0.8
CB B:SER389 4.2 16.0 0.8
CB B:ASP379 4.3 9.0 0.8
C B:ASP387 4.4 14.9 0.8
N B:GLY382 4.4 9.4 0.8
C B:ASN381 4.5 10.5 0.8
CA B:GLY382 4.5 9.5 0.8
N B:PHE390 4.5 13.6 0.8
N B:ASN381 4.6 10.0 0.8
CB B:ASN381 4.6 10.8 0.8
CB B:ASP387 4.6 15.5 0.8
O B:HOH3087 4.7 19.7 0.8
CA B:ASN381 4.7 9.9 0.8
OG B:SER319 4.8 12.9 0.8
CA B:PHE390 4.8 13.1 0.8
C B:SER388 4.8 15.6 0.8
O B:ASN381 4.9 11.3 0.8
O B:HOH3260 4.9 34.7 0.8
CA B:ASP387 4.9 14.6 0.8
CA B:ASP379 4.9 9.3 0.8

Calcium binding site 5 out of 5 in 3cye

Go back to Calcium Binding Sites List in 3cye
Calcium binding site 5 out of 5 in the Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cyrstal Structure of the Native 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:11.5
occ:0.77
 OD2 B:ASP324 2.3 9.6 0.8
O B:GLY345 2.3 14.1 0.8
O B:ASN347 2.4 11.6 0.8
O B:GLY297 2.4 12.8 0.8
O B:HOH3057 2.4 15.1 0.8
O B:ASP293 2.4 11.8 0.8
CG B:ASP324 3.4 11.5 0.8
C B:GLY345 3.5 14.6 0.8
C B:GLY297 3.5 12.5 0.8
C B:ASN347 3.5 12.0 0.8
C B:ASP293 3.6 10.9 0.8
CA B:GLY348 4.0 11.4 0.8
O B:HOH3013 4.1 10.6 0.8
CA B:GLY345 4.1 14.0 0.8
O B:ALA346 4.2 13.9 0.8
C B:ALA346 4.2 13.0 0.8
CB B:ASP324 4.2 10.8 0.8
N B:GLY348 4.2 11.2 0.8
CA B:ASN294 4.3 11.3 0.8
N B:GLY297 4.3 12.6 0.8
OD1 B:ASP324 4.3 10.8 0.8
N B:SER298 4.3 11.4 0.8
CA B:SER298 4.4 12.3 0.8
N B:ASN347 4.4 12.9 0.8
N B:ASN294 4.4 10.9 0.8
CA B:GLY297 4.5 12.2 0.8
N B:ALA346 4.5 14.3 0.8
CA B:ASP293 4.6 11.1 0.8
CA B:ASN347 4.6 13.2 0.8
O B:ASN344 4.6 15.7 0.8
C B:ASN294 4.7 11.6 0.8
CA B:ALA346 4.7 13.6 0.8
CB B:ASP293 4.7 11.5 0.8
N B:ASP293 4.8 10.8 0.8
OD1 B:ASP293 4.8 12.1 0.8
O B:PRO326 4.9 13.5 0.8

Reference:

X.Zhu, X.Xu, I.A.Wilson. Structure Determination of the 1918 H1N1 Neuraminidase From A Crystal with Lattice-Translocation Defects Acta Crystallogr.,Sect.D V. 64 843 2008.
ISSN: ISSN 0907-4449
PubMed: 18645233
DOI: 10.1107/S0907444908016648
Page generated: Sat Jul 13 08:47:43 2024

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