Zinc in PDB 5bvr: Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe

The structure of Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe, PDB code: 5bvr was solved by K.Persson, L.Backman, B.Addario, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.97 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.537, 79.468, 91.933, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.7

The binding sites of Zinc atom in the Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe (pdb code 5bvr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe, PDB code: 5bvr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.4 occ:0.93 ND1 A:HIS166 1.9 19.7 1.0 OD2 A:ASP233 2.0 19.8 1.0 O A:HOH608 2.0 24.4 1.0 O A:HOH618 2.3 11.5 1.0 CG A:ASP233 2.8 25.4 1.0 CE1 A:HIS166 2.8 24.1 1.0 OD1 A:ASP233 2.9 24.2 1.0 CG A:HIS166 3.0 20.9 1.0 HE1 A:HIS166 3.0 28.9 1.0 HB2 A:HIS166 3.1 24.1 1.0 HA A:HIS166 3.2 25.8 1.0 HB3 A:PHE229 3.3 19.4 1.0 CB A:HIS166 3.4 20.1 1.0 CA A:HIS166 3.8 21.5 1.0 O A:HOH439 3.9 28.7 1.0 O A:HOH513 3.9 31.6 1.0 HZ2 A:LYS136 3.9 31.4 1.0 NE2 A:HIS166 4.0 23.1 1.0 O A:HOH629 4.0 49.7 1.0 O A:HOH466 4.0 25.9 1.0 CD2 A:HIS166 4.1 23.6 1.0 HE22 A:GLN165 4.2 24.9 1.0 CB A:PHE229 4.2 16.2 1.0 CB A:ASP233 4.2 22.8 1.0 O A:PHE229 4.3 19.1 1.0 O A:HIS166 4.3 26.4 1.0 HB3 A:HIS166 4.4 24.1 1.0 HD2 A:PHE229 4.4 26.5 1.0 HB2 A:ASP233 4.4 27.3 1.0 HA A:PHE229 4.5 20.6 1.0 HB3 A:ASP233 4.5 27.3 1.0 CG A:PHE229 4.5 19.7 1.0 C A:HIS166 4.5 25.5 1.0 HZ1 A:LYS136 4.5 31.4 1.0 CD2 A:PHE229 4.6 22.1 1.0 NZ A:LYS136 4.6 26.2 1.0 HE2 A:HIS166 4.7 27.7 1.0 CA A:PHE229 4.7 17.2 1.0 C A:PHE229 4.7 17.0 1.0 NE2 A:GLN165 4.8 20.8 1.0 HE3 A:LYS136 4.9 26.4 1.0 HB2 A:PHE229 4.9 19.4 1.0 HD2 A:HIS166 4.9 28.3 1.0 N A:HIS166 5.0 20.2 1.0

Zinc binding site 2 out of 3 in the Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.5 occ:0.81 OD1 A:ASP211 1.9 31.5 1.0 O A:HOH575 2.3 14.5 1.0 CG A:ASP211 2.7 35.3 1.0 OD2 A:ASP211 2.8 32.5 1.0 HH12 A:ARG151 3.5 62.7 1.0 HH22 A:ARG151 3.7 42.9 1.0 NH1 A:ARG151 4.0 52.3 1.0 CB A:ASP211 4.1 19.6 1.0 NH2 A:ARG151 4.2 35.7 1.0 O A:HOH492 4.2 48.2 1.0 HB2 A:ASP211 4.4 23.5 1.0 CZ A:ARG151 4.4 40.2 1.0 HH11 A:ARG151 4.5 62.7 1.0 HA A:ASP211 4.6 24.9 1.0 HG3 A:ARG212 4.7 42.8 1.0 HB3 A:ASP211 4.7 23.5 1.0 O A:ASP211 4.7 22.4 1.0 HH21 A:ARG151 4.8 42.9 1.0 CA A:ASP211 4.8 20.7 1.0 NH2 A:ARG212 4.8 53.7 1.0 HH21 A:ARG212 4.9 64.4 1.0 HH22 A:ARG212 5.0 64.4 1.0 CZ A:ARG212 5.0 57.8 1.0 C A:ASP211 5.0 22.3 1.0

Zinc binding site 3 out of 3 in the Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Actin Binding Domain of Alpha-Actinin From Schizosaccharomyces Pombe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:26.3 occ:0.38 H A:ARG216 2.1 19.5 1.0 HG3 A:ARG216 2.6 19.6 1.0 OD1 A:ASP214 2.8 19.8 1.0 N A:ARG216 2.9 16.3 1.0 HB2 A:ARG216 2.9 17.1 1.0 HB3 A:GLU215 3.0 18.9 1.0 H A:GLU215 3.1 18.8 1.0 HE21 A:GLN10 3.1 22.2 1.0 HE22 A:GLN10 3.2 22.2 1.0 HD2 A:ARG216 3.2 24.4 1.0 CG A:ARG216 3.3 16.4 1.0 CG A:ASP214 3.3 18.4 1.0 O A:HOH539 3.3 56.2 1.0 O A:HOH576 3.4 23.8 1.0 N A:GLU215 3.4 15.7 1.0 CB A:ARG216 3.4 14.2 1.0 OD2 A:ASP214 3.5 16.9 1.0 NE2 A:GLN10 3.5 18.5 1.0 O A:HOH587 3.5 35.9 1.0 CD A:ARG216 3.7 20.4 1.0 CA A:ARG216 3.8 14.1 1.0 CB A:GLU215 3.8 15.7 1.0 C A:GLU215 3.8 14.3 1.0 CA A:GLU215 3.9 14.4 1.0 HA A:ASP214 3.9 22.1 1.0 C A:ASP214 4.1 15.9 1.0 HG2 A:ARG216 4.1 19.6 1.0 HB2 A:GLU215 4.2 18.9 1.0 H A:SER217 4.2 16.4 1.0 O A:HOH514 4.3 38.1 1.0 HB3 A:ARG216 4.3 17.1 1.0 HE A:ARG216 4.4 26.1 1.0 NE A:ARG216 4.4 21.8 1.0 CA A:ASP214 4.4 18.4 1.0 HA A:ARG216 4.4 16.9 1.0 CB A:ASP214 4.5 16.8 1.0 HD3 A:ARG216 4.5 24.4 1.0 CD A:GLN10 4.8 21.1 1.0 O A:HOH510 4.8 27.6 1.0 HA A:GLU215 4.8 17.3 1.0 O A:ASP214 4.8 14.2 1.0 N A:SER217 4.8 13.7 1.0 C A:ARG216 4.9 15.6 1.0 O A:HOH559 4.9 40.0 1.0

B.Addario, L.Sandblad, K.Persson, L.Backman. Characterisation of Schizosaccharomyces Pombe Alpha-Actinin. Peerj V. 4 E1858 2016.
ISSN: ESSN 2167-8359
PubMed: 27069798
DOI: 10.7717/PEERJ.1858