Ytterbium in PDB 8rki: Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment

The structure of Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment, PDB code: 8rki was solved by B.Wiseman, S.Zamora-Caballero, D.De Sanctis, S.Yasumasu, L.Jovine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.06 / 4.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.35, 108.35, 255.07, 90, 90, 120
R / Rfree (%)	32.9 / 36.8

The binding sites of Ytterbium atom in the Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment (pdb code 8rki). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 4 binding sites of Ytterbium where determined in the Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment, PDB code: 8rki:
Jump to Ytterbium binding site number: 1; 2; 3; 4;

Ytterbium binding site 1 out of 4 in the Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb1001 b:274.0 occ:0.82 OE1 A:GLU176 2.2 287.0 1.0 OE2 A:GLU176 2.4 263.3 1.0 CD A:GLU176 2.6 267.0 1.0 HE2 A:HIS178 3.7 356.2 1.0 HE1 A:HIS178 3.8 339.2 1.0 CG A:GLU176 4.1 272.2 1.0 NE2 A:HIS178 4.3 296.4 1.0 CE1 A:HIS178 4.3 282.3 1.0 HG2 A:GLU176 4.4 327.1 1.0 HB3 A:GLU176 4.6 331.2 1.0 HG3 A:GLU176 4.6 327.1 1.0 HG11 A:VAL148 4.7 358.6 1.0 HB2 A:GLU176 4.8 331.2 1.0 CB A:GLU176 4.8 275.6 1.0

Ytterbium binding site 2 out of 4 in the Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb1002 b:311.0 occ:0.73 OE2 A:GLU144 2.6 266.8 1.0 OD1 A:ASP145 3.0 265.7 1.0 OD2 A:ASP145 3.0 266.0 1.0 CG A:ASP145 3.4 280.7 1.0 CD A:GLU144 3.7 279.7 1.0 OE1 A:GLU144 4.3 276.4 1.0 HG2 A:GLU144 4.4 336.6 1.0 CG A:GLU144 4.7 280.1 1.0 CB A:ASP145 4.9 290.1 1.0

Ytterbium binding site 3 out of 4 in the Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Yb1001 b:262.0 occ:0.72 OD1 C:ASP311 2.3 235.2 1.0 OD2 C:ASP311 2.3 209.6 1.0 CG C:ASP311 2.5 216.9 1.0 O C:SER312 2.8 256.0 1.0 H C:SER312 3.3 302.9 1.0 N C:SER312 3.7 252.0 1.0 C C:SER312 3.9 247.9 1.0 CB C:ASP311 3.9 215.4 1.0 HA C:ASP311 4.1 284.2 1.0 C C:ASP311 4.2 238.8 1.0 CA C:ASP311 4.3 236.4 1.0 HB3 C:ASP311 4.3 258.9 1.0 CA C:SER312 4.3 240.6 1.0 HB2 C:ASP311 4.5 258.9 1.0 HA C:SER312 4.6 289.2 1.0 HB3 C:ASN313 4.6 317.9 1.0 HA C:ASN313 4.9 288.1 1.0 N C:ASN313 5.0 250.4 1.0

Ytterbium binding site 4 out of 4 in the Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Molecular Basis of ZP3/ZP1 Heteropolymerization: Crystal Structure of A Native Vertebrate Egg Coat Filament Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Yb1002 b:394.5 occ:0.76 OD2 C:ASP294 2.3 280.0 1.0 OD1 C:ASP294 2.4 250.6 1.0 CG C:ASP294 2.6 276.4 1.0 OE2 C:GLU296 2.7 239.6 1.0 OE1 C:GLU296 3.0 244.2 1.0 CD C:GLU296 3.2 258.4 1.0 CB C:ASP294 4.1 273.8 1.0 HB3 C:ASP294 4.3 329.1 1.0 HA C:ASP294 4.5 319.9 1.0 CG C:GLU296 4.6 266.8 1.0 HB2 C:ASP294 4.6 329.1 1.0 HG2 C:GLU296 4.8 320.7 1.0 HZ1 C:LYS286 4.8 331.6 1.0 CA C:ASP294 4.8 266.2 1.0 H C:LEU295 4.8 322.5 1.0 H C:GLU296 4.9 340.4 1.0

S.Nishio, C.Emori, B.Wiseman, D.Fahrenkamp, E.Dioguardi, S.Zamora-Caballero, M.Bokhove, L.Han, A.Stsiapanava, B.Algarra, Y.Lu, M.Kodani, R.E.Bainbridge, K.M.Komondor, A.E.Carlson, M.Landreh, D.De Sanctis, S.Yasumasu, M.Ikawa, L.Jovine. ZP2 Cleavage Blocks Polyspermy By Modulating the Architecture of the Egg Coat Cell(Cambridge,Mass.) 2024.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2024.02.013