Zinc in PDB 6gf7: Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer

The structure of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer, PDB code: 6gf7 was solved by K.Nishimura, L.Jovine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.32 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.410, 75.410, 100.780, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 27.2

The binding sites of Zinc atom in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer (pdb code 6gf7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer, PDB code: 6gf7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:84.4 occ:0.88 O A:HOH305 2.2 70.1 0.4 O A:HOH312 2.2 84.4 0.9 NE2 A:HIS91 2.2 70.5 0.6 NE2 A:HIS71 2.3 72.7 1.0 CE1 A:HIS71 3.0 71.6 1.0 CE1 A:HIS91 3.0 55.5 0.6 CD2 A:HIS91 3.3 66.0 0.6 O A:HOH313 3.5 51.3 1.0 CD2 A:HIS71 3.5 50.4 1.0 SG A:CYS69 3.7 85.0 0.6 CB A:CYS69 4.0 68.4 0.6 CB A:CYS69 4.0 68.8 0.4 NE1 B:TRP72 4.0 64.2 1.0 SG A:CYS69 4.1 81.3 0.4 ND1 A:HIS91 4.2 59.0 0.6 ND1 A:HIS71 4.2 70.5 1.0 CG A:HIS91 4.4 59.9 0.6 CG A:HIS71 4.5 58.8 1.0 ND1 A:HIS91 4.6 57.4 0.4 CD1 B:TRP72 4.7 61.1 1.0 CB A:CYS90 4.9 68.2 0.4 O B:ASN65 4.9 100.0 1.0

Zinc binding site 2 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:65.1 occ:1.00 OD2 A:ASP31 2.0 67.1 1.0 NE2 A:HIS29 2.0 56.5 1.0 O A:HOH315 2.2 65.1 1.0 O A:HOH314 2.2 65.1 1.0 CG A:ASP31 2.7 67.3 1.0 OD1 A:ASP31 2.8 57.5 1.0 CD2 A:HIS29 3.0 53.1 1.0 CE1 A:HIS29 3.0 57.0 1.0 CD1 A:LEU40 3.7 80.3 1.0 ND1 A:HIS29 4.1 58.3 1.0 CG A:HIS29 4.1 43.6 1.0 CB A:ASP31 4.2 49.7 1.0 CG A:LEU40 4.7 50.8 1.0

Zinc binding site 3 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:65.1 occ:0.88 ND1 A:HIS50 2.1 65.2 1.0 OE2 A:GLU62 2.1 82.1 1.0 O A:HOH306 2.2 65.1 0.7 O A:HOH304 2.2 65.1 0.9 CD A:GLU62 2.7 69.4 1.0 OE1 A:GLU62 2.8 86.2 1.0 CE1 A:HIS50 3.0 56.1 1.0 CG A:HIS50 3.1 56.7 1.0 O A:HOH306 3.3 96.2 0.3 CB A:HIS50 3.4 54.6 1.0 CG A:GLU62 4.0 53.6 1.0 NE2 A:HIS50 4.2 55.5 1.0 CD2 A:HIS50 4.2 61.6 1.0 SD A:MET108 4.3 81.2 1.0 OE1 A:GLU106 4.7 96.2 1.0 CA A:HIS50 4.9 59.9 1.0 CE A:LYS52 5.0 56.4 1.0

Zinc binding site 4 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:0.3 occ:0.70 OE1 A:GLU106 2.2 96.2 1.0 OE2 A:GLU106 2.2 0.0 1.0 O A:HOH306 2.2 96.2 0.3 O A:HOH303 2.2 0.0 0.7 NZ A:LYS52 2.3 91.7 1.0 CD A:GLU106 2.5 89.9 1.0 CE A:LYS52 3.2 56.4 1.0 O A:HOH306 3.3 65.1 0.7 CG A:GLU106 4.0 63.3 1.0 CG2 A:VAL114 4.1 62.3 1.0 CD A:LYS52 4.3 67.7 1.0 CB A:GLU106 4.8 64.1 1.0

Zinc binding site 5 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:0.1 occ:0.91 O A:HOH308 2.2 0.1 0.9 O A:HOH309 2.2 0.1 0.9 O A:HOH316 2.2 0.1 0.9 OD2 A:ASP34 2.4 99.6 1.0 CG A:ASP34 3.1 89.5 1.0 OD1 A:ASP34 3.2 84.5 1.0 CB A:ASP34 4.4 81.8 1.0

Zinc binding site 6 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:85.5 occ:0.54 ND1 B:HIS71 2.2 68.3 1.0 CE1 B:HIS71 3.1 79.9 1.0 CG B:HIS71 3.2 56.5 1.0 CD2 B:HIS91 3.3 85.8 1.0 O B:CYS69 3.3 79.9 1.0 CB B:HIS71 3.5 55.7 1.0 CB B:CYS69 3.9 67.7 1.0 N B:CYS90 4.0 85.2 1.0 NE2 B:HIS91 4.1 78.8 1.0 N B:HIS91 4.2 61.5 1.0 C B:CYS69 4.2 61.2 1.0 CB B:CYS90 4.2 93.3 1.0 NE2 B:HIS71 4.2 72.7 1.0 CD2 B:HIS71 4.3 62.3 1.0 CG B:HIS91 4.3 93.4 1.0 N B:HIS71 4.5 54.3 1.0 CA B:CYS90 4.6 88.7 1.0 O B:MET70 4.6 64.3 1.0 CA B:HIS71 4.6 57.1 1.0 C B:MET70 4.6 59.7 1.0 CA B:CYS69 4.7 64.8 1.0 CB B:HIS91 4.8 86.9 1.0 SG B:CYS69 4.8 0.3 1.0 C B:GLY89 4.9 71.4 1.0 CG2 B:VAL53 4.9 52.6 1.0 CA B:GLY89 4.9 61.2 1.0 C B:CYS90 4.9 78.5 1.0

Zinc binding site 7 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:79.5 occ:0.73 OD1 B:ASP31 1.9 79.0 1.0 O B:HOH306 2.2 79.5 1.0 NE2 B:HIS29 2.2 77.8 1.0 CE1 B:HIS29 2.6 82.6 1.0 CG B:ASP31 2.7 68.2 1.0 OD2 B:ASP31 2.9 73.0 1.0 CD2 B:HIS29 3.5 71.2 1.0 ZN B:ZN204 3.8 0.1 0.9 ND1 B:HIS29 3.9 83.9 1.0 CB B:ASP31 4.1 54.6 1.0 CG B:HIS29 4.4 76.0 1.0 O B:TYR30 4.5 61.9 1.0 CA B:ASP31 4.7 66.6 1.0

Zinc binding site 8 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:0.1 occ:0.85 O B:HOH306 2.2 79.5 1.0 ZN B:ZN203 3.8 79.5 0.7

Zinc binding site 9 out of 9 in the Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Molecular Basis of Egg Coat Filament Cross-Linking: Zn-Sad Structure of the Partially Deglycosylated ZP1 Zp-N1 Domain Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:1.0 occ:1.00 O B:HOH303 2.2 85.7 1.0 OE1 B:GLU106 2.2 0.3 1.0 ND1 B:HIS50 2.4 85.7 1.0 CG B:HIS50 3.3 77.7 1.0 CD B:GLU106 3.3 0.5 1.0 CE1 B:HIS50 3.3 0.4 1.0 CB B:HIS50 3.5 73.2 1.0 OE2 B:GLU106 3.8 0.1 1.0 SD B:MET108 4.2 95.4 1.0 CD2 B:HIS50 4.4 67.7 1.0 NE2 B:HIS50 4.4 93.7 1.0 CG B:GLU106 4.5 0.0 1.0 CE B:LYS52 4.6 0.6 1.0 CB B:GLU106 4.7 0.7 1.0 NZ B:LYS52 4.8 81.3 1.0 CD B:LYS52 5.0 98.8 1.0

K.Nishimura, E.Dioguardi, S.Nishio, A.Villa, L.Han, T.Matsuda, L.Jovine. Molecular Basis of Egg Coat Cross-Linking Sheds Light on ZP1-Associated Female Infertility. Nat Commun V. 10 3086 2019.
ISSN: ESSN 2041-1723
PubMed: 31300655
DOI: 10.1038/S41467-019-10931-5