Calcium in PDB 3d4g: Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)

The structure of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II), PDB code: 3d4g was solved by L.Jovine, M.Monne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	91.050, 91.960, 140.480, 89.99, 90.18, 89.98
R / Rfree (%)	20.1 / 22.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) (pdb code 3d4g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II), PDB code: 3d4g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca483 b:70.6 occ:1.00 O A:HOH486 2.5 41.2 1.0 O A:HOH488 2.5 36.1 1.0 O A:HOH631 2.9 59.4 1.0 O A:HOH663 3.7 45.2 1.0 OD1 A:ASP42 3.8 52.3 1.0 O A:HOH725 4.1 63.0 1.0 N A:LYS43 4.4 42.9 1.0 O A:HOH526 4.5 39.2 1.0 OE2 A:GLU45 4.5 35.4 1.0 OD1 A:ASN13 4.5 40.2 1.0 OE1 A:GLU45 4.6 33.3 1.0 CA A:LYS43 4.7 41.5 1.0 CH2 A:TRP63 4.8 30.0 1.0 O A:HOH542 4.9 30.8 1.0 CG A:ASP42 5.0 51.8 1.0

Calcium binding site 2 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca484 b:57.7 occ:1.00 O A:VAL182 2.4 53.8 1.0 OD1 A:ASP185 2.4 58.6 1.0 OE1 A:GLN366 2.4 60.0 1.0 O A:HOH529 2.5 56.2 1.0 CG A:ASP185 3.3 58.2 1.0 CD A:GLN366 3.4 54.4 1.0 OD2 A:ASP185 3.5 61.3 1.0 C A:VAL182 3.6 51.1 1.0 O A:HOH643 3.8 59.9 1.0 CG A:GLN366 4.2 51.1 1.0 N A:VAL182 4.2 52.3 1.0 NE2 A:GLN366 4.3 54.9 1.0 CA A:VAL182 4.4 50.0 1.0 N A:GLY183 4.5 50.2 1.0 CA A:GLY183 4.6 51.4 1.0 CB A:GLN366 4.6 47.7 1.0 CB A:ASP185 4.7 56.1 1.0 OD1 A:ASP181 4.8 58.8 1.0 CB A:VAL182 4.8 48.3 1.0 N A:ASP185 4.8 52.9 1.0

Calcium binding site 3 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca485 b:61.1 occ:1.00 O A:ASP297 2.4 56.2 1.0 O A:LYS296 2.4 59.3 1.0 OG A:SER234 2.4 59.6 1.0 O A:HOH675 2.9 52.0 1.0 C A:ASP297 3.2 54.6 1.0 C A:LYS296 3.5 57.9 1.0 CB A:SER234 3.5 56.1 1.0 CA A:ASP297 3.6 55.8 1.0 O A:HOH666 3.9 46.5 1.0 O A:HOH705 3.9 54.1 1.0 N A:ASP297 4.0 56.2 1.0 N A:LYS298 4.4 52.2 1.0 CA A:SER234 4.5 57.5 1.0 OD1 A:ASP297 4.6 56.2 1.0 O A:HOH569 4.7 49.3 1.0 CA A:LYS296 4.8 58.3 1.0 CA A:LYS298 4.9 51.0 1.0 CB A:ASP297 5.0 54.4 1.0

Calcium binding site 4 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca483 b:93.6 occ:1.00 O B:HOH489 2.4 55.6 1.0 O B:HOH490 2.5 50.2 1.0 O B:HOH612 2.6 59.7 1.0 OD1 B:ASP42 3.6 56.0 1.0 N B:LYS43 4.3 49.0 1.0 OE2 B:GLU45 4.5 40.5 1.0 CA B:LYS43 4.6 47.7 1.0 OD1 B:ASN13 4.7 50.6 1.0 OE1 B:GLU45 4.7 40.1 1.0 O B:HOH526 4.8 48.5 1.0 CG B:ASP42 4.8 55.5 1.0 CD B:LYS43 4.9 53.5 1.0 O B:HOH575 4.9 58.2 1.0 CG B:LYS43 5.0 51.2 1.0

Calcium binding site 5 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca484 b:54.7 occ:1.00 O A:HOH731 2.3 48.8 1.0 O A:HOH761 2.3 43.5 1.0 OD1 B:ASP185 2.4 57.4 1.0 O B:VAL182 2.4 55.5 1.0 OE1 B:GLN366 2.4 60.7 1.0 O B:HOH636 2.6 49.3 1.0 CG B:ASP185 3.2 57.4 1.0 OD2 B:ASP185 3.4 58.1 1.0 CD B:GLN366 3.4 54.5 1.0 C B:VAL182 3.6 54.5 1.0 O B:HOH618 3.9 45.5 1.0 CG B:GLN366 4.2 52.1 1.0 N B:VAL182 4.2 55.4 1.0 OE1 A:GLU310 4.2 72.7 1.0 NE2 B:GLN366 4.3 53.8 1.0 CA B:VAL182 4.4 53.2 1.0 N B:GLY183 4.5 54.7 1.0 CB B:GLN366 4.6 49.5 1.0 CA B:GLY183 4.6 56.3 1.0 CB B:ASP185 4.6 55.9 1.0 OD1 B:ASP181 4.7 59.5 1.0 CB B:VAL182 4.8 50.7 1.0 N B:ASP185 4.9 54.9 1.0

Calcium binding site 6 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca485 b:59.9 occ:1.00 O B:ASP297 2.4 76.5 1.0 O B:LYS296 2.4 85.2 1.0 OG B:SER234 2.4 76.3 1.0 O B:HOH666 2.5 68.3 1.0 O B:HOH632 2.6 53.8 1.0 C B:ASP297 3.2 76.7 1.0 C B:LYS296 3.4 85.1 1.0 CB B:SER234 3.5 73.0 1.0 CA B:ASP297 3.5 79.5 1.0 O B:HOH567 3.5 51.4 1.0 N B:ASP297 3.9 82.4 1.0 N B:LYS298 4.3 74.7 1.0 CA B:SER234 4.4 73.9 1.0 OD1 B:ASP297 4.7 76.0 1.0 CA B:LYS296 4.7 88.3 1.0 O B:HOH634 4.8 67.2 1.0 CA B:LYS298 4.8 72.3 1.0 CB B:ASP297 5.0 78.0 1.0

Calcium binding site 7 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca483 b:64.4 occ:1.00 O C:HOH635 2.4 52.4 1.0 O C:HOH504 2.6 40.1 1.0 O C:HOH503 2.6 44.4 1.0 O C:HOH665 3.4 41.2 1.0 OD1 C:ASP42 4.0 55.4 1.0 OE2 C:GLU45 4.3 37.8 1.0 O C:HOH751 4.4 48.3 1.0 OD1 C:ASN13 4.5 40.0 1.0 OE1 C:GLU45 4.5 35.1 1.0 N C:LYS43 4.5 44.3 1.0 CH2 C:TRP63 4.6 31.8 1.0 O C:HOH539 4.6 36.1 1.0 O C:HOH555 4.7 30.6 1.0 CA C:LYS43 4.7 42.7 1.0 O C:HOH732 4.8 56.1 1.0 CD C:GLU45 4.8 35.9 1.0 OE2 C:GLU154 5.0 42.5 1.0

Calcium binding site 8 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca484 b:57.6 occ:1.00 O C:VAL182 2.4 53.7 1.0 OD1 C:ASP185 2.4 58.1 1.0 OE1 C:GLN366 2.4 61.5 1.0 O C:HOH542 2.6 46.9 1.0 CG C:ASP185 3.3 57.8 1.0 CD C:GLN366 3.3 56.2 1.0 OD2 C:ASP185 3.5 60.5 1.0 C C:VAL182 3.6 51.3 1.0 CG C:GLN366 4.1 53.0 1.0 N C:VAL182 4.2 52.5 1.0 NE2 C:GLN366 4.2 57.5 1.0 CA C:VAL182 4.4 50.1 1.0 N C:GLY183 4.5 50.5 1.0 CB C:GLN366 4.6 49.3 1.0 CA C:GLY183 4.6 51.5 1.0 CB C:ASP185 4.7 55.8 1.0 CB C:VAL182 4.8 48.5 1.0 OE1 D:GLU310 4.8 0.9 1.0 OD1 C:ASP181 4.9 60.2 1.0 N C:ASP185 4.9 52.8 1.0

Calcium binding site 9 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca485 b:61.5 occ:1.00 O C:ASP297 2.4 57.2 1.0 O C:LYS296 2.4 60.5 1.0 OG C:SER234 2.4 60.6 1.0 O C:HOH676 2.9 51.1 1.0 C C:ASP297 3.2 55.5 1.0 CB C:SER234 3.5 57.4 1.0 C C:LYS296 3.5 59.0 1.0 CA C:ASP297 3.6 56.6 1.0 N C:ASP297 4.0 57.1 1.0 O C:HOH708 4.0 47.3 1.0 N C:LYS298 4.4 53.0 1.0 O C:HOH670 4.4 60.5 1.0 CA C:SER234 4.4 58.9 1.0 O C:HOH581 4.6 46.1 1.0 OD1 C:ASP297 4.6 56.4 1.0 CA C:LYS296 4.8 59.5 1.0 CA C:LYS298 4.9 51.9 1.0 CB C:ASP297 5.0 55.0 1.0

Calcium binding site 10 out of 24 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca483 b:95.2 occ:1.00 O D:HOH683 2.2 56.5 1.0 O D:HOH488 2.6 54.4 1.0 O D:HOH665 2.9 58.4 1.0 O D:HOH641 3.0 45.6 1.0 O D:HOH490 3.0 51.4 1.0 OE2 D:GLU154 4.5 47.1 1.0 OE2 D:GLU45 4.5 43.0 1.0 O D:HOH544 4.5 33.1 1.0 O D:HOH581 4.6 53.3 1.0 OD1 D:ASP42 4.6 62.2 1.0 CH2 D:TRP63 4.8 42.6 1.0 OD1 D:ASN13 4.9 50.6 1.0

M.Monne, L.Han, T.Schwend, S.Burendahl, L.Jovine. Crystal Structure of the Zp-N Domain of ZP3 Reveals the Core Fold of Animal Egg Coats Nature V. 456 653 2008.
ISSN: ISSN 0028-0836
PubMed: 19052627
DOI: 10.1038/NATURE07599