Calcium in PDB 4zi9: Structure of Mouse Clustered PCDHGA1 EC1-3

The structure of Structure of Mouse Clustered PCDHGA1 EC1-3, PDB code: 4zi9 was solved by J.M.Nicoludis, S.-Y.Lau, C.P.I.Scharfe, D.S.Marks, W.A.Weihofen, R.Gaudet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.51 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.751, 63.687, 107.486, 90.00, 99.69, 90.00
R / Rfree (%)	23 / 26.6

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Structure of Mouse Clustered PCDHGA1 EC1-3 (pdb code 4zi9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Structure of Mouse Clustered PCDHGA1 EC1-3, PDB code: 4zi9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:31.4 occ:1.00 O A:ASN246 2.3 30.6 1.0 O A:ASN210 2.3 29.6 1.0 OD1 A:ASN208 2.3 27.5 1.0 OD2 A:ASP242 2.4 28.9 1.0 OD2 A:ASP240 2.5 32.3 1.0 OD2 A:ASP295 2.6 31.8 1.0 OD1 A:ASP240 2.6 39.7 1.0 CG A:ASP240 2.8 43.7 1.0 CG A:ASP242 3.4 37.0 1.0 C A:ASN246 3.5 37.0 1.0 CG A:ASP295 3.5 30.4 1.0 CG A:ASN208 3.5 33.5 1.0 C A:ASN210 3.5 29.5 1.0 CB A:ASP242 3.6 37.9 1.0 CB A:ASP295 3.7 34.0 1.0 ND2 A:ASN208 4.0 25.1 1.0 N A:ASN210 4.3 28.1 1.0 CA A:ASN210 4.3 29.0 1.0 CB A:ASP240 4.3 34.5 1.0 N A:GLY247 4.4 33.8 1.0 CA A:ASN246 4.4 38.0 1.0 CA A:GLY247 4.4 37.0 1.0 CB A:ASN210 4.5 30.1 1.0 N A:PRO211 4.5 32.7 1.0 OD1 A:ASP242 4.5 31.8 1.0 CB A:ASN246 4.5 33.4 1.0 OD1 A:ASP295 4.6 30.1 1.0 CD1 A:LEU299 4.6 30.3 1.0 CA A:PRO211 4.6 35.1 1.0 C A:PRO211 4.7 32.2 1.0 N A:ASP242 4.7 33.9 1.0 CB A:ASN208 4.8 23.8 1.0 CA A:ASP242 4.8 35.2 1.0 CA A:ASN208 4.9 27.1 1.0 N A:PRO212 4.9 33.5 1.0 CB A:LEU299 4.9 29.6 1.0 CD A:PRO212 5.0 32.6 1.0

Calcium binding site 2 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:32.1 occ:1.00 OD1 A:ASP206 2.3 30.2 1.0 OE2 A:GLU175 2.3 25.9 1.0 OE1 A:GLU116 2.3 25.0 1.0 OD1 A:ASP209 2.4 29.2 1.0 OD1 A:ASP242 2.4 31.8 1.0 O A:VAL207 2.5 22.4 1.0 OE1 A:GLU175 2.6 26.6 1.0 CD A:GLU175 2.8 24.6 1.0 CD A:GLU116 3.4 22.7 1.0 CG A:ASP242 3.4 37.0 1.0 CG A:ASP206 3.5 30.2 1.0 CG A:ASP209 3.5 31.4 1.0 C A:VAL207 3.6 26.6 1.0 OE2 A:GLU116 3.8 26.9 1.0 N A:VAL207 3.8 23.7 1.0 CA A:CA503 3.9 31.9 1.0 ND2 A:ASN210 4.0 32.2 1.0 OD2 A:ASP206 4.1 29.5 1.0 CB A:ASP242 4.1 37.9 1.0 N A:ASP209 4.1 25.6 1.0 OD2 A:ASP209 4.1 32.5 1.0 CG A:GLU175 4.2 25.9 1.0 CA A:ASP242 4.3 35.2 1.0 CA A:VAL207 4.3 23.1 1.0 OD2 A:ASP242 4.4 28.9 1.0 NE A:ARG174 4.4 34.4 1.0 CB A:ASP206 4.6 23.7 1.0 CA A:ASP206 4.6 26.0 1.0 C A:ASP206 4.7 26.9 1.0 CG A:GLU116 4.7 23.0 1.0 N A:ASN208 4.7 22.4 1.0 CB A:ASP209 4.7 28.1 1.0 CA A:ASN208 4.8 27.1 1.0 CA A:ASP209 4.9 32.8 1.0 CB A:ARG174 4.9 21.1 1.0 CB A:VAL207 4.9 26.6 1.0 C A:ASN208 5.0 21.9 1.0 NH2 A:ARG174 5.0 34.5 1.0

Calcium binding site 3 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:31.9 occ:1.00 OE1 A:GLU175 2.3 26.6 1.0 OD1 A:ASP173 2.3 23.8 1.0 O A:HOH766 2.4 27.0 1.0 OE2 A:GLU116 2.4 26.9 1.0 O A:HOH769 2.5 27.9 1.0 OD2 A:ASP209 2.5 32.5 1.0 CG A:ASP209 3.2 31.4 1.0 CG A:ASP173 3.2 28.2 1.0 OD1 A:ASP209 3.2 29.2 1.0 CD A:GLU116 3.3 22.7 1.0 CD A:GLU175 3.5 24.6 1.0 OE1 A:GLU116 3.7 25.0 1.0 OD2 A:ASP173 3.9 31.6 1.0 CA A:CA502 3.9 32.1 1.0 O A:HOH629 4.0 26.6 1.0 CB A:ASP173 4.1 26.1 1.0 CA A:ASP173 4.2 29.8 1.0 ND2 A:ASN210 4.2 32.2 1.0 N A:ARG174 4.3 24.1 1.0 N A:GLU175 4.3 32.0 1.0 CB A:GLU175 4.3 27.2 1.0 CG A:GLU175 4.4 25.9 1.0 OE2 A:GLU175 4.4 25.9 1.0 C A:ASP173 4.5 27.7 1.0 O A:HOH651 4.5 30.6 1.0 CG A:GLU116 4.5 23.0 1.0 CB A:ASP209 4.7 28.1 1.0 O A:HOH722 4.7 31.1 1.0 CA A:GLU175 5.0 31.2 1.0 CB A:GLU116 5.0 21.5 1.0

Calcium binding site 4 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:33.6 occ:1.00 OE2 A:GLU65 2.3 39.8 1.0 OD1 A:ASP100 2.4 35.3 1.0 OE2 A:GLU9 2.4 31.1 1.0 OD1 A:ASP133 2.4 24.0 1.0 O A:ILE98 2.4 29.7 1.0 OD1 A:ASP97 2.5 36.0 1.0 OE1 A:GLU65 2.5 32.5 1.0 CD A:GLU65 2.7 33.4 1.0 CD A:GLU9 3.3 40.9 1.0 CG A:ASP133 3.4 35.6 1.0 CG A:ASP100 3.5 37.7 1.0 CG A:ASP97 3.6 37.2 1.0 OE1 A:GLU9 3.6 37.6 1.0 C A:ILE98 3.6 28.9 1.0 N A:ILE98 3.8 30.2 1.0 ND2 A:ASN101 3.8 31.5 1.0 CA A:CA506 4.0 36.9 1.0 OD2 A:ASP100 4.0 37.9 1.0 N A:ASP100 4.1 28.1 1.0 CB A:ASP133 4.1 37.4 1.0 OD2 A:ASP97 4.1 39.7 1.0 CG A:GLU65 4.2 40.3 1.0 OD2 A:ASP133 4.3 32.9 1.0 CA A:ILE98 4.3 29.0 1.0 CA A:ASP133 4.3 33.9 1.0 CG1 A:ILE98 4.4 30.3 1.0 NE A:ARG64 4.4 40.1 1.0 C A:ASP97 4.6 32.5 1.0 CA A:ASP97 4.6 32.3 1.0 CB A:ASP97 4.7 33.0 1.0 N A:ASN99 4.7 28.7 1.0 CG A:GLU9 4.7 31.0 1.0 CB A:ASP100 4.7 29.1 1.0 NH2 A:ARG64 4.8 36.9 1.0 CA A:ASN99 4.9 27.9 1.0 CA A:ASP100 4.9 31.0 1.0 C A:ASN99 5.0 27.4 1.0

Calcium binding site 5 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:31.8 occ:1.00 OD1 A:ASN99 2.3 28.4 1.0 O A:ASN101 2.4 29.1 1.0 OD2 A:ASP188 2.4 32.9 1.0 O A:ASN137 2.4 28.4 1.0 OD2 A:ASP133 2.4 32.9 1.0 OD2 A:ASP131 2.4 25.7 1.0 OD1 A:ASP131 2.7 33.6 1.0 CG A:ASP131 2.9 30.0 1.0 CG A:ASP188 3.3 30.0 1.0 CG A:ASP133 3.4 35.6 1.0 CG A:ASN99 3.4 27.4 1.0 C A:ASN101 3.5 31.3 1.0 C A:ASN137 3.6 28.4 1.0 CB A:ASP188 3.7 29.9 1.0 CB A:ASP133 3.7 37.4 1.0 ND2 A:ASN99 4.0 31.9 1.0 N A:ASN101 4.2 31.8 1.0 CA A:ASN101 4.2 36.8 1.0 CB A:ASN137 4.3 32.3 1.0 CA A:ASN137 4.3 32.9 1.0 CB A:ASP131 4.4 26.4 1.0 CB A:ASN101 4.4 31.0 1.0 OD1 A:ASP188 4.4 26.6 1.0 N A:THR102 4.5 22.5 1.0 OD1 A:ASP133 4.5 24.0 1.0 N A:SER138 4.6 28.1 1.0 CA A:THR102 4.7 27.8 1.0 CD A:PRO103 4.7 23.7 1.0 CB A:ASN99 4.7 27.2 1.0 CA A:SER138 4.7 27.6 1.0 CA A:ASN99 4.7 27.9 1.0 ND1 A:HIS194 4.8 41.5 1.0 N A:ASP133 4.9 25.0 1.0 C A:ASN99 4.9 27.4 1.0 CA A:ASP133 4.9 33.9 1.0

Calcium binding site 6 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:36.9 occ:1.00 OD1 A:ASP63 2.2 37.3 1.0 OE1 A:GLU65 2.3 32.5 1.0 OE1 A:GLU9 2.4 37.6 1.0 OD2 A:ASP100 2.4 37.9 1.0 OE2 A:GLU10 2.5 39.5 1.0 O A:HOH775 2.5 34.8 1.0 CG A:ASP100 3.3 37.7 1.0 CG A:ASP63 3.4 33.8 1.0 CD A:GLU9 3.4 40.9 1.0 OD1 A:ASP100 3.5 35.3 1.0 CD A:GLU10 3.5 41.0 1.0 CD A:GLU65 3.5 33.4 1.0 CG A:GLU10 3.8 30.9 1.0 OE2 A:GLU9 3.8 31.1 1.0 CA A:CA504 4.0 33.6 1.0 OD2 A:ASP63 4.2 35.6 1.0 CB A:ASP63 4.2 38.6 1.0 CA A:ASP63 4.2 38.7 1.0 N A:ARG64 4.3 34.4 1.0 NH2 A:ARG61 4.3 42.5 1.0 N A:GLU65 4.3 41.6 1.0 CG A:GLU65 4.4 40.3 1.0 CB A:GLU65 4.4 43.9 1.0 ND2 A:ASN101 4.4 31.5 1.0 OE2 A:GLU65 4.4 39.8 1.0 O A:HOH682 4.4 45.1 1.0 CG A:GLU9 4.5 31.0 1.0 C A:ASP63 4.5 34.7 1.0 O A:HOH768 4.6 35.7 1.0 OE1 A:GLU10 4.6 42.5 1.0 CB A:ASP100 4.7 29.1 1.0 O A:HOH808 4.7 43.2 1.0 CB A:GLU9 4.9 31.8 1.0

Calcium binding site 7 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:31.4 occ:1.00 O B:ASN101 2.3 35.1 1.0 O B:ASN137 2.3 33.8 1.0 OD1 B:ASN99 2.4 35.0 1.0 OD2 B:ASP131 2.4 33.0 1.0 OD2 B:ASP133 2.4 33.3 1.0 OD2 B:ASP188 2.6 38.8 1.0 OD1 B:ASP131 2.7 35.0 1.0 CG B:ASP131 2.8 31.9 1.0 CG B:ASP133 3.4 39.0 1.0 CG B:ASP188 3.4 36.5 1.0 C B:ASN101 3.5 35.3 1.0 C B:ASN137 3.5 34.7 1.0 CG B:ASN99 3.5 40.0 1.0 CB B:ASP188 3.6 36.6 1.0 CB B:ASP133 3.7 40.1 1.0 ND2 B:ASN99 4.1 37.0 1.0 N B:ASN101 4.2 37.7 1.0 CA B:ASN101 4.3 34.7 1.0 CB B:ASN137 4.3 39.8 1.0 CA B:ASN137 4.3 39.3 1.0 CB B:ASP131 4.3 34.2 1.0 N B:THR102 4.5 31.8 1.0 CB B:ASN101 4.5 35.1 1.0 N B:SER138 4.5 36.5 1.0 CA B:SER138 4.5 40.1 1.0 OD1 B:ASP133 4.5 34.0 1.0 OD1 B:ASP188 4.6 36.4 1.0 CA B:THR102 4.7 31.2 1.0 CB B:ASN99 4.7 30.7 1.0 CD B:PRO103 4.7 32.5 1.0 CA B:ASN99 4.8 30.4 1.0 N B:ASP133 4.8 33.7 1.0 ND1 B:HIS194 4.9 45.1 1.0 CA B:ASP133 4.9 43.8 1.0 C B:ASN99 4.9 30.4 1.0

Calcium binding site 8 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:30.8 occ:1.00 OD1 B:ASP97 2.3 34.0 1.0 OD1 B:ASP100 2.3 34.6 1.0 OE2 B:GLU9 2.4 34.1 1.0 OD1 B:ASP133 2.4 34.0 1.0 OE2 B:GLU65 2.4 40.6 1.0 O B:ILE98 2.6 36.9 1.0 OE1 B:GLU65 2.7 32.0 1.0 CD B:GLU65 2.9 32.9 1.0 CD B:GLU9 3.4 35.4 1.0 CG B:ASP133 3.4 39.0 1.0 CG B:ASP100 3.5 35.4 1.0 CG B:ASP97 3.5 31.3 1.0 OE1 B:GLU9 3.7 34.0 1.0 C B:ILE98 3.7 34.8 1.0 ND2 B:ASN101 3.8 33.5 1.0 N B:ILE98 3.9 28.7 1.0 CA B:CA503 4.0 37.5 1.0 OD2 B:ASP100 4.0 38.0 1.0 N B:ASP100 4.1 36.0 1.0 CB B:ASP133 4.1 40.1 1.0 OD2 B:ASP97 4.2 35.9 1.0 OD2 B:ASP133 4.3 33.3 1.0 CG B:GLU65 4.3 34.2 1.0 CA B:ASP133 4.3 43.8 1.0 NE B:ARG64 4.4 35.1 1.0 CG1 B:ILE98 4.4 32.3 1.0 CA B:ILE98 4.4 28.4 1.0 CA B:ASP97 4.6 33.9 1.0 CB B:ASP97 4.6 30.8 1.0 C B:ASP97 4.7 32.3 1.0 CG B:GLU9 4.7 29.8 1.0 CB B:ASP100 4.7 29.9 1.0 N B:ASN99 4.8 33.0 1.0 NH2 B:ARG64 4.8 43.5 1.0 CA B:ASP100 4.9 30.7 1.0 CA B:ASN99 4.9 30.4 1.0 C B:ASN99 5.0 30.4 1.0

Calcium binding site 9 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:37.5 occ:1.00 OD2 B:ASP100 2.4 38.0 1.0 O B:HOH719 2.4 38.2 1.0 OE1 B:GLU65 2.4 32.0 1.0 OE2 B:GLU10 2.4 37.0 1.0 OE1 B:GLU9 2.4 34.0 1.0 OD1 B:ASP63 2.4 40.0 1.0 CG B:ASP100 3.3 35.4 1.0 CD B:GLU9 3.4 35.4 1.0 CD B:GLU10 3.4 42.0 1.0 CG B:ASP63 3.4 44.2 1.0 OD1 B:ASP100 3.5 34.6 1.0 CD B:GLU65 3.6 32.9 1.0 CG B:GLU10 3.8 38.4 1.0 OE2 B:GLU9 3.8 34.1 1.0 CA B:CA502 4.0 30.8 1.0 CB B:ASP63 4.2 38.2 1.0 OD2 B:ASP63 4.2 40.5 1.0 CA B:ASP63 4.2 33.5 1.0 N B:ARG64 4.3 31.1 1.0 NH2 B:ARG61 4.4 43.6 1.0 N B:GLU65 4.4 37.2 1.0 OE2 B:GLU65 4.4 40.6 1.0 ND2 B:ASN101 4.5 33.5 1.0 CG B:GLU65 4.5 34.2 1.0 CG B:GLU9 4.5 29.8 1.0 CB B:GLU65 4.5 40.3 1.0 C B:ASP63 4.6 32.2 1.0 OE1 B:GLU10 4.6 37.6 1.0 CB B:ASP100 4.7 29.9 1.0 O B:HOH791 4.7 38.4 1.0 O B:HOH804 4.8 42.1 1.0 CB B:GLU9 5.0 30.7 1.0

Calcium binding site 10 out of 12 in the Structure of Mouse Clustered PCDHGA1 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Mouse Clustered PCDHGA1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:23.3 occ:1.00 O B:ASN246 2.2 22.9 1.0 O B:ASN210 2.2 19.2 1.0 OD1 B:ASN208 2.3 29.6 1.0 OD2 B:ASP240 2.4 34.4 1.0 OD2 B:ASP242 2.4 24.4 1.0 OD2 B:ASP295 2.5 24.6 1.0 OD1 B:ASP240 2.7 27.1 1.0 CG B:ASP240 2.9 37.0 1.0 CG B:ASP295 3.4 28.5 1.0 CG B:ASP242 3.4 30.2 1.0 C B:ASN246 3.4 27.9 1.0 CG B:ASN208 3.5 28.7 1.0 C B:ASN210 3.5 27.8 1.0 CB B:ASP242 3.7 26.8 1.0 CB B:ASP295 3.7 28.3 1.0 ND2 B:ASN208 4.0 29.5 1.0 CA B:ASN210 4.3 26.4 1.0 N B:ASN210 4.3 23.1 1.0 CA B:ASN246 4.3 32.3 1.0 N B:GLY247 4.3 26.1 1.0 CB B:ASP240 4.4 25.6 1.0 CA B:GLY247 4.4 30.1 1.0 N B:PRO211 4.5 25.2 1.0 OD1 B:ASP295 4.5 26.3 1.0 CB B:ASN246 4.5 30.1 1.0 CB B:ASN210 4.5 27.1 1.0 OD1 B:ASP242 4.6 20.9 1.0 CA B:PRO211 4.6 24.6 1.0 CD1 B:LEU299 4.6 23.5 1.0 C B:PRO211 4.7 22.6 1.0 CB B:ASN208 4.7 28.2 1.0 N B:ASP242 4.8 27.7 1.0 CA B:ASP242 4.8 28.9 1.0 CA B:ASN208 4.9 27.8 1.0 N B:PRO212 4.9 30.1 1.0 CB B:LEU299 5.0 21.6 1.0

J.M.Nicoludis, S.Y.Lau, C.P.Scharfe, D.S.Marks, W.A.Weihofen, R.Gaudet. Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions That Mediate Homophilic Specificity. Structure V. 23 2087 2015.
ISSN: ISSN 0969-2126
PubMed: 26481813
DOI: 10.1016/J.STR.2015.09.005