Calcium in PDB 4by5: Crystal Structure of Drosophila FRQ2

The structure of Crystal Structure of Drosophila FRQ2, PDB code: 4by5 was solved by S.Banos-Mateos, A.Chaves-Sanjuan, M.J.Sanchez-Barrena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.93 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.984, 131.192, 56.710, 90.00, 91.07, 90.00
R / Rfree (%)	21.068 / 27.052

The structure of Crystal Structure of Drosophila FRQ2 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Drosophila FRQ2 (pdb code 4by5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Drosophila FRQ2, PDB code: 4by5:
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 Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1183 b:24.2 occ:1.00 O A:ALA79 2.1 15.8 1.0 OD1 A:ASN75 2.2 24.8 1.0 OD1 A:ASP73 2.2 13.4 1.0 O A:HOH2069 2.4 24.3 1.0 OE2 A:GLU84 2.5 14.2 1.0 OE1 A:GLU84 2.7 16.1 1.0 OD1 A:ASP77 2.7 30.2 1.0 CD A:GLU84 3.0 15.8 1.0 CG A:ASN75 3.2 25.6 1.0 C A:ALA79 3.3 14.4 1.0 CG A:ASP77 3.4 28.2 1.0 CG A:ASP73 3.4 15.6 1.0 OD2 A:ASP77 3.5 34.4 1.0 ND2 A:ASN75 3.7 26.7 1.0 CA A:ASP73 4.1 16.4 1.0 N A:ALA79 4.2 13.9 1.0 CB A:ASP73 4.2 15.3 1.0 N A:ASP77 4.2 20.5 1.0 CA A:ALA79 4.2 16.0 1.0 N A:ILE80 4.3 15.2 1.0 OD2 A:ASP73 4.3 14.4 1.0 N A:ASN75 4.3 20.5 1.0 CA A:ILE80 4.3 16.1 1.0 N A:GLU81 4.4 19.4 1.0 C A:ASP73 4.4 17.3 1.0 CG A:GLU84 4.5 15.1 1.0 CB A:ASN75 4.5 23.2 1.0 CB A:ASP77 4.6 24.6 1.0 N A:GLU74 4.6 20.1 1.0 N A:ASN76 4.6 25.3 1.0 CA A:ASN75 4.8 25.4 1.0 CB A:ALA79 4.8 14.4 1.0 C A:ASN75 4.8 29.1 1.0 CA A:ASP77 4.8 19.4 1.0 C A:ILE80 4.9 18.6 1.0 CD A:GLU81 4.9 45.7 1.0 CG A:GLU81 4.9 32.6 1.0 N A:GLY78 4.9 16.3 1.0 OE1 A:GLU81 4.9 44.9 1.0 C A:ASP77 5.0 18.6 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1184 b:20.2 occ:1.00 OD1 A:ASP109 2.2 18.9 1.0 OD1 A:ASP113 2.2 24.9 1.0 O A:TYR115 2.2 15.9 1.0 OD1 A:ASP111 2.4 34.1 1.0 OE1 A:GLU120 2.4 14.5 1.0 OE2 A:GLU120 2.5 20.4 1.0 O A:HOH2081 2.6 21.3 1.0 CD A:GLU120 2.8 18.5 1.0 CG A:ASP113 3.2 23.2 1.0 CG A:ASP109 3.4 21.1 1.0 CG A:ASP111 3.4 32.9 1.0 C A:TYR115 3.4 17.1 1.0 OD2 A:ASP113 3.5 23.3 1.0 OD2 A:ASP111 3.7 27.8 1.0 CA A:ASP109 4.0 21.1 1.0 N A:TYR115 4.2 16.5 1.0 OD2 A:ASP109 4.2 20.1 1.0 CB A:ASP109 4.2 19.2 1.0 N A:ASP113 4.2 24.1 1.0 CG A:GLU120 4.3 18.2 1.0 CA A:TYR115 4.3 15.8 1.0 CB A:ASP113 4.4 20.0 1.0 C A:ASP109 4.4 23.0 1.0 N A:ILE116 4.4 16.0 1.0 N A:ASP111 4.4 27.2 1.0 CA A:ILE116 4.5 16.8 1.0 O A:HOH2080 4.5 33.4 1.0 N A:VAL110 4.6 24.8 1.0 N A:ASN112 4.6 27.3 1.0 CB A:TYR115 4.6 17.6 1.0 N A:THR117 4.6 22.1 1.0 CB A:ASP111 4.7 27.4 1.0 CA A:ASP113 4.8 21.7 1.0 N A:GLY114 4.9 22.2 1.0 CA A:ASP111 4.9 27.4 1.0 CG2 A:THR117 4.9 25.1 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1185 b:23.3 occ:1.00 O A:ARG162 2.2 21.1 1.0 O A:HOH2093 2.2 23.6 1.0 OD1 A:ASP156 2.2 18.0 1.0 OD1 A:ASN158 2.3 19.5 1.0 OE2 A:GLU167 2.4 19.4 1.0 OD1 A:ASP160 2.5 21.1 1.0 OE1 A:GLU167 2.6 20.0 1.0 CD A:GLU167 2.9 17.8 1.0 CG A:ASP156 3.4 20.4 1.0 C A:ARG162 3.4 18.6 1.0 CG A:ASP160 3.4 21.9 1.0 CG A:ASN158 3.5 21.8 1.0 OD2 A:ASP160 3.8 22.8 1.0 ND2 A:ASN158 4.0 19.6 1.0 OD2 A:ASP156 4.1 19.6 1.0 N A:ARG162 4.3 19.1 1.0 N A:LEU163 4.3 17.2 1.0 CA A:ASP156 4.3 20.9 1.0 CB A:ASP156 4.3 19.2 1.0 CA A:ARG162 4.3 20.7 1.0 N A:ASP160 4.4 19.2 1.0 CA A:LEU163 4.4 16.6 1.0 N A:ASN158 4.4 23.1 1.0 CG A:GLU167 4.4 17.8 1.0 O A:HOH2092 4.5 23.1 1.0 C A:ASP156 4.6 20.9 1.0 N A:LYS157 4.6 20.9 1.0 CB A:ASP160 4.7 19.8 1.0 N A:HIS159 4.7 22.9 1.0 CB A:ASN158 4.7 20.7 1.0 O A:HOH2094 4.8 34.8 1.0 N A:THR164 4.8 15.4 1.0 CA A:ASN158 4.9 22.5 1.0 C A:ASN158 4.9 21.1 1.0 CB A:ARG162 4.9 22.3 1.0 CD2 A:LEU163 4.9 15.8 1.0 CA A:ASP160 5.0 18.4 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1185 b:26.6 occ:1.00 O B:ALA79 2.3 19.9 1.0 O B:HOH2029 2.3 40.0 1.0 OD1 B:ASP73 2.3 22.6 1.0 OD1 B:ASN75 2.3 26.9 1.0 OD1 B:ASP77 2.5 29.4 1.0 OE1 B:GLU84 2.5 21.9 1.0 OE2 B:GLU84 2.6 18.7 1.0 CD B:GLU84 3.0 18.5 1.0 CG B:ASP77 3.2 33.7 1.0 CG B:ASN75 3.3 28.7 1.0 CG B:ASP73 3.4 23.9 1.0 C B:ALA79 3.4 20.6 1.0 OD2 B:ASP77 3.5 36.4 1.0 ND2 B:ASN75 3.7 30.1 1.0 N B:ALA79 4.1 23.2 1.0 CA B:ASP73 4.1 23.2 1.0 CB B:ASP73 4.2 22.4 1.0 OD2 B:ASP73 4.2 21.0 1.0 N B:ASP77 4.3 29.9 1.0 CA B:ALA79 4.3 24.8 1.0 N B:ILE80 4.3 20.1 1.0 CA B:ILE80 4.3 20.6 1.0 CB B:ASP77 4.4 30.0 1.0 N B:ASN75 4.4 29.5 1.0 C B:ASP73 4.4 24.5 1.0 CG B:GLU84 4.5 18.1 1.0 CB B:ASN75 4.6 27.6 1.0 N B:GLU81 4.6 21.8 1.0 N B:GLU74 4.7 27.8 1.0 N B:ASN76 4.7 35.5 1.0 CA B:ASP77 4.8 28.9 1.0 OE2 B:GLU81 4.8 41.3 1.0 CA B:ASN75 4.9 29.7 1.0 N B:GLY78 4.9 27.1 1.0 O B:HOH2032 4.9 36.1 1.0 CB B:ALA79 4.9 20.2 1.0 C B:ASN75 4.9 34.8 1.0 C B:ILE80 4.9 20.7 1.0 C B:ASP77 5.0 28.0 1.0 O B:ASP73 5.0 28.7 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1186 b:19.7 occ:1.00 OD1 B:ASN158 2.2 23.7 1.0 OD1 B:ASP160 2.2 19.2 1.0 O B:HOH2055 2.3 18.1 1.0 OD1 B:ASP156 2.3 20.4 1.0 O B:ARG162 2.5 18.4 1.0 OE1 B:GLU167 2.5 16.4 1.0 OE2 B:GLU167 2.5 17.4 1.0 CD B:GLU167 2.9 15.3 1.0 CG B:ASP160 3.2 21.6 1.0 CG B:ASN158 3.4 26.1 1.0 CG B:ASP156 3.5 20.5 1.0 C B:ARG162 3.6 16.8 1.0 OD2 B:ASP160 3.6 22.7 1.0 ND2 B:ASN158 4.0 26.2 1.0 OD2 B:ASP156 4.2 17.8 1.0 N B:ARG162 4.3 17.6 1.0 N B:ASP160 4.3 24.0 1.0 CA B:ASP156 4.3 20.7 1.0 N B:ASN158 4.3 25.5 1.0 CB B:ASP156 4.4 18.9 1.0 CA B:LEU163 4.4 16.2 1.0 CG B:GLU167 4.4 15.0 1.0 N B:LEU163 4.5 16.3 1.0 CA B:ARG162 4.5 18.1 1.0 CB B:ASP160 4.5 20.0 1.0 C B:ASP156 4.5 23.0 1.0 O B:HOH2056 4.5 22.3 1.0 O B:HOH2060 4.6 17.4 1.0 N B:LYS157 4.6 23.1 1.0 CB B:ASN158 4.6 23.9 1.0 N B:HIS159 4.7 23.9 1.0 CG B:ARG162 4.7 20.4 1.0 CA B:ASN158 4.8 24.0 1.0 C B:ASN158 4.8 21.4 1.0 N B:THR164 4.8 15.8 1.0 CD2 B:LEU163 4.9 16.1 1.0 CA B:ASP160 4.9 20.9 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1187 b:19.5 occ:1.00 OD1 B:ASP109 2.2 21.7 1.0 O B:TYR115 2.3 18.9 1.0 OD1 B:ASP113 2.4 16.9 1.0 O B:HOH2043 2.4 23.4 1.0 OD1 B:ASP111 2.4 28.4 1.0 OE1 B:GLU120 2.5 19.0 1.0 OE2 B:GLU120 2.5 21.8 1.0 CD B:GLU120 2.9 21.4 1.0 CG B:ASP113 3.2 18.2 1.0 CG B:ASP109 3.3 20.4 1.0 CG B:ASP111 3.4 31.2 1.0 C B:TYR115 3.5 16.6 1.0 OD2 B:ASP113 3.6 17.4 1.0 OD2 B:ASP111 3.8 34.3 1.0 N B:ASP113 4.0 21.5 1.0 N B:TYR115 4.1 16.2 1.0 OD2 B:ASP109 4.1 20.1 1.0 CA B:ASP109 4.2 22.7 1.0 CB B:ASP109 4.2 20.9 1.0 CB B:ASP113 4.2 18.6 1.0 CA B:TYR115 4.3 16.8 1.0 CG B:GLU120 4.4 19.2 1.0 CA B:ILE116 4.5 16.8 1.0 N B:ILE116 4.5 16.3 1.0 N B:ASP111 4.5 25.8 1.0 C B:ASP109 4.5 23.1 1.0 CB B:TYR115 4.6 17.9 1.0 CA B:ASP113 4.6 18.7 1.0 N B:ASN112 4.6 23.2 1.0 N B:VAL110 4.7 27.4 1.0 CB B:ASP111 4.7 29.6 1.0 N B:GLY114 4.8 15.9 1.0 N B:THR117 4.8 21.5 1.0 C B:ASP111 4.9 27.1 1.0 CA B:ASP111 4.9 28.7 1.0 C B:ASP113 4.9 16.7 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1185 b:23.8 occ:1.00 OD1 C:ASN75 1.8 34.7 1.0 O C:ALA79 2.3 22.1 1.0 OD1 C:ASP73 2.3 19.6 1.0 O C:HOH2020 2.5 32.9 1.0 OE1 C:GLU84 2.5 25.2 1.0 OE2 C:GLU84 2.7 20.9 1.0 OD1 C:ASP77 2.7 25.0 1.0 CD C:GLU84 2.9 22.0 1.0 CG C:ASN75 3.0 32.7 1.0 CG C:ASP77 3.3 27.2 1.0 CG C:ASP73 3.5 21.4 1.0 C C:ALA79 3.5 22.7 1.0 OD2 C:ASP77 3.5 28.4 1.0 ND2 C:ASN75 3.6 35.1 1.0 CA C:ASP73 4.2 22.4 1.0 CB C:ASN75 4.3 28.4 1.0 N C:ASN75 4.3 29.1 1.0 N C:ALA79 4.3 21.8 1.0 CB C:ASP73 4.3 20.8 1.0 OD2 C:ASP73 4.3 22.4 1.0 N C:ASP77 4.4 26.9 1.0 N C:ILE80 4.4 20.6 1.0 CA C:ALA79 4.4 25.8 1.0 CG C:GLU84 4.4 18.8 1.0 CB C:ASP77 4.4 25.6 1.0 CA C:ILE80 4.5 20.3 1.0 N C:GLU81 4.5 19.2 1.0 C C:ASP73 4.5 24.1 1.0 CA C:ASN75 4.6 31.9 1.0 OE1 C:GLU81 4.6 36.6 1.0 N C:ASN76 4.7 28.7 1.0 C C:ASN75 4.7 32.1 1.0 N C:GLU74 4.8 25.6 1.0 CA C:ASP77 4.8 27.2 1.0 CG C:GLU81 4.8 28.7 1.0 CB C:ALA79 4.9 25.8 1.0 N C:GLY78 4.9 24.9 1.0 C C:ILE80 5.0 17.8 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1186 b:31.2 occ:1.00 OD1 C:ASP113 2.1 27.5 1.0 OE1 C:GLU120 2.3 27.4 1.0 OE2 C:GLU120 2.4 24.1 1.0 OD1 C:ASP111 2.5 30.9 1.0 O C:TYR115 2.5 25.0 1.0 OD1 C:ASP109 2.5 26.9 1.0 O C:HOH2033 2.6 32.4 1.0 CD C:GLU120 2.6 25.3 1.0 CG C:ASP113 3.1 33.2 1.0 CG C:ASP111 3.4 32.4 1.0 OD2 C:ASP113 3.6 33.8 1.0 CG C:ASP109 3.7 28.3 1.0 C C:TYR115 3.7 26.9 1.0 OD2 C:ASP111 3.8 33.2 1.0 CG C:GLU120 4.1 25.9 1.0 CA C:ASP109 4.2 26.9 1.0 N C:ASP111 4.2 27.8 1.0 CB C:ASP113 4.3 34.5 1.0 CA C:ILE116 4.4 28.3 1.0 C C:ASP109 4.4 26.6 1.0 N C:VAL110 4.4 27.5 1.0 N C:ASP113 4.4 31.7 1.0 CG2 C:THR117 4.4 30.0 1.0 CB C:ASP109 4.4 26.0 1.0 N C:TYR115 4.4 27.6 1.0 N C:ILE116 4.5 24.9 1.0 N C:THR117 4.5 35.5 1.0 OD2 C:ASP109 4.6 30.4 1.0 CA C:TYR115 4.6 27.6 1.0 N C:ASN112 4.6 33.3 1.0 CB C:TYR115 4.7 31.8 1.0 CB C:ASP111 4.7 33.5 1.0 CA C:ASP111 4.8 32.3 1.0 CA C:ASP113 4.8 32.9 1.0 C C:ILE116 4.9 33.0 1.0 C C:ASP111 4.9 32.8 1.0 CB C:GLU120 5.0 24.3 1.0 O C:ASP109 5.0 26.9 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1187 b:41.1 occ:1.00 O C:HOH2036 2.2 31.6 1.0 O C:ARG162 2.4 45.8 1.0 OD1 C:ASP156 2.5 40.1 1.0 OE1 C:GLU167 2.5 50.2 1.0 OD1 C:ASP160 2.7 50.6 1.0 OD1 C:ASN158 2.9 52.7 1.0 CD C:GLU167 3.1 55.8 1.0 OE2 C:GLU167 3.2 56.7 1.0 CG C:ASP160 3.5 49.1 1.0 C C:ARG162 3.6 45.9 1.0 CG C:ASP156 3.7 53.1 1.0 OD2 C:ASP160 3.9 48.2 1.0 N C:ASP160 4.0 60.8 1.0 CG C:ASN158 4.0 62.6 1.0 CA C:ASP156 4.1 52.5 1.0 N C:ARG162 4.1 51.4 1.0 C C:ASP156 4.2 57.4 1.0 N C:HIS159 4.2 63.4 1.0 N C:ASN158 4.3 65.2 1.0 N C:LYS157 4.3 65.3 1.0 CD2 C:LEU163 4.4 30.3 1.0 CA C:LEU163 4.4 31.5 1.0 CA C:ARG162 4.5 49.2 1.0 N C:LEU163 4.5 37.1 1.0 CB C:ASP156 4.5 51.7 1.0 CG C:GLU167 4.5 46.7 1.0 N C:ASP161 4.6 60.9 1.0 CB C:ASP160 4.6 50.7 1.0 C C:ASN158 4.6 60.1 1.0 OD2 C:ASP156 4.6 52.8 1.0 O C:ASP156 4.7 56.4 1.0 CA C:ASP160 4.7 57.1 1.0 ND2 C:ASN158 4.8 63.5 1.0 CA C:ASN158 4.8 59.7 1.0 CG C:ARG162 4.8 47.1 1.0 CA C:HIS159 4.9 69.7 1.0 C C:HIS159 4.9 65.2 1.0 C C:ASP160 4.9 56.8 1.0 N C:THR164 5.0 31.6 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Drosophila FRQ2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Drosophila FRQ2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1183 b:48.9 occ:1.00 OD1 D:ASP73 1.9 37.6 1.0 O D:ALA79 2.1 41.6 1.0 O D:HOH2005 2.1 39.4 1.0 OD1 D:ASN75 2.3 47.5 1.0 OE1 D:GLU84 2.5 45.0 1.0 OD1 D:ASP77 2.7 48.4 1.0 OE2 D:GLU84 2.8 45.8 1.0 CD D:GLU84 3.0 52.2 1.0 CG D:ASP73 3.1 35.5 1.0 CG D:ASP77 3.3 52.8 1.0 C D:ALA79 3.3 44.8 1.0 OD2 D:ASP77 3.5 50.6 1.0 CG D:ASN75 3.5 47.5 1.0 OD2 D:ASP73 4.0 33.3 1.0 ND2 D:ASN75 4.1 42.9 1.0 N D:ALA79 4.2 52.1 1.0 CA D:ALA79 4.2 49.4 1.0 CB D:ASP73 4.2 35.2 1.0 N D:ILE80 4.3 40.6 1.0 CA D:ASP73 4.3 37.1 1.0 N D:ASN75 4.3 45.8 1.0 N D:ASP77 4.4 50.8 1.0 CB D:ASP77 4.4 53.0 1.0 CA D:ILE80 4.5 37.2 1.0 CG D:GLU84 4.5 47.0 1.0 N D:GLU81 4.6 48.7 1.0 N D:GLU74 4.6 38.1 1.0 C D:ASP73 4.7 41.1 1.0 N D:ASN76 4.7 47.5 1.0 CB D:ASN75 4.7 43.3 1.0 C D:ASN75 4.7 45.1 1.0 CA D:ASN75 4.8 46.4 1.0 CB D:ALA79 4.8 43.4 1.0 CA D:ASP77 4.8 55.8 1.0

J.Romero-Pozuelo, J.S.Dason, A.Mansilla, S.Banos-Mateos, J.L.Sardina, A.Chaves-Sanjuan, J.Jurado-Gomez, E.Santana, H.L.Atwood, A.Hernandez-Hernandez, M.Sanchez-Barrena, A.Ferrus. The Guanine-Exchange Factor RIC8A Binds the Calcium Sensor Ncs-1 to Regulate Synapse Number and Probability of Release. J.Cell.Sci. 2014.
ISSN: ESSN 1477-9137
PubMed: 25074811
DOI: 10.1242/JCS.152603