Calcium in PDB 4yru: Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus

The structure of Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus, PDB code: 4yru was solved by S.Pandalaneni, V.Karrupiah, O.Mayans, J.P.Derrick, L.Y.Lian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.59 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.680, 88.800, 100.670, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 29.1

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus (pdb code 4yru). 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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus, PDB code: 4yru:
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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:63.6 occ:1.00 OE1 A:GLU81 2.4 0.9 1.0 OD1 A:ASP73 2.4 46.8 1.0 OD1 A:ASN75 2.4 73.0 1.0 O A:ARG79 2.5 75.4 1.0 OD1 A:ASP77 2.5 64.7 1.0 OE1 A:GLU84 2.5 59.5 1.0 OE2 A:GLU84 2.6 62.1 1.0 OD2 A:ASP77 2.8 68.7 1.0 CD A:GLU84 2.8 61.4 1.0 CG A:ASP77 2.9 66.0 1.0 CD A:GLU81 3.2 0.9 1.0 CG A:ASN75 3.2 70.5 1.0 OE2 A:GLU81 3.3 0.2 1.0 ND2 A:ASN75 3.4 71.8 1.0 CG A:ASP73 3.5 48.5 1.0 C A:ARG79 3.6 71.9 1.0 CG A:GLU84 4.2 60.8 1.0 OD2 A:ASP73 4.2 50.5 1.0 N A:GLU81 4.3 71.4 1.0 CB A:ASP77 4.3 65.9 1.0 N A:ARG79 4.4 60.8 1.0 N A:ASP77 4.4 63.2 1.0 CA A:ARG79 4.4 67.0 1.0 N A:ILE80 4.5 71.3 1.0 CB A:ASP73 4.5 45.9 1.0 CA A:ILE80 4.5 48.3 1.0 CA A:ASP73 4.6 49.7 1.0 CG A:GLU81 4.6 97.4 1.0 CB A:ARG79 4.6 75.3 1.0 CB A:ASN75 4.6 65.4 1.0 N A:ASN75 4.7 58.5 1.0 N A:LYS76 4.8 56.4 1.0 CA A:ASP77 4.9 65.4 1.0 C A:ASP73 4.9 54.0 1.0 C A:ILE80 4.9 65.7 1.0 N A:GLU74 5.0 56.1 1.0 CB A:GLU81 5.0 87.7 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:34.2 occ:1.00 OE1 A:GLU120 2.4 42.6 1.0 OD1 A:ASP111 2.4 55.7 1.0 OD1 A:ASP113 2.4 58.6 1.0 O A:TYR115 2.5 61.5 1.0 OE2 A:GLU120 2.6 46.1 1.0 OD1 A:ASP109 2.7 33.7 1.0 CD A:GLU120 2.8 46.1 1.0 CG A:ASP113 3.3 56.1 1.0 CG A:ASP111 3.4 53.2 1.0 C A:TYR115 3.5 46.9 1.0 OD2 A:ASP113 3.5 54.6 1.0 OD2 A:ASP111 3.7 55.3 1.0 CG A:ASP109 3.8 37.3 1.0 CA A:TYR115 4.3 44.2 1.0 CG2 A:THR117 4.3 57.0 1.0 N A:TYR115 4.3 40.1 1.0 CG A:GLU120 4.3 34.6 1.0 N A:ILE116 4.4 40.3 1.0 CA A:ASP109 4.4 35.1 1.0 CB A:TYR115 4.4 48.8 1.0 CA A:ILE116 4.4 37.7 1.0 N A:THR117 4.4 46.8 1.0 N A:ASP111 4.5 51.3 1.0 N A:LEU110 4.6 46.2 1.0 N A:ASP113 4.6 47.3 1.0 CB A:ASP109 4.6 31.2 1.0 CB A:ASP113 4.6 52.5 1.0 OD2 A:ASP109 4.7 37.7 1.0 CB A:ASP111 4.7 55.8 1.0 C A:ASP109 4.7 42.2 1.0 N A:ASN112 4.9 44.0 1.0 C A:ILE116 4.9 41.9 1.0 OG1 A:THR117 4.9 73.4 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:34.8 occ:1.00 OD1 A:ASN159 2.4 39.5 1.0 OE1 A:GLU168 2.4 38.6 1.0 OD1 A:ASP161 2.4 39.8 1.0 O A:LYS163 2.5 47.9 1.0 OE2 A:GLU168 2.5 35.3 1.0 OD1 A:ASP157 2.5 43.5 1.0 CD A:GLU168 2.8 33.8 1.0 OD2 A:ASP161 3.0 40.6 1.0 CG A:ASP161 3.0 41.2 1.0 CG A:ASN159 3.3 40.9 1.0 ND2 A:ASN159 3.6 41.9 1.0 C A:LYS163 3.6 35.2 1.0 CG A:ASP157 3.7 44.8 1.0 CG A:GLU168 4.3 32.5 1.0 OD2 A:ASP157 4.4 48.4 1.0 CB A:ASP161 4.4 47.7 1.0 N A:LYS163 4.4 38.8 1.0 N A:ASP161 4.5 43.7 1.0 CA A:LYS163 4.5 37.0 1.0 N A:LEU164 4.5 33.6 1.0 CA A:LEU164 4.5 32.2 1.0 CA A:ASP157 4.7 45.4 1.0 CB A:ASN159 4.7 48.7 1.0 CB A:LYS163 4.7 37.9 1.0 CB A:ASP157 4.8 37.4 1.0 N A:ASN159 4.8 40.5 1.0 N A:THR165 4.8 31.7 1.0 CG2 A:THR165 4.9 33.9 1.0 CA A:ASP161 4.9 44.7 1.0 N A:ALA160 4.9 47.3 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:53.7 occ:1.00 OE1 B:GLU81 2.4 89.6 1.0 OD1 B:ASP73 2.4 45.5 1.0 OD1 B:ASP77 2.4 63.5 1.0 O B:ARG79 2.4 60.5 1.0 OD1 B:ASN75 2.5 53.1 1.0 OE1 B:GLU84 2.5 50.9 1.0 OE2 B:GLU84 2.6 53.6 1.0 CD B:GLU84 2.8 52.0 1.0 OD2 B:ASP77 2.9 60.3 1.0 CG B:ASP77 3.0 58.1 1.0 CD B:GLU81 3.1 89.9 1.0 OE2 B:GLU81 3.2 92.9 1.0 CG B:ASN75 3.4 53.5 1.0 CG B:ASP73 3.5 51.4 1.0 C B:ARG79 3.5 58.1 1.0 ND2 B:ASN75 3.7 57.3 1.0 CG B:GLU84 4.2 57.0 1.0 OD2 B:ASP73 4.3 51.9 1.0 N B:GLU81 4.3 61.0 1.0 N B:ARG79 4.3 63.9 1.0 CA B:ARG79 4.3 62.2 1.0 CB B:ASP73 4.4 51.1 1.0 CA B:ASP73 4.4 55.5 1.0 CB B:ASP77 4.4 57.8 1.0 N B:ILE80 4.5 58.7 1.0 N B:ASP77 4.5 57.1 1.0 CG B:GLU81 4.5 84.3 1.0 CB B:ARG79 4.5 67.6 1.0 CA B:ILE80 4.5 38.5 1.0 N B:ASN75 4.7 53.6 1.0 CB B:ASN75 4.8 55.8 1.0 C B:ASP73 4.8 53.1 1.0 N B:GLU74 4.9 53.9 1.0 N B:LYS76 4.9 49.4 1.0 C B:ILE80 4.9 62.4 1.0 CA B:ASP77 4.9 55.8 1.0 CB B:GLU81 5.0 75.5 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:44.0 occ:1.00 OD1 B:ASP111 2.4 54.7 1.0 O B:TYR115 2.4 56.9 1.0 OE1 B:GLU120 2.4 56.3 1.0 OD1 B:ASP113 2.4 51.9 1.0 OD1 B:ASP109 2.7 53.3 1.0 OE2 B:GLU120 2.8 54.9 1.0 CD B:GLU120 3.0 53.4 1.0 CG B:ASP113 3.3 54.8 1.0 CG B:ASP111 3.3 54.3 1.0 C B:TYR115 3.4 51.9 1.0 OD2 B:ASP113 3.6 47.8 1.0 OD2 B:ASP111 3.6 46.7 1.0 CG B:ASP109 3.9 53.6 1.0 CA B:TYR115 4.2 49.7 1.0 N B:TYR115 4.3 50.5 1.0 N B:ILE116 4.3 49.1 1.0 CB B:TYR115 4.4 52.9 1.0 CG2 B:THR117 4.4 60.7 1.0 CA B:ILE116 4.4 51.0 1.0 CA B:ASP109 4.4 45.7 1.0 CG B:GLU120 4.4 54.0 1.0 N B:THR117 4.5 44.0 1.0 N B:ASP111 4.5 47.0 1.0 N B:ASP113 4.6 61.0 1.0 CB B:ASP113 4.6 47.3 1.0 CB B:ASP111 4.7 51.0 1.0 CB B:ASP109 4.7 38.3 1.0 N B:LEU110 4.7 48.3 1.0 OD2 B:ASP109 4.7 54.5 1.0 C B:ASP109 4.8 48.9 1.0 N B:ASN112 4.8 49.4 1.0 C B:ILE116 4.9 52.7 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:46.0 occ:1.00 OD1 B:ASN159 2.4 67.0 1.0 O B:LYS163 2.4 56.5 1.0 OE1 B:GLU168 2.4 53.0 1.0 OD1 B:ASP157 2.5 51.7 1.0 OD1 B:ASP161 2.5 62.0 1.0 OE2 B:GLU168 2.6 65.4 1.0 CD B:GLU168 2.9 48.0 1.0 OD2 B:ASP161 3.1 55.0 1.0 CG B:ASP161 3.1 55.3 1.0 CG B:ASN159 3.4 68.8 1.0 C B:LYS163 3.6 47.8 1.0 CG B:ASP157 3.7 57.6 1.0 ND2 B:ASN159 3.7 68.6 1.0 CG B:GLU168 4.4 46.5 1.0 OD2 B:ASP157 4.4 60.0 1.0 CA B:LEU164 4.4 44.5 1.0 N B:LEU164 4.4 45.7 1.0 N B:LYS163 4.5 54.2 1.0 CA B:LYS163 4.5 49.1 1.0 CB B:ASP161 4.5 58.4 1.0 N B:ASP161 4.6 57.8 1.0 CA B:ASP157 4.6 68.0 1.0 N B:ASN159 4.7 56.1 1.0 N B:THR165 4.7 44.2 1.0 CB B:ASN159 4.7 58.3 1.0 CB B:ASP157 4.8 50.9 1.0 N B:LYS158 4.8 55.2 1.0 CB B:LYS163 4.8 52.6 1.0 CG2 B:THR165 4.8 47.1 1.0 CD2 B:LEU164 4.9 45.1 1.0 N B:ALA160 5.0 58.0 1.0 C B:ASP157 5.0 52.1 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:41.0 occ:1.00 OD1 C:ASN75 2.4 51.6 1.0 O C:ARG79 2.4 33.8 1.0 OE1 C:GLU84 2.4 36.2 1.0 OE2 C:GLU84 2.5 33.1 1.0 OD1 C:ASP73 2.5 49.8 1.0 OD1 C:ASP77 2.5 60.6 1.0 OE1 C:GLU81 2.6 54.1 1.0 CD C:GLU84 2.8 32.6 1.0 OD2 C:ASP77 3.1 60.4 1.0 CG C:ASP77 3.1 58.2 1.0 CG C:ASN75 3.4 52.3 1.0 CG C:ASP73 3.6 44.3 1.0 CD C:GLU81 3.6 55.7 1.0 C C:ARG79 3.6 38.3 1.0 ND2 C:ASN75 3.8 51.2 1.0 OE2 C:GLU81 4.0 54.9 1.0 CA C:ASP73 4.1 39.5 1.0 CG C:GLU84 4.2 32.2 1.0 CB C:ASP73 4.3 39.9 1.0 N C:GLU81 4.3 39.9 1.0 CA C:ILE80 4.4 42.0 1.0 N C:ASP77 4.4 51.0 1.0 N C:ILE80 4.5 40.7 1.0 N C:ARG79 4.5 43.9 1.0 CB C:ASP77 4.5 55.3 1.0 OD2 C:ASP73 4.5 40.4 1.0 N C:GLU74 4.6 37.6 1.0 C C:ASP73 4.6 37.0 1.0 N C:ASN75 4.6 60.8 1.0 CA C:ARG79 4.6 41.4 1.0 CB C:ASN75 4.7 54.6 1.0 N C:LYS76 4.7 49.4 1.0 C C:ILE80 4.9 41.9 1.0 CG C:GLU81 4.9 35.7 1.0 CA C:ASP77 5.0 50.4 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:54.8 occ:1.00 OE2 C:GLU120 2.4 38.4 1.0 OD1 C:ASP113 2.4 63.8 1.0 OD1 C:ASP111 2.5 39.4 1.0 OD1 C:ASP109 2.5 49.3 1.0 OE1 C:GLU120 2.5 38.8 1.0 O C:TYR115 2.6 42.2 1.0 CD C:GLU120 2.8 38.5 1.0 OD2 C:ASP113 2.9 65.2 1.0 CG C:ASP113 2.9 59.8 1.0 CG C:ASP111 3.4 40.1 1.0 C C:TYR115 3.5 45.7 1.0 CG C:ASP109 3.6 45.3 1.0 OD2 C:ASP111 3.7 41.5 1.0 CA C:TYR115 4.2 48.9 1.0 N C:TYR115 4.2 56.6 1.0 CB C:TYR115 4.2 49.9 1.0 CG C:GLU120 4.3 43.3 1.0 CB C:ASP113 4.3 56.2 1.0 OD2 C:ASP109 4.3 50.6 1.0 N C:ASP113 4.4 49.8 1.0 CG2 C:THR117 4.4 47.8 1.0 CA C:ASP109 4.4 43.5 1.0 N C:ILE116 4.5 39.9 1.0 CB C:ASP109 4.5 42.8 1.0 CA C:ILE116 4.6 47.5 1.0 N C:ASP111 4.6 37.1 1.0 N C:THR117 4.7 40.7 1.0 N C:LEU110 4.8 35.4 1.0 CB C:ASP111 4.8 42.7 1.0 C C:ASP109 4.8 45.1 1.0 CA C:ASP113 4.8 49.6 1.0 N C:ASN112 4.8 42.5 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:71.1 occ:1.00 OD1 C:ASN159 2.4 64.3 1.0 OD1 C:ASP161 2.4 73.5 1.0 OE1 C:GLU168 2.5 60.9 1.0 OE2 C:GLU168 2.5 63.0 1.0 O C:LYS163 2.7 47.9 1.0 CD C:GLU168 2.8 58.9 1.0 OD2 C:ASP161 2.8 74.3 1.0 OD1 C:ASP157 2.9 49.3 1.0 CG C:ASP161 2.9 71.5 1.0 CG C:ASN159 3.2 64.1 1.0 ND2 C:ASN159 3.4 66.8 1.0 C C:LYS163 3.8 54.3 1.0 CG C:ASP157 4.1 49.5 1.0 CG C:GLU168 4.3 52.5 1.0 CB C:ASP161 4.4 72.5 1.0 CG2 C:THR165 4.4 48.0 1.0 CA C:LYS163 4.6 59.8 1.0 N C:LEU164 4.6 51.1 1.0 CB C:ASN159 4.6 62.0 1.0 N C:THR165 4.6 42.6 1.0 CA C:LEU164 4.6 42.6 1.0 N C:LYS163 4.7 69.2 1.0 OD2 C:ASP157 4.7 50.3 1.0 N C:ASP161 4.7 63.2 1.0 CB C:LYS163 4.7 64.1 1.0 N C:ASN159 4.9 61.5 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus


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 C-Terminally Truncated Neuronal Calcium Sensor (Ncs-1) From Rattus Norvegicus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:47.0 occ:1.00 O D:ARG79 2.3 46.4 1.0 OD1 D:ASN75 2.4 50.4 1.0 OE1 D:GLU84 2.4 35.5 1.0 OE1 D:GLU81 2.5 49.6 1.0 OD1 D:ASP77 2.5 52.2 1.0 OD1 D:ASP73 2.5 59.1 1.0 OE2 D:GLU84 2.6 36.2 1.0 CD D:GLU84 2.8 35.6 1.0 OD2 D:ASP77 3.0 54.5 1.0 CG D:ASP77 3.1 53.5 1.0 CG D:ASN75 3.4 48.4 1.0 CD D:GLU81 3.5 47.3 1.0 C D:ARG79 3.5 46.7 1.0 CG D:ASP73 3.6 45.6 1.0 ND2 D:ASN75 3.7 54.1 1.0 OE2 D:GLU81 3.8 46.8 1.0 CA D:ASP73 4.2 39.3 1.0 N D:GLU81 4.2 46.4 1.0 CG D:GLU84 4.2 35.0 1.0 CB D:ASP73 4.3 40.4 1.0 CA D:ILE80 4.3 45.0 1.0 N D:ILE80 4.4 44.6 1.0 N D:ARG79 4.4 38.8 1.0 N D:ASP77 4.4 40.4 1.0 OD2 D:ASP73 4.4 43.1 1.0 CB D:ASP77 4.5 42.3 1.0 CA D:ARG79 4.5 38.4 1.0 N D:ASN75 4.6 48.1 1.0 C D:ASP73 4.7 40.8 1.0 CB D:ASN75 4.7 45.8 1.0 N D:GLU74 4.7 42.5 1.0 N D:LYS76 4.8 58.7 1.0 CG D:GLU81 4.8 44.5 1.0 C D:ILE80 4.8 36.1 1.0 CA D:ASP77 4.9 41.9 1.0 CB D:ARG79 4.9 53.2 1.0

S.Pandalaneni, V.Karrupiah, O.Mayans, J.P.Derrick, L.Y.Lian. Structures of Neuronal Calcium Sensor-1 Complexes with the D2 Dopamine Receptor and Gpcr Kinase 1 (GRK1) Peptides Shows Different Modes of Interactions To Be Published.