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Calcium in PDB 5aeq: Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus

Protein crystallography data

The structure of Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus, PDB code: 5aeq was solved by M.Saleem, V.Karuppiah, S.Pandalaneni, R.Burgoyne, 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) 77.13 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.910, 55.490, 77.360, 90.00, 94.42, 90.00
R / Rfree (%) 22.499 / 25.37

Other elements in 5aeq:

The structure of Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus (pdb code 5aeq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus, PDB code: 5aeq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5aeq

Go back to Calcium Binding Sites List in 5aeq
Calcium binding site 1 out of 6 in the 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 Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca200

b:16.5
occ:1.00
O A:ARG79 2.3 21.0 1.0
OD1 A:ASN75 2.3 24.3 1.0
O A:HOH2035 2.3 20.7 1.0
OE2 A:GLU84 2.3 18.9 1.0
OD1 A:ASP73 2.3 19.4 1.0
OD1 A:ASP77 2.3 26.0 1.0
OE1 A:GLU84 2.3 17.6 1.0
CD A:GLU84 2.7 16.5 1.0
CG A:ASP77 3.3 26.2 1.0
CG A:ASN75 3.3 24.4 1.0
CG A:ASP73 3.5 19.2 1.0
C A:ARG79 3.5 21.6 1.0
OD2 A:ASP77 3.7 26.9 1.0
ND2 A:ASN75 3.9 25.1 1.0
N A:ASP77 4.2 25.8 1.0
CA A:ASP73 4.2 16.9 1.0
CG A:GLU84 4.2 15.1 1.0
N A:ASN75 4.2 22.6 1.0
N A:ARG79 4.3 24.8 1.0
OD2 A:ASP73 4.3 18.5 1.0
CB A:ASP73 4.4 17.8 1.0
CA A:ARG79 4.4 25.5 1.0
C A:ASP73 4.4 18.1 1.0
N A:ILE80 4.5 18.9 1.0
CB A:ASP77 4.5 26.9 1.0
CA A:ILE80 4.5 17.4 1.0
N A:LYS76 4.5 25.3 1.0
CB A:ASN75 4.5 24.3 1.0
N A:GLU74 4.6 18.4 1.0
N A:GLU81 4.6 17.1 1.0
CA A:ASN75 4.7 24.1 1.0
O A:HOH2033 4.7 34.0 1.0
CA A:ASP77 4.8 26.2 1.0
C A:ASN75 4.8 25.2 1.0
OE2 A:GLU81 4.8 24.3 1.0
CB A:ARG79 4.9 28.8 1.0
O A:ASP73 5.0 18.5 1.0
CG A:GLU81 5.0 20.3 1.0
N A:GLY78 5.0 24.9 1.0

Calcium binding site 2 out of 6 in 5aeq

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Calcium binding site 2 out of 6 in the 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 Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:10.6
occ:1.00
OD1 A:ASP109 2.3 14.6 1.0
O A:TYR115 2.3 14.2 1.0
OD1 A:ASP111 2.3 16.4 1.0
O A:HOH2047 2.3 13.6 1.0
OD1 A:ASP113 2.3 16.6 1.0
OE2 A:GLU120 2.3 15.3 1.0
OE1 A:GLU120 2.3 14.4 1.0
CD A:GLU120 2.7 14.7 1.0
CG A:ASP113 3.2 17.5 1.0
CG A:ASP111 3.3 16.7 1.0
CG A:ASP109 3.5 14.0 1.0
C A:TYR115 3.5 13.3 1.0
OD2 A:ASP113 3.7 18.0 1.0
OD2 A:ASP111 3.8 18.0 1.0
N A:ASP111 4.1 14.0 1.0
N A:ASP113 4.2 16.1 1.0
CA A:ASP109 4.2 13.0 1.0
N A:TYR115 4.2 14.1 1.0
CG A:GLU120 4.2 14.8 1.0
OD2 A:ASP109 4.3 14.6 1.0
CB A:ASP113 4.3 17.8 1.0
C A:ASP109 4.3 12.9 1.0
N A:LEU110 4.4 12.7 1.0
CA A:TYR115 4.4 13.5 1.0
CB A:ASP109 4.4 13.4 1.0
CB A:ASP111 4.5 16.6 1.0
N A:ILE116 4.5 12.7 1.0
CA A:ILE116 4.5 12.7 1.0
N A:ASN112 4.5 14.7 1.0
CA A:ASP111 4.6 15.4 1.0
O A:HOH2048 4.7 23.1 1.0
C A:ASP111 4.7 15.5 1.0
CA A:ASP113 4.7 17.0 1.0
N A:THR117 4.7 14.6 1.0
CB A:TYR115 4.7 14.3 1.0
O A:HOH2046 4.8 14.6 1.0
CG2 A:THR117 4.9 17.0 1.0
O A:ASP109 4.9 12.3 1.0
N A:GLY114 4.9 15.2 1.0

Calcium binding site 3 out of 6 in 5aeq

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Calcium binding site 3 out of 6 in the 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 Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:13.0
occ:1.00
OD1 A:ASP157 2.3 16.1 1.0
O A:LYS163 2.3 16.4 1.0
OD1 A:ASP161 2.3 18.8 1.0
OD1 A:ASN159 2.3 20.7 1.0
OE1 A:GLU168 2.3 16.5 1.0
OE2 A:GLU168 2.3 17.2 1.0
O A:HOH2067 2.4 18.4 1.0
CD A:GLU168 2.7 15.9 1.0
CG A:ASP161 3.3 20.3 1.0
CG A:ASP157 3.4 15.7 1.0
CG A:ASN159 3.4 23.7 1.0
C A:LYS163 3.5 16.0 1.0
OD2 A:ASP161 3.7 19.8 1.0
ND2 A:ASN159 4.0 24.0 1.0
OD2 A:ASP157 4.1 15.0 1.0
CG A:GLU168 4.3 15.3 1.0
N A:LYS163 4.3 17.2 1.0
N A:ASP161 4.4 21.6 1.0
N A:ASN159 4.4 24.4 1.0
CA A:ASP157 4.4 15.5 1.0
N A:LEU164 4.4 14.9 1.0
CA A:LEU164 4.4 13.5 1.0
N A:LYS158 4.5 20.7 1.0
CB A:ASP157 4.5 15.4 1.0
CA A:LYS163 4.5 17.6 1.0
O A:HOH2070 4.6 21.0 1.0
CB A:ASP161 4.6 21.3 1.0
C A:ASP157 4.7 17.5 1.0
CB A:ASN159 4.7 24.9 1.0
N A:THR165 4.8 13.0 1.0
CG A:LYS163 4.8 20.9 1.0
N A:ALA160 4.8 24.4 1.0
CA A:ASN159 4.9 25.1 1.0
CA A:ASP161 4.9 21.4 1.0
CD2 A:LEU164 5.0 12.6 1.0
C A:ASN159 5.0 25.4 1.0

Calcium binding site 4 out of 6 in 5aeq

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Calcium binding site 4 out of 6 in the 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 Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca200

b:28.6
occ:1.00
O B:HOH2028 2.0 17.2 1.0
OD1 B:ASN75 2.3 37.1 1.0
O B:ARG79 2.3 31.1 1.0
OE2 B:GLU84 2.3 30.0 1.0
OE1 B:GLU84 2.3 29.2 1.0
OD1 B:ASP77 2.3 38.6 1.0
OD1 B:ASP73 2.4 38.8 1.0
CD B:GLU84 2.7 27.3 1.0
OE2 B:GLU81 2.8 40.2 1.0
CG B:ASP77 3.2 37.1 1.0
CG B:ASN75 3.2 39.4 1.0
OD2 B:ASP77 3.4 37.3 1.0
ND2 B:ASN75 3.5 40.3 1.0
C B:ARG79 3.6 28.9 1.0
CG B:ASP73 3.6 34.0 1.0
CD B:GLU81 3.8 34.5 1.0
CG B:GLU84 4.1 25.8 1.0
N B:GLU81 4.4 26.2 1.0
OD2 B:ASP73 4.5 35.2 1.0
N B:ASN75 4.5 37.3 1.0
N B:ILE80 4.5 27.3 1.0
CB B:ASP77 4.5 37.2 1.0
CG B:GLU81 4.5 31.2 1.0
CB B:ASN75 4.5 38.6 1.0
CA B:ILE80 4.5 26.2 1.0
N B:ASP77 4.5 35.9 1.0
CA B:ARG79 4.5 30.6 1.0
N B:ARG79 4.6 30.6 1.0
CA B:ASP73 4.6 31.1 1.0
CB B:ASP73 4.7 32.7 1.0
C B:ASP73 4.8 32.5 1.0
OE1 B:GLU81 4.8 37.3 1.0
N B:GLU74 4.9 34.8 1.0
CA B:ASN75 4.9 37.8 1.0
CB B:ARG79 4.9 32.2 1.0
N B:LYS76 4.9 36.8 1.0
C B:ILE80 4.9 26.7 1.0
CA B:ASP77 5.0 35.8 1.0

Calcium binding site 5 out of 6 in 5aeq

Go back to Calcium Binding Sites List in 5aeq
Calcium binding site 5 out of 6 in the 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 Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:19.0
occ:1.00
OD1 B:ASP109 2.3 23.4 1.0
O B:TYR115 2.3 23.8 1.0
O B:HOH2038 2.3 20.6 1.0
OD1 B:ASP111 2.3 24.8 1.0
OD1 B:ASP113 2.3 25.7 1.0
OE1 B:GLU120 2.3 22.1 1.0
OE2 B:GLU120 2.3 22.1 1.0
CD B:GLU120 2.7 21.1 1.0
CG B:ASP113 3.2 25.7 1.0
CG B:ASP111 3.3 25.1 1.0
CG B:ASP109 3.5 21.9 1.0
C B:TYR115 3.5 22.7 1.0
OD2 B:ASP113 3.7 26.3 1.0
OD2 B:ASP111 3.8 27.0 1.0
N B:ASP111 4.2 23.0 1.0
CG B:GLU120 4.2 19.9 1.0
CA B:ASP109 4.2 20.0 1.0
N B:ASP113 4.2 26.2 1.0
OD2 B:ASP109 4.3 21.6 1.0
N B:TYR115 4.3 23.9 1.0
CB B:ASP113 4.4 25.7 1.0
C B:ASP109 4.4 19.9 1.0
CB B:ASP109 4.4 20.5 1.0
CA B:TYR115 4.4 24.0 1.0
N B:LEU110 4.4 20.0 1.0
N B:ILE116 4.5 20.9 1.0
CA B:ILE116 4.5 20.2 1.0
CB B:ASP111 4.5 25.0 1.0
CG2 B:THR117 4.6 20.6 1.0
N B:ASN112 4.6 26.2 1.0
N B:THR117 4.6 20.0 1.0
CA B:ASP111 4.7 24.7 1.0
CB B:TYR115 4.8 26.0 1.0
CA B:ASP113 4.8 25.7 1.0
C B:ASP111 4.8 26.1 1.0
O B:ASP109 5.0 19.3 1.0
N B:GLY114 5.0 24.6 1.0

Calcium binding site 6 out of 6 in 5aeq

Go back to Calcium Binding Sites List in 5aeq
Calcium binding site 6 out of 6 in the 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 Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:22.1
occ:1.00
OD1 B:ASP157 2.3 26.4 1.0
O B:HOH2057 2.3 27.1 1.0
O B:LYS163 2.3 25.8 1.0
OD1 B:ASN159 2.3 35.4 1.0
OE1 B:GLU168 2.3 27.6 1.0
OD1 B:ASP161 2.3 31.6 1.0
OE2 B:GLU168 2.3 28.2 1.0
CD B:GLU168 2.7 26.2 1.0
CG B:ASP161 3.3 31.2 1.0
CG B:ASN159 3.4 36.7 1.0
CG B:ASP157 3.4 26.0 1.0
C B:LYS163 3.5 25.1 1.0
OD2 B:ASP161 3.7 31.5 1.0
ND2 B:ASN159 3.9 37.9 1.0
OD2 B:ASP157 4.1 25.5 1.0
CG B:GLU168 4.2 25.7 1.0
N B:ASN159 4.4 35.9 1.0
N B:LYS163 4.4 24.9 1.0
CA B:ASP157 4.4 25.5 1.0
N B:LEU164 4.4 23.3 1.0
CA B:LEU164 4.4 22.6 1.0
N B:ASP161 4.4 31.1 1.0
CB B:ASP157 4.5 25.0 1.0
CA B:LYS163 4.5 25.6 1.0
N B:LYS158 4.5 30.0 1.0
CB B:ASP161 4.6 30.9 1.0
O B:HOH2059 4.6 33.2 1.0
CB B:ASN159 4.7 36.2 1.0
C B:ASP157 4.7 27.5 1.0
CG B:LYS163 4.7 29.0 1.0
N B:THR165 4.8 22.7 1.0
N B:ALA160 4.8 34.9 1.0
CA B:ASN159 4.9 36.0 1.0
CA B:ASP161 5.0 30.6 1.0
CD2 B:LEU164 5.0 21.2 1.0
C B:ASN159 5.0 35.5 1.0

Reference:

S.Pandalaneni, V.Karuppiah, M.Saleem, L.P.Haynes, R.Burgoyne, O.Mayans, J.P.Derrick, L.Y.Lian. Structures of Ncs-1 Complexes with the D2 Dopamine Receptor and Gpcr Kinase 1 (GRK1) Peptides Shows Different Modes of Interactions To Be Published.
Page generated: Sat Dec 12 05:17:24 2020

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