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Calcium in PDB 5afp: Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens

Protein crystallography data

The structure of Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens, PDB code: 5afp 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) 47.86 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.690, 93.690, 55.710, 90.00, 92.25, 90.00
R / Rfree (%) 22.556 / 25.515

Other elements in 5afp:

The structure of Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens (pdb code 5afp). 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-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens, PDB code: 5afp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5afp

Go back to Calcium Binding Sites List in 5afp
Calcium binding site 1 out of 6 in the Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens


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-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1185

b:39.9
occ:1.00
O A:ARG79 2.3 43.6 1.0
OD1 A:ASN75 2.3 46.6 1.0
O A:HOH2007 2.3 39.8 1.0
OD1 A:ASP73 2.3 41.9 1.0
OD1 A:ASP77 2.3 48.9 1.0
OE2 A:GLU84 2.3 43.7 1.0
OE1 A:GLU84 2.3 41.9 1.0
CD A:GLU84 2.7 38.7 1.0
CG A:ASP77 3.2 46.4 1.0
CG A:ASN75 3.4 43.5 1.0
CG A:ASP73 3.5 38.9 1.0
C A:ARG79 3.5 42.1 1.0
OD2 A:ASP77 3.7 48.6 1.0
ND2 A:ASN75 3.9 40.9 1.0
CG A:GLU84 4.2 35.4 1.0
CA A:ASP73 4.2 37.2 1.0
N A:ASP77 4.2 43.3 1.0
N A:ARG79 4.3 44.1 1.0
OD2 A:ASP73 4.3 39.7 1.0
CB A:ASP77 4.4 45.4 1.0
CA A:ARG79 4.4 45.2 1.0
CB A:ASP73 4.4 37.4 1.0
N A:ILE80 4.4 39.5 1.0
N A:ASN75 4.4 42.1 1.0
CA A:ILE80 4.5 35.5 1.0
N A:GLU81 4.5 36.1 1.0
C A:ASP73 4.6 39.7 1.0
N A:LYS76 4.6 41.8 1.0
CB A:ASN75 4.6 42.9 1.0
N A:GLU74 4.7 42.7 1.0
CB A:ARG79 4.8 49.9 1.0
CA A:ASP77 4.8 44.9 1.0
CA A:ASN75 4.8 43.6 1.0
C A:ASN75 4.9 43.7 1.0
CG A:GLU81 4.9 41.7 1.0
N A:GLY78 4.9 44.5 1.0
OE2 A:GLU81 5.0 48.9 1.0

Calcium binding site 2 out of 6 in 5afp

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Calcium binding site 2 out of 6 in the Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens


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-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1186

b:45.1
occ:1.00
O A:TYR115 2.3 47.5 1.0
OD1 A:ASP109 2.3 45.5 1.0
OD1 A:ASP111 2.3 55.1 1.0
O A:HOH2011 2.3 47.8 1.0
OE2 A:GLU120 2.3 45.8 1.0
OD1 A:ASP113 2.3 55.5 1.0
OE1 A:GLU120 2.3 46.5 1.0
CD A:GLU120 2.7 42.4 1.0
CG A:ASP111 3.2 53.4 1.0
CG A:ASP113 3.2 55.1 1.0
CG A:ASP109 3.5 43.9 1.0
C A:TYR115 3.5 42.1 1.0
OD2 A:ASP111 3.6 57.4 1.0
OD2 A:ASP113 3.7 54.1 1.0
N A:ASP111 4.2 47.8 1.0
N A:ASP113 4.2 54.0 1.0
CG A:GLU120 4.2 41.9 1.0
OD2 A:ASP109 4.2 44.6 1.0
CA A:ASP109 4.3 40.7 1.0
N A:TYR115 4.3 44.4 1.0
CB A:ASP111 4.4 51.4 1.0
CA A:TYR115 4.4 44.7 1.0
CB A:ASP113 4.4 56.8 1.0
N A:ASN112 4.4 49.6 1.0
C A:ASP109 4.4 43.5 1.0
CB A:ASP109 4.5 41.6 1.0
N A:ILE116 4.5 39.6 1.0
CA A:ILE116 4.5 37.6 1.0
N A:LEU110 4.5 43.8 1.0
N A:THR117 4.6 38.1 1.0
CA A:ASP111 4.6 50.3 1.0
CB A:TYR115 4.6 45.8 1.0
C A:ASP111 4.7 49.2 1.0
CA A:ASP113 4.8 55.7 1.0
CG2 A:THR117 4.9 40.8 1.0
O A:ASP109 5.0 44.9 1.0

Calcium binding site 3 out of 6 in 5afp

Go back to Calcium Binding Sites List in 5afp
Calcium binding site 3 out of 6 in the Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens


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-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1187

b:38.5
occ:1.00
O A:LYS163 2.3 44.9 1.0
OD1 A:ASN159 2.3 49.0 1.0
OD1 A:ASP157 2.3 42.6 1.0
OE2 A:GLU168 2.3 39.7 1.0
OD1 A:ASP161 2.3 48.2 1.0
OE1 A:GLU168 2.3 41.8 1.0
CD A:GLU168 2.7 38.8 1.0
CG A:ASP161 3.3 49.4 1.0
CG A:ASN159 3.4 48.5 1.0
CG A:ASP157 3.5 39.5 1.0
C A:LYS163 3.5 42.0 1.0
OD2 A:ASP161 3.7 51.7 1.0
ND2 A:ASN159 3.9 48.9 1.0
CG A:GLU168 4.2 38.5 1.0
OD2 A:ASP157 4.2 39.4 1.0
CA A:ASP157 4.2 37.2 1.0
N A:LYS163 4.3 45.7 1.0
N A:ASN159 4.4 45.1 1.0
CB A:ASP157 4.4 38.3 1.0
CA A:LYS163 4.4 44.9 1.0
N A:ASP161 4.4 48.4 1.0
N A:LEU164 4.4 38.9 1.0
CA A:LEU164 4.5 36.6 1.0
C A:ASP157 4.5 39.3 1.0
N A:LYS158 4.5 41.5 1.0
CB A:ASP161 4.6 50.7 1.0
CB A:ASN159 4.7 48.2 1.0
CB A:LYS163 4.7 48.6 1.0
N A:ALA160 4.7 46.3 1.0
CD2 A:LEU164 4.8 36.6 1.0
N A:THR165 4.9 36.2 1.0
CA A:ASN159 4.9 47.3 1.0
CA A:ASP161 5.0 49.8 1.0
C A:ASN159 5.0 45.8 1.0

Calcium binding site 4 out of 6 in 5afp

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Calcium binding site 4 out of 6 in the Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens


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-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1185

b:43.1
occ:1.00
O B:HOH2003 2.3 51.0 1.0
OD1 B:ASP77 2.3 56.6 1.0
OE2 B:GLU84 2.3 49.6 1.0
O B:ARG79 2.3 45.1 1.0
OD1 B:ASN75 2.3 53.6 1.0
OD1 B:ASP73 2.3 48.9 1.0
OE1 B:GLU84 2.3 46.9 1.0
CD B:GLU84 2.7 44.9 1.0
CG B:ASP77 3.2 53.9 1.0
CG B:ASP73 3.4 45.4 1.0
CG B:ASN75 3.4 50.0 1.0
C B:ARG79 3.5 43.4 1.0
OD2 B:ASP77 3.7 57.3 1.0
ND2 B:ASN75 4.0 49.9 1.0
CG B:GLU84 4.2 41.8 1.0
OD2 B:ASP73 4.2 46.8 1.0
N B:ASP77 4.2 46.3 1.0
CA B:ASP73 4.2 40.3 1.0
N B:ARG79 4.2 47.0 1.0
CB B:ASP73 4.4 42.0 1.0
CB B:ASP77 4.4 52.2 1.0
CA B:ARG79 4.4 47.2 1.0
N B:ILE80 4.5 40.4 1.0
CA B:ILE80 4.5 38.7 1.0
N B:ASN75 4.5 44.8 1.0
C B:ASP73 4.6 41.7 1.0
N B:LYS76 4.6 43.4 1.0
N B:GLU81 4.6 37.4 1.0
CB B:ASN75 4.7 48.8 1.0
N B:GLU74 4.7 42.2 1.0
CA B:ASP77 4.7 49.1 1.0
N B:GLY78 4.8 48.5 1.0
C B:ASN75 4.9 45.2 1.0
CB B:ARG79 4.9 50.6 1.0
CG B:GLU81 4.9 42.3 1.0
CA B:ASN75 4.9 46.6 1.0
C B:ASP77 5.0 48.5 1.0

Calcium binding site 5 out of 6 in 5afp

Go back to Calcium Binding Sites List in 5afp
Calcium binding site 5 out of 6 in the Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens


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-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1186

b:49.1
occ:1.00
O B:TYR115 2.3 55.3 1.0
OD1 B:ASP111 2.3 62.0 1.0
O B:HOH2005 2.3 55.8 1.0
OD1 B:ASP109 2.3 55.2 1.0
OE2 B:GLU120 2.3 56.2 1.0
OD1 B:ASP113 2.3 64.3 1.0
OE1 B:GLU120 2.3 55.8 1.0
CD B:GLU120 2.7 51.6 1.0
CG B:ASP113 3.2 65.2 1.0
CG B:ASP111 3.2 61.1 1.0
CG B:ASP109 3.5 52.0 1.0
C B:TYR115 3.5 53.3 1.0
OD2 B:ASP113 3.5 66.1 1.0
OD2 B:ASP111 3.7 60.9 1.0
N B:ASP111 4.2 54.6 1.0
OD2 B:ASP109 4.2 52.7 1.0
CG B:GLU120 4.2 50.0 1.0
CA B:ASP109 4.3 46.2 1.0
CB B:ASP111 4.4 59.8 1.0
CA B:TYR115 4.4 56.8 1.0
N B:ASP113 4.4 63.0 1.0
N B:TYR115 4.4 57.2 1.0
CB B:ASP113 4.4 66.0 1.0
N B:ILE116 4.4 49.4 1.0
CB B:ASP109 4.4 48.9 1.0
C B:ASP109 4.4 47.9 1.0
N B:LEU110 4.5 48.3 1.0
CA B:ILE116 4.5 47.8 1.0
N B:ASN112 4.5 56.0 1.0
N B:THR117 4.6 48.9 1.0
CA B:ASP111 4.6 57.1 1.0
CB B:TYR115 4.6 59.3 1.0
C B:ASP111 4.7 55.8 1.0
CA B:ASP113 4.9 64.7 1.0
CG2 B:THR117 4.9 54.2 1.0
C B:ASP113 5.0 65.1 1.0

Calcium binding site 6 out of 6 in 5afp

Go back to Calcium Binding Sites List in 5afp
Calcium binding site 6 out of 6 in the Neuronal Calcium Sensor-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens


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-1 (Ncs-1)From Rattus Norvegicus Complex with Rhodopsin Kinase Peptide From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1187

b:51.4
occ:1.00
O B:LYS163 2.3 62.8 1.0
OD1 B:ASN159 2.3 70.5 1.0
OD1 B:ASP157 2.3 60.2 1.0
OE2 B:GLU168 2.3 58.0 1.0
OD1 B:ASP161 2.3 64.0 1.0
OE1 B:GLU168 2.3 56.4 1.0
CD B:GLU168 2.7 52.0 1.0
CG B:ASP161 3.3 61.6 1.0
CG B:ASN159 3.4 69.9 1.0
CG B:ASP157 3.5 58.0 1.0
C B:LYS163 3.5 57.3 1.0
OD2 B:ASP161 3.7 60.9 1.0
ND2 B:ASN159 3.8 70.0 1.0
O B:HOH2010 4.1 54.4 1.0
CG B:GLU168 4.2 50.1 1.0
N B:LYS163 4.3 58.7 1.0
OD2 B:ASP157 4.3 58.0 1.0
CA B:ASP157 4.3 54.8 1.0
N B:ASN159 4.4 66.4 1.0
CA B:LYS163 4.4 58.9 1.0
CB B:ASP157 4.4 55.6 1.0
N B:ASP161 4.4 62.4 1.0
N B:LEU164 4.4 54.1 1.0
CA B:LEU164 4.5 50.4 1.0
N B:LYS158 4.5 59.7 1.0
CB B:ASP161 4.6 63.1 1.0
CB B:ASN159 4.6 70.1 1.0
C B:ASP157 4.6 57.3 1.0
CB B:LYS163 4.7 61.2 1.0
N B:ALA160 4.7 66.1 1.0
CA B:ASN159 4.9 68.3 1.0
N B:THR165 4.9 51.4 1.0
CA B:ASP161 4.9 62.6 1.0
C B:ASN159 5.0 67.4 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 05:17:28 2020

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