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Sodium 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:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5afp

Go back to Sodium Binding Sites List in 5afp
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na1188

b:32.0
occ:1.00
O A:THR20 2.2 33.9 1.0
O A:THR17 2.2 37.4 1.0
O A:PHE22 2.2 36.6 1.0
C A:THR20 3.2 32.5 1.0
N A:PHE22 3.3 30.6 1.0
C A:THR17 3.3 38.6 1.0
C A:PHE22 3.3 33.0 1.0
C A:TYR21 3.7 31.5 1.0
CG2 A:THR17 3.8 36.7 1.0
OG1 A:THR20 3.9 31.0 1.0
CA A:THR17 3.9 36.0 1.0
CA A:PHE22 3.9 31.2 1.0
CA A:TYR21 3.9 31.6 1.0
N A:TYR21 4.0 31.6 1.0
N A:THR20 4.2 35.4 1.0
CA A:THR20 4.2 32.3 1.0
N A:THR23 4.4 33.3 1.0
N A:ARG18 4.5 40.8 1.0
CB A:THR17 4.5 37.4 1.0
O A:TYR21 4.6 33.1 1.0
CB A:THR20 4.6 32.2 1.0
O A:LEU16 4.8 33.4 1.0
CA A:ARG18 4.9 44.8 1.0
CA A:THR23 4.9 35.1 1.0
CB A:PHE22 4.9 29.4 1.0
C A:ARG18 5.0 46.1 1.0

Sodium binding site 2 out of 2 in 5afp

Go back to Sodium Binding Sites List in 5afp
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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:Na1189

b:38.4
occ:1.00
O A:ALA175 2.2 40.6 1.0
C A:ALA175 3.3 37.4 1.0
CD A:PRO177 3.8 40.6 1.0
CG A:PRO177 3.8 42.5 1.0
CA A:ALA175 4.0 38.1 1.0
N A:ASP176 4.2 38.4 1.0
O A:LYS174 4.3 41.5 1.0
N A:PRO177 4.3 40.7 1.0
CA A:ASP176 4.6 39.5 1.0
C A:ASP176 4.7 39.0 1.0
CB A:PRO177 4.8 42.0 1.0
CA A:PRO177 4.9 40.6 1.0
CB A:ALA175 5.0 37.3 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: Tue Dec 15 10:20:04 2020

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