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Sodium 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:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus, PDB code: 5aeq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5aeq

Go back to Sodium Binding Sites List in 5aeq
Sodium binding site 1 out of 2 in the Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus


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 (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:11.1
occ:1.00
O A:HOH2074 2.2 10.9 1.0
O A:ALA175 2.3 13.7 1.0
C A:ALA175 3.2 13.8 1.0
CD A:PRO177 3.8 15.6 1.0
CG A:PRO177 3.8 16.1 1.0
CA A:ALA175 3.9 13.3 1.0
N A:ASP176 4.2 14.8 1.0
O A:LYS174 4.2 13.5 1.0
N A:PRO177 4.3 14.9 1.0
CA A:ASP176 4.6 16.0 1.0
C A:ASP176 4.7 14.8 1.0
CB A:ALA175 4.8 12.8 1.0
CA A:PRO177 4.9 15.3 1.0
CB A:PRO177 4.9 16.1 1.0
N A:ALA175 4.9 13.0 1.0
C A:LYS174 5.0 13.7 1.0

Sodium binding site 2 out of 2 in 5aeq

Go back to Sodium Binding Sites List in 5aeq
Sodium binding site 2 out of 2 in the Neuronal Calcium Sensor (Ncs-1)From Rattus Norvegicus


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 (Ncs-1)From Rattus Norvegicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:17.6
occ:1.00
O B:HOH2005 2.2 20.2 1.0
O B:THR17 2.2 26.7 1.0
O B:THR20 2.2 25.0 1.0
O B:PHE22 2.2 23.3 1.0
C B:THR20 3.3 23.7 1.0
C B:PHE22 3.3 22.1 1.0
C B:THR17 3.4 26.6 1.0
N B:PHE22 3.5 21.4 1.0
CG2 B:THR17 3.8 25.2 1.0
C B:TYR21 3.8 21.7 1.0
OG1 B:THR20 4.0 24.6 1.0
CA B:THR17 4.0 25.4 1.0
CA B:PHE22 4.0 21.5 1.0
CA B:TYR21 4.0 22.2 1.0
N B:TYR21 4.0 22.3 1.0
CA B:THR20 4.3 24.3 1.0
N B:THR20 4.3 26.0 1.0
N B:THR23 4.4 22.2 1.0
N B:ARG18 4.5 29.4 1.0
CB B:THR17 4.6 25.6 1.0
O B:TYR21 4.6 21.4 1.0
CB B:THR20 4.8 24.1 1.0
CA B:ARG18 4.8 32.2 1.0
CA B:THR23 4.8 23.0 1.0
CB B:PHE22 5.0 21.5 1.0
O B:LEU16 5.0 23.5 1.0
C B:ARG18 5.0 31.9 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 10:19:05 2020

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