Atomistry » Sodium » PDB 5ack-5b07 » 5afp
Atomistry »
  Sodium »
    PDB 5ack-5b07 »
      5afp »

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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy