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Sodium in PDB 5iyu: ALGE_CIM

Protein crystallography data

The structure of ALGE_CIM, PDB code: 5iyu was solved by P.Ma, D.Weichert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.32 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 56.830, 73.390, 114.530, 90.00, 101.93, 90.00
R / Rfree (%) 22.3 / 28.3

Sodium Binding Sites:

The binding sites of Sodium atom in the ALGE_CIM (pdb code 5iyu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the ALGE_CIM, PDB code: 5iyu:

Sodium binding site 1 out of 1 in 5iyu

Go back to Sodium Binding Sites List in 5iyu
Sodium binding site 1 out of 1 in the ALGE_CIM


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of ALGE_CIM within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:51.3
occ:1.00
O A:ALA136 2.5 41.1 1.0
O A:THR139 2.7 50.4 1.0
O A:TYR141 2.8 53.6 1.0
C A:TYR141 3.2 51.9 1.0
CA A:PRO142 3.5 49.1 1.0
N A:PRO142 3.6 54.7 1.0
C A:ALA136 3.6 38.8 1.0
O A:GLU144 3.7 43.2 1.0
C A:THR139 3.8 55.0 1.0
C A:ALA140 3.8 60.4 1.0
CB A:ALA136 3.9 35.3 1.0
N A:TYR141 3.9 60.9 1.0
O A:ALA140 4.1 51.0 1.0
CA A:TYR141 4.2 57.7 1.0
OE2 A:GLU144 4.2 56.6 1.0
CA A:ALA140 4.3 53.1 1.0
CA A:ALA136 4.3 35.2 1.0
C A:PRO142 4.5 47.1 1.0
N A:ALA140 4.5 57.7 1.0
N A:GLY137 4.6 44.7 1.0
CB A:PRO142 4.6 49.8 1.0
OG1 A:THR139 4.6 46.6 1.0
CD A:PRO142 4.7 57.4 1.0
CA A:GLY137 4.7 51.1 1.0
C A:GLU144 4.8 43.1 1.0
O A:PRO142 4.8 60.1 1.0
N A:THR139 4.8 41.6 1.0
CA A:THR139 4.9 42.9 1.0
OD1 A:ASP83 5.0 47.8 1.0

Reference:

P.Ma, D.Weichert, L.A.Aleksandrov, T.J.Jensen, J.R.Riordan, X.Liu, B.K.Kobilka, M.Caffrey. The Cubicon Method For Concentrating Membrane Proteins in the Cubic Mesophase. Nat Protoc V. 12 1745 2017.
ISSN: ISSN 1750-2799
PubMed: 28771236
DOI: 10.1038/NPROT.2017.057
Page generated: Tue Dec 15 11:06:50 2020

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