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Sodium in PDB 3fgr: Two Chain Form of the 66.3 kDa Protein at 1.8 Angstroem

Protein crystallography data

The structure of Two Chain Form of the 66.3 kDa Protein at 1.8 Angstroem, PDB code: 3fgr was solved by K.Lakomek, A.Dickmanns, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.26 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.737, 89.560, 64.811, 90.00, 98.69, 90.00
R / Rfree (%) 15.2 / 18.2

Other elements in 3fgr:

The structure of Two Chain Form of the 66.3 kDa Protein at 1.8 Angstroem also contains other interesting chemical elements:

Xenon (Xe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Two Chain Form of the 66.3 kDa Protein at 1.8 Angstroem (pdb code 3fgr). 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 Two Chain Form of the 66.3 kDa Protein at 1.8 Angstroem, PDB code: 3fgr:

Sodium binding site 1 out of 1 in 3fgr

Go back to Sodium Binding Sites List in 3fgr
Sodium binding site 1 out of 1 in the Two Chain Form of the 66.3 kDa Protein at 1.8 Angstroem


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Two Chain Form of the 66.3 kDa Protein at 1.8 Angstroem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:28.0
occ:1.00
OD2 B:OCS249 2.8 26.4 0.5
OE1 B:GLU328 2.8 18.0 1.0
OG1 B:THR330 2.8 17.6 1.0
OH B:TYR379 2.8 25.4 1.0
O B:ASP315 2.9 16.1 1.0
OD1 B:OCS249 3.0 27.3 0.5
OE2 B:GLU328 3.0 16.1 1.0
OG A:SER246 3.1 44.2 1.0
CD B:GLU328 3.3 17.2 1.0
SG B:OCS249 3.4 31.5 1.0
C B:ASP315 3.7 16.0 1.0
CZ B:TYR379 3.7 24.4 1.0
CB A:SER246 3.9 42.7 1.0
O B:GLY314 4.0 21.0 1.0
CE2 B:TYR379 4.0 22.9 1.0
CB B:THR330 4.1 14.8 1.0
N B:THR330 4.1 13.7 1.0
N B:ASP316 4.3 14.2 1.0
OD3 B:OCS249 4.3 30.0 0.5
O B:GLU328 4.4 13.1 1.0
CA B:THR330 4.6 14.8 1.0
CA B:THR329 4.6 12.8 1.0
OD1 B:ASN381 4.7 15.4 1.0
CB B:OCS249 4.7 22.2 1.0
C B:THR329 4.7 13.8 1.0
CG B:GLU328 4.7 15.0 1.0
CA B:ASP315 4.8 15.8 1.0
CE1 B:TYR379 4.8 21.1 1.0
OD1 B:ASP316 4.9 21.4 1.0
C A:SER246 4.9 42.0 1.0
C B:GLU328 5.0 12.2 1.0

Reference:

K.Lakomek, A.Dickmanns, M.Kettwig, H.Urlaub, R.Ficner, T.Luebke. Initial Insight Into the Function of the Lysosomal 66.3 kDa Protein From Mouse By Means of X-Ray Crystallography Bmc Struct.Biol. V. 9 56 2009.
ISSN: ESSN 1472-6807
PubMed: 19706171
DOI: 10.1186/1472-6807-9-56
Page generated: Tue Dec 15 06:10:44 2020

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