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Sodium in PDB 5jid: Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)

Protein crystallography data

The structure of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa), PDB code: 5jid was solved by A.Begum, J.Zhang, A.Olofsson, P.Andersson, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.18 / 1.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.653, 85.674, 63.420, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 16.3

Other elements in 5jid:

The structure of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) also contains other interesting chemical elements:

Fluorine (F) 30 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) (pdb code 5jid). 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 Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa), PDB code: 5jid:

Sodium binding site 1 out of 1 in 5jid

Go back to Sodium Binding Sites List in 5jid
Sodium binding site 1 out of 1 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:44.3
occ:1.00
O B:ASP99 2.2 29.3 1.0
O B:HOH406 2.2 34.9 1.0
O B:HOH459 2.3 30.0 1.0
O B:HOH480 2.6 39.2 1.0
C B:ASP99 3.4 29.4 1.0
HB2 B:ASP99 3.6 42.4 1.0
OE2 B:GLU66 3.9 26.5 1.0
HA B:ASP99 3.9 35.1 1.0
HA B:SER100 3.9 39.5 1.0
O B:HOH488 3.9 41.2 1.0
CA B:ASP99 4.1 29.3 1.0
CB B:ASP99 4.3 35.3 1.0
N B:SER100 4.4 30.6 1.0
CD B:GLU66 4.5 25.9 1.0
OE1 B:GLU66 4.6 24.9 1.0
CA B:SER100 4.6 32.9 1.0

Reference:

J.Zhang, A.Begum, K.Brannstrom, C.Grundstrom, I.Iakovleva, A.Olofsson, A.E.Sauer-Eriksson, P.L.Andersson. Structure-Based Virtual Screening Protocol For in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Environ. Sci. Technol. V. 50 11984 2016.
ISSN: ISSN 1520-5851
PubMed: 27668830
DOI: 10.1021/ACS.EST.6B02771
Page generated: Tue Dec 15 11:08:11 2020

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