Sodium in PDB 5u9j: Crystal Structure of the Fkbp Domain of Human Aryl Hydrocarbon Receptor-Interacting Protein-Like 1 (AIPL1) Complexed with Geranyl Geranyl Pyrophoshate

The structure of Crystal Structure of the Fkbp Domain of Human Aryl Hydrocarbon Receptor-Interacting Protein-Like 1 (AIPL1) Complexed with Geranyl Geranyl Pyrophoshate, PDB code: 5u9j was solved by R.P.Yadav, L.Gakhar, Y.Liping, N.O.Artemyev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.15 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.340, 51.170, 106.970, 90.00, 93.09, 90.00
R / Rfree (%)	23.8 / 29.4

The binding sites of Sodium atom in the Crystal Structure of the Fkbp Domain of Human Aryl Hydrocarbon Receptor-Interacting Protein-Like 1 (AIPL1) Complexed with Geranyl Geranyl Pyrophoshate (pdb code 5u9j). 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 the Fkbp Domain of Human Aryl Hydrocarbon Receptor-Interacting Protein-Like 1 (AIPL1) Complexed with Geranyl Geranyl Pyrophoshate, PDB code: 5u9j:

Sodium binding site 1 out of 1 in the Crystal Structure of the Fkbp Domain of Human Aryl Hydrocarbon Receptor-Interacting Protein-Like 1 (AIPL1) Complexed with Geranyl Geranyl Pyrophoshate


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 the Fkbp Domain of Human Aryl Hydrocarbon Receptor-Interacting Protein-Like 1 (AIPL1) Complexed with Geranyl Geranyl Pyrophoshate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:30.5 occ:1.00 HH21 B:ARG38 2.0 29.4 1.0 O B:HOH452 2.4 27.2 1.0 O B:ARG46 2.8 24.6 1.0 NH2 B:ARG38 2.8 24.5 1.0 OE2 A:GLU152 2.9 26.3 1.0 HB3 B:ARG46 3.1 30.5 1.0 HH22 B:ARG38 3.1 29.4 1.0 HB2 B:ARG46 3.1 30.5 1.0 SD B:MET40 3.2 26.1 1.0 CB B:ARG46 3.5 25.4 1.0 HG23 B:VAL48 3.5 26.5 1.0 HH11 A:ARG53 3.6 29.8 1.0 HG2 B:MET40 3.7 32.5 1.0 HE B:ARG38 3.7 31.6 1.0 HG22 B:VAL48 3.7 26.5 1.0 CD A:GLU152 3.7 33.5 1.0 O A:HOH407 3.8 22.0 1.0 C B:ARG46 3.8 23.1 1.0 O B:GLU45 3.8 28.0 1.0 CZ B:ARG38 3.9 34.7 1.0 OE1 A:GLU152 3.9 32.5 1.0 CG2 B:VAL48 4.0 22.1 1.0 CG B:MET40 4.1 27.1 1.0 HE B:ARG46 4.1 28.9 1.0 NH1 A:ARG53 4.1 24.8 1.0 NE B:ARG38 4.2 26.3 1.0 HH12 A:ARG53 4.2 29.8 1.0 CA B:ARG46 4.2 24.4 1.0 O A:HOH434 4.2 28.7 1.0 HG21 B:VAL48 4.4 26.5 1.0 HB3 B:MET40 4.5 27.0 1.0 HG21 A:VAL84 4.6 23.0 1.0 NE B:ARG46 4.8 24.1 1.0 HD3 B:ARG46 4.8 27.8 1.0 HG3 B:MET40 4.8 32.5 1.0 CG B:ARG46 4.8 26.5 1.0 C B:GLU45 4.8 26.6 1.0 CE B:MET40 4.9 27.4 1.0 HE A:ARG53 4.9 47.9 1.0 CB B:MET40 4.9 22.5 1.0 H B:VAL48 4.9 22.4 1.0 N B:THR47 4.9 25.6 1.0 CZ A:ARG53 5.0 24.1 1.0 HA B:ARG46 5.0 29.2 1.0

R.P.Yadav, L.Gakhar, L.Yu, N.O.Artemyev. Unique Structural Features of the AIPL1-Fkbp Domain That Support Prenyl Lipid Binding and Underlie Protein Malfunction in Blindness. Proc. Natl. Acad. Sci. V. 114 E6536 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28739921
DOI: 10.1073/PNAS.1704782114