Sodium in PDB 5i8f: Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin

The structure of Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin, PDB code: 5i8f was solved by J.Sliwiak, Z.Dauter, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.860, 89.639, 76.410, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 15.3

The binding sites of Sodium atom in the Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin (pdb code 5i8f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin, PDB code: 5i8f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin


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 St. John'S Wort Hyp-1 Protein in Complex with Melatonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:17.6 occ:1.00 O A:HOH455 2.3 22.9 1.0 O A:HIS63 2.3 16.5 1.0 O A:LEU65 2.3 15.5 1.0 O A:VAL60 2.5 16.8 1.0 O A:HOH369 2.5 20.6 0.5 O A:HOH369 2.5 29.9 0.5 O A:ASP61 3.2 20.2 1.0 C A:HIS63 3.3 16.1 1.0 C A:LEU65 3.4 15.3 1.0 C A:ASP61 3.5 19.1 1.0 C A:VAL60 3.6 16.9 1.0 N A:HIS63 3.6 17.0 1.0 CA A:ASP61 3.7 19.8 1.0 CA A:HIS63 3.9 17.1 1.0 CB A:HIS63 4.0 18.4 1.0 CA A:THR66 4.1 17.0 1.0 N A:ASP61 4.1 19.2 1.0 N A:LEU65 4.2 16.2 1.0 CB A:PHE59 4.2 16.6 1.0 N A:THR66 4.2 16.0 1.0 C A:PRO64 4.3 17.3 1.0 O A:PHE59 4.3 18.3 1.0 N A:GLY62 4.3 18.8 1.0 C A:GLY62 4.4 17.3 1.0 OG1 A:THR66 4.4 24.1 1.0 N A:PRO64 4.4 17.1 1.0 CA A:LEU65 4.5 16.2 1.0 O A:HOH353 4.5 33.0 1.0 C A:PHE59 4.5 17.0 1.0 O A:PRO64 4.5 19.8 1.0 CA A:PRO64 4.7 17.9 1.0 N A:VAL60 4.8 17.1 1.0 CA A:VAL60 4.8 17.7 1.0 CB A:THR66 4.8 20.4 1.0 CA A:GLY62 4.9 19.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:56.8 occ:1.00 O A:HOH439 2.2 39.0 1.0 O A:GLU11 2.3 22.6 1.0 OE2 A:GLU10 2.4 31.8 0.6 O A:HOH458 2.4 50.8 1.0 O A:HOH401 2.5 51.5 1.0 OH A:TYR144 2.6 33.7 1.0 CD A:GLU10 3.4 31.8 0.6 O A:HOH304 3.5 53.5 1.0 C A:GLU11 3.6 20.8 1.0 CZ A:TYR144 3.8 29.6 1.0 NZ A:LYS145 3.9 37.1 1.0 CG A:GLU10 4.0 31.4 0.6 OE2 A:GLU148 4.1 27.4 1.0 CE2 A:TYR144 4.1 28.5 1.0 N A:GLU11 4.3 22.6 1.0 OE1 A:GLU10 4.4 32.3 0.6 CA A:SER12 4.5 18.1 1.0 N A:SER12 4.5 18.4 1.0 CA A:GLU11 4.5 22.2 1.0 OE1 A:GLU148 4.6 31.9 1.0 CD A:GLU148 4.8 28.3 1.0 O2 A:GOL212 4.8 66.7 1.0 OE1 A:GLU10 4.8 31.2 0.4 C1 A:GOL213 4.9 50.9 0.7 CE1 A:TYR144 5.0 27.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of St. John'S Wort Hyp-1 Protein in Complex with Melatonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:39.0 occ:0.50 OE2 A:GLU137 2.1 29.0 0.6 O A:HOH344 2.2 55.7 1.0 O A:HOH315 2.4 44.5 1.0 O A:HOH393 2.4 55.4 1.0 CD A:GLU137 3.2 26.7 0.6 N A:GLU137 3.7 17.1 0.4 N A:GLU137 3.7 16.8 0.6 C A:GLY136 3.7 16.6 1.0 CG A:GLU137 3.8 22.5 0.6 O A:GLY136 3.9 17.7 1.0 CA A:GLU137 3.9 17.9 0.6 CA A:GLU137 3.9 18.2 0.4 CG1 A:VAL118 4.0 19.3 1.0 O A:HOH452 4.2 46.7 1.0 OE1 A:GLU137 4.2 28.8 0.6 CA A:GLY136 4.3 17.1 1.0 CG2 A:VAL118 4.4 20.2 1.0 CE2 A:TYR101 4.4 19.5 1.0 CB A:GLU137 4.5 20.0 0.6 CB A:GLU137 4.5 20.4 0.4 O A:HOH477 4.5 64.7 1.0 OH A:TYR120 4.6 20.8 1.0 OH A:TYR101 4.6 22.7 1.0 O A:VAL133 4.7 18.3 1.0 CB A:VAL118 4.7 18.1 1.0 O A:HOH338 4.8 48.5 1.0 O A:HOH454 4.8 50.4 1.0 CE2 A:TYR120 4.9 17.9 1.0 CB A:ALA140 4.9 19.8 1.0

J.Sliwiak, Z.Dauter, M.Jaskolski. Crystal Structure of Hyp-1, A Hypericum Perforatum Pr-10 Protein, in Complex with Melatonin. Front Plant Sci V. 7 668 2016.
ISSN: ESSN 1664-462X
PubMed: 27242869
DOI: 10.3389/FPLS.2016.00668