Sodium in PDB 5z7w: Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)

The structure of Crystal Structure of Striga Hermonthica HTL1 (SHHTL1), PDB code: 5z7w was solved by Y.Xu, T.Miyakawa, A.Nakamura, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.95 / 1.66
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.170, 138.770, 49.410, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.9

The structure of Crystal Structure of Striga Hermonthica HTL1 (SHHTL1) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1) (pdb code 5z7w). 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 Striga Hermonthica HTL1 (SHHTL1), PDB code: 5z7w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)


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 Striga Hermonthica HTL1 (SHHTL1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:30.9 occ:0.92 O A:PHE112 2.3 27.6 1.0 O A:HOH658 2.3 28.8 1.0 O A:PRO109 2.4 27.0 1.0 O A:HOH647 2.4 44.4 1.0 O A:HOH651 2.5 33.8 1.0 C A:PRO109 3.5 26.7 1.0 C A:PHE112 3.5 27.4 1.0 CG2 A:VAL207 3.9 24.1 1.0 N A:PHE112 4.3 26.7 1.0 O A:HOH518 4.3 24.3 1.0 O A:HOH464 4.3 36.7 1.0 N A:ASP110 4.3 26.4 1.0 CA A:PRO109 4.3 26.4 1.0 CA A:ASP110 4.4 28.2 1.0 N A:THR113 4.4 25.8 1.0 CA A:PHE112 4.4 26.8 1.0 CA A:THR113 4.5 24.3 1.0 CB A:PRO109 4.5 28.1 1.0 O A:HOH557 4.5 46.5 1.0 C A:ASP110 4.5 28.1 1.0 O A:ASP110 4.7 29.3 1.0 O A:HOH668 4.7 44.6 1.0 CB A:VAL207 4.9 23.0 1.0 O A:HOH525 4.9 49.6 1.0 CG1 A:VAL207 4.9 25.8 1.0 CB A:PHE112 4.9 26.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)


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 Striga Hermonthica HTL1 (SHHTL1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:73.5 occ:1.00 O B:HOH401 2.7 32.2 1.0 O B:HOH706 2.8 39.4 1.0 O B:HOH503 3.2 42.7 1.0 OE2 B:GLU144 5.0 23.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)


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 Striga Hermonthica HTL1 (SHHTL1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:33.0 occ:0.78 O B:HOH728 2.4 37.6 1.0 O B:HOH655 2.4 33.9 1.0 O B:PHE112 2.6 25.1 1.0 O B:PRO109 2.6 21.3 1.0 C B:PRO109 3.6 21.1 1.0 CG2 B:VAL207 3.6 23.8 1.0 C B:PHE112 3.8 20.8 1.0 CB B:PRO109 4.2 21.0 1.0 CA B:PRO109 4.3 21.0 1.0 CA B:THR113 4.4 22.7 1.0 N B:ASP110 4.5 19.9 1.0 N B:THR113 4.5 21.9 1.0 O B:HOH571 4.6 37.0 1.0 CA B:ASP110 4.7 20.3 1.0 CB B:VAL207 4.8 22.6 1.0 N B:PHE112 4.8 18.8 1.0 CA B:PHE112 4.8 19.0 1.0 CG1 B:VAL207 5.0 22.8 1.0

Y.Xu, T.Miyakawa, S.Nosaki, A.Nakamura, Y.Lyu, H.Nakamura, U.Ohto, H.Ishida, T.Shimizu, T.Asami, M.Tanokura. Structural Analysis of Htl and D14 Proteins Reveals the Basis For Ligand Selectivity in Striga. Nat Commun V. 9 3947 2018.
ISSN: ESSN 2041-1723
PubMed: 30258184
DOI: 10.1038/S41467-018-06452-2