Sodium in PDB 5dnu: Crystal Structure of Striga KAI2-Like Protein in Complex with Karrikin

The structure of Crystal Structure of Striga KAI2-Like Protein in Complex with Karrikin, PDB code: 5dnu 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)	19.70 / 1.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.757, 75.757, 181.266, 90.00, 90.00, 120.00
R / Rfree (%)	14 / 15.5

The binding sites of Sodium atom in the Crystal Structure of Striga KAI2-Like Protein in Complex with Karrikin (pdb code 5dnu). 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 KAI2-Like Protein in Complex with Karrikin, PDB code: 5dnu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Striga KAI2-Like Protein in Complex with Karrikin


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 KAI2-Like Protein in Complex with Karrikin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:33.6 occ:1.00 OD1 A:ASP267 2.5 35.0 1.0 O2 A:FMT302 2.8 24.8 1.0 NZ A:LYS114 2.8 16.3 1.0 N A:ASP267 3.1 18.1 1.0 C A:ASN266 3.2 16.7 1.0 CE A:LYS114 3.4 19.3 1.0 O A:ASN266 3.5 17.7 1.0 NE2 A:GLN113 3.5 23.4 1.0 O A:HOH557 3.5 37.2 1.0 C A:FMT302 3.5 21.4 1.0 CG A:ASP267 3.5 32.0 1.0 CA A:ASP267 3.5 21.5 1.0 CA A:ASN266 3.7 17.3 1.0 N A:ASN266 3.8 16.3 1.0 O A:LYS265 3.8 20.3 1.0 O A:HOH567 3.9 37.2 1.0 C A:LYS265 3.9 16.4 1.0 O A:ILE264 3.9 15.1 1.0 CB A:ASP267 4.1 27.3 1.0 O A:HOH517 4.4 30.0 1.0 OD2 A:ASP267 4.5 43.8 1.0 O1 A:FMT302 4.6 21.5 1.0 O A:HOH519 4.7 25.4 1.0 C A:ILE264 4.8 14.1 1.0 CD A:GLN113 4.8 20.5 1.0 CD A:LYS114 4.8 17.5 1.0 CA A:LYS265 4.9 16.1 1.0 C A:ASP267 4.9 25.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Striga KAI2-Like Protein in Complex with Karrikin


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 KAI2-Like Protein in Complex with Karrikin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:43.2 occ:1.00 OE2 A:GLU83 2.6 49.5 1.0 NH2 A:ARG8 3.2 21.1 1.0 OE1 A:GLU83 3.2 43.3 1.0 CD A:GLU83 3.2 37.4 1.0 NH1 A:ARG8 3.3 22.2 1.0 CG1 A:VAL79 3.6 18.2 1.0 CZ A:ARG8 3.7 19.5 1.0 CG1 A:VAL4 3.7 28.9 1.0 OE2 A:GLU5 4.4 37.0 1.0 CG A:GLU83 4.7 33.4 1.0 CD A:GLU5 4.9 30.1 1.0 CB A:VAL79 4.9 16.0 1.0 NE A:ARG8 4.9 18.0 1.0 NH1 A:ARG66 5.0 21.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Striga KAI2-Like Protein in Complex with Karrikin


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 KAI2-Like Protein in Complex with Karrikin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:33.5 occ:1.00 O A:HOH401 2.2 27.8 1.0 O A:PHE64 2.9 18.4 1.0 OG A:SER68 3.0 24.1 1.0 CD2 A:HIS63 3.4 22.7 1.0 O A:HIS63 3.5 23.1 1.0 OE2 A:GLU65 3.6 40.6 0.5 N A:SER68 3.6 16.2 1.0 C A:PHE64 3.6 17.5 1.0 CA A:GLU65 3.7 19.0 0.5 CA A:GLU65 3.7 19.1 0.5 O A:HOH573 3.7 27.8 1.0 O A:GLU65 3.7 16.8 1.0 NE2 A:HIS63 3.9 22.0 1.0 C A:GLU65 3.9 17.1 1.0 C A:TYR67 3.9 16.3 1.0 N A:GLU65 4.0 18.8 1.0 CA A:SER68 4.0 16.7 1.0 CB A:SER68 4.1 17.9 1.0 CG A:HIS63 4.1 22.0 1.0 C A:HIS63 4.2 20.6 1.0 N A:TYR67 4.3 15.3 1.0 CA A:TYR67 4.4 15.6 1.0 CB A:TYR67 4.4 17.2 1.0 O A:TYR67 4.5 17.0 1.0 O A:HOH452 4.6 22.2 1.0 O2 A:FMT306 4.6 33.4 1.0 CB A:HIS63 4.6 21.8 1.0 CE1 A:HIS63 4.7 21.7 1.0 CD A:GLU65 4.7 32.8 0.5 N A:PHE64 4.8 20.0 1.0 CA A:PHE64 4.8 18.9 1.0 ND1 A:HIS63 4.8 21.4 1.0 N A:ARG66 4.9 16.4 1.0 CB A:GLU65 4.9 22.9 0.5 C A:FMT306 4.9 33.5 1.0

Y.Xu, T.Miyakawa, H.Nakamura, A.Nakamura, Y.Imamura, T.Asami, M.Tanokura. Structural Basis of Unique Ligand Specificity of KAI2-Like Protein From Parasitic Weed Striga Hermonthica Sci Rep V. 6 31386 2016.
ISSN: ESSN 2045-2322
PubMed: 27507097
DOI: 10.1038/SREP31386