Sodium in PDB 5dnw: Crystal Structure of KAI2-Like Protein From Striga (Apo State 1)

The structure of Crystal Structure of KAI2-Like Protein From Striga (Apo State 1), PDB code: 5dnw 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)	19.74 / 2.02
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.940, 75.940, 181.470, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 22.5

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

Sodium binding site 1 out of 3 in the Crystal Structure of KAI2-Like Protein From Striga (Apo State 1)


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 KAI2-Like Protein From Striga (Apo State 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:23.6 occ:1.00 O A:HOH514 2.3 29.1 1.0 O A:PHE112 2.4 19.8 1.0 O A:HOH591 2.4 38.5 1.0 O A:PRO109 2.4 18.4 1.0 O A:HOH554 2.5 35.4 1.0 C A:PHE112 3.4 18.8 1.0 C A:PRO109 3.4 18.9 1.0 CG1 A:VAL207 3.7 17.5 1.0 CA A:ASP110 4.1 21.2 1.0 N A:ASP110 4.1 20.2 1.0 N A:PHE112 4.2 18.4 1.0 N A:GLN113 4.2 18.8 1.0 C A:ASP110 4.3 21.0 1.0 CA A:PHE112 4.3 18.0 1.0 O A:ASP110 4.3 22.2 1.0 C1 A:EDO309 4.3 41.2 1.0 CA A:GLN113 4.4 20.8 1.0 O2 A:EDO309 4.4 39.8 1.0 CA A:PRO109 4.5 18.5 1.0 CB A:VAL207 4.6 17.0 1.0 O A:HOH629 4.6 49.6 1.0 O A:HOH604 4.7 49.3 1.0 C2 A:EDO309 4.8 40.8 1.0 O A:GLN113 4.8 18.9 1.0 CB A:PHE112 4.8 17.1 1.0 C A:GLN113 4.8 20.1 1.0 CB A:PRO109 4.8 19.7 1.0 N A:LEU111 4.9 21.0 1.0 O A:HOH415 4.9 44.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of KAI2-Like Protein From Striga (Apo State 1)


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 KAI2-Like Protein From Striga (Apo State 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:45.3 occ:1.00 O A:HOH618 2.2 40.5 1.0 O A:HOH508 2.5 27.2 1.0 O A:HOH622 2.5 40.8 1.0 O A:HOH409 2.7 30.7 1.0 NA A:NA312 3.3 39.1 1.0 O A:HOH520 4.0 28.4 1.0 O A:GLY234 4.2 21.6 1.0 N A:SER236 4.2 20.4 1.0 CA A:ARG235 4.3 23.6 1.0 O A:HOH487 4.5 27.3 1.0 OG A:SER236 4.6 24.7 1.0 C A:ARG235 4.7 22.3 1.0 O A:HOH606 4.7 48.3 1.0 O A:SER236 4.8 18.5 1.0 O A:HOH574 4.8 45.5 1.0 C A:GLY234 4.9 22.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of KAI2-Like Protein From Striga (Apo State 1)


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 KAI2-Like Protein From Striga (Apo State 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:39.1 occ:1.00 O A:HOH431 2.3 32.6 1.0 O A:HOH409 2.4 30.7 1.0 O A:HOH487 2.5 27.3 1.0 O A:HOH520 2.6 28.4 1.0 NA A:NA311 3.3 45.3 1.0 O A:GLY234 3.9 21.6 1.0 O A:HOH618 3.9 40.5 1.0 O A:VAL232 4.0 22.1 1.0 O A:HIS229 4.1 18.0 1.0 OG A:SER236 4.6 24.7 1.0 O A:HOH622 4.7 40.8 1.0 O A:HOH445 4.7 31.3 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