Sodium in PDB 2wnh: Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase

All present enzymatic activity of Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase:
3.1.3.8;

The structure of Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase, PDB code: 2wnh was solved by K.Bohm, J.J.Mueller, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.49 / 1.68
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	133.680, 133.680, 111.240, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 20.7

The structure of Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase (pdb code 2wnh). 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 Analysis of Klebsiella Sp ASR1 Phytase, PDB code: 2wnh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1407 b:32.2 occ:1.00 O A:HOH2050 2.3 30.8 1.0 O A:HOH2059 2.3 34.9 1.0 O A:HOH2062 2.4 29.1 1.0 O A:TRP49 2.5 19.1 1.0 O A:THR51 2.6 17.1 1.0 O A:HOH2063 2.8 26.9 1.0 C A:THR51 3.5 16.9 1.0 C A:TRP49 3.6 17.6 1.0 CA A:HIS52 3.8 19.0 1.0 N A:TRP49 3.8 17.0 1.0 N A:HIS52 4.0 17.3 1.0 OE1 A:GLU48 4.0 31.9 1.0 N A:ASP53 4.0 17.0 1.0 O A:HOH2053 4.1 43.6 1.0 CA A:TRP49 4.2 15.4 1.0 C A:HIS52 4.2 17.9 1.0 O A:HOH2049 4.3 26.9 1.0 OD1 A:ASP53 4.4 19.1 1.0 N A:THR51 4.4 16.3 1.0 C A:GLU48 4.4 18.9 1.0 O A:HOH2060 4.5 38.8 1.0 C A:THR50 4.5 18.1 1.0 N A:THR50 4.6 16.6 1.0 CA A:THR51 4.6 16.9 1.0 CB A:TRP49 4.6 14.5 1.0 O A:HOH2056 4.7 37.6 1.0 CB A:GLU48 4.8 20.8 1.0 O A:THR50 4.8 19.8 1.0 CA A:GLU48 4.8 19.6 1.0 CA A:THR50 4.8 18.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1407 b:45.8 occ:1.00 O B:HOH2228 2.4 33.9 1.0 O B:HOH2106 2.4 46.1 1.0 O B:HOH2282 2.5 42.7 1.0 O B:HOH2226 2.5 27.2 1.0 O B:HOH2105 3.2 36.3 1.0 NH2 B:ARG312 3.7 22.3 1.0 O B:HOH2225 3.8 26.0 1.0 OE1 B:GLU247 3.8 24.8 1.0 O B:HOH2232 3.9 29.9 1.0 O B:HOH2107 4.1 32.9 1.0 OD2 B:ASP250 4.4 24.2 1.0 O B:HOH2111 4.9 41.6 1.0 CZ B:ARG312 4.9 22.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of Klebsiella Sp ASR1 Phytase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1408 b:13.5 occ:0.50 O B:ARG76 2.4 18.9 1.0 C B:ARG76 3.4 16.4 1.0 O B:GLN77 4.2 19.1 1.0 N B:GLN77 4.2 17.7 1.0 CA B:GLN77 4.2 17.7 1.0 C B:GLN77 4.4 19.1 1.0 CA B:ARG76 4.4 16.1 1.0 N B:GLY79 4.4 20.7 1.0 CA B:GLY79 4.5 20.2 1.0 CB B:ARG76 4.6 15.5 1.0 O B:LEU81 4.8 19.5 1.0

K.Bohm, T.Herter, J.J.Mueller, R.Borriss, U.Heinemann. Crystal Structure of Klebsiella Sp. ASR1 Phytase Suggests Substrate Binding to A Preformed Active Site That Meets the Requirements of A Plant Rhizosphere Enzyme. Febs J. V. 277 1284 2010.
ISSN: ISSN 1742-464X
PubMed: 20392204
DOI: 10.1111/J.1742-4658.2010.07559.X