Sodium in PDB 1ud8: Crystal Structure of AMYK38 with Lithium Ion

All present enzymatic activity of Crystal Structure of AMYK38 with Lithium Ion:
3.2.1.1;

The structure of Crystal Structure of AMYK38 with Lithium Ion, PDB code: 1ud8 was solved by T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.28 / 2.88
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	132.553, 132.553, 132.553, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26.8

The binding sites of Sodium atom in the Crystal Structure of AMYK38 with Lithium Ion (pdb code 1ud8). 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 AMYK38 with Lithium Ion, PDB code: 1ud8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of AMYK38 with Lithium Ion


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 AMYK38 with Lithium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:21.1 occ:1.00 O A:HIS235 2.3 32.3 1.0 OD1 A:ASN104 2.4 28.5 1.0 OD1 A:ASP194 2.4 23.9 1.0 O A:ASP194 2.5 25.5 1.0 OD1 A:ASN200 2.6 38.3 1.0 C A:HIS235 3.3 28.4 1.0 CG A:ASN200 3.4 35.4 1.0 ND2 A:ASN200 3.4 36.6 1.0 CG A:ASN104 3.5 25.6 1.0 C A:ASP194 3.5 26.5 1.0 CG A:ASP194 3.6 26.7 1.0 CB A:HIS235 3.8 29.4 1.0 CA A:ASP194 4.0 28.4 1.0 O A:ASN104 4.0 26.4 1.0 ND2 A:ASN104 4.1 26.4 1.0 N A:ILE236 4.1 27.1 1.0 CA A:HIS235 4.2 27.5 1.0 ND2 A:ASN183 4.2 26.8 1.0 CA A:ILE236 4.3 26.4 1.0 CB A:ASP194 4.4 26.4 1.0 OD2 A:ASP194 4.4 26.9 1.0 O A:HOH2086 4.4 44.8 1.0 CB A:ASN104 4.6 24.9 1.0 N A:TYR195 4.7 25.2 1.0 O A:ILE201 4.7 34.4 1.0 CG1 A:ILE236 4.8 22.3 1.0 CA A:ASN104 4.8 25.3 1.0 C A:ASN104 4.8 24.7 1.0 CB A:ASN200 4.8 31.9 1.0 CG A:ASN183 5.0 28.7 1.0 CD A:PRO237 5.0 27.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of AMYK38 with Lithium Ion


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 AMYK38 with Lithium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:37.8 occ:1.00 O A:GLY300 2.2 25.0 1.0 OD1 A:ASP404 2.3 22.4 1.0 O A:TYR302 2.4 29.9 1.0 O A:TRP403 2.5 30.5 1.0 O A:HOH2018 2.5 14.2 1.0 OD1 A:ASN427 3.1 32.5 1.0 ND2 A:ASN427 3.3 27.4 1.0 C A:GLY300 3.4 26.6 1.0 C A:TRP403 3.4 30.2 1.0 CG A:ASP404 3.5 19.0 1.0 CG A:ASN427 3.6 31.2 1.0 C A:TYR302 3.6 27.2 1.0 CA A:ASP404 3.8 24.4 1.0 N A:ASP404 4.0 26.4 1.0 C A:SER301 4.1 25.4 1.0 N A:MET304 4.2 24.4 1.0 CA A:GLY300 4.2 27.5 1.0 CB A:ASP404 4.2 20.2 1.0 O A:SER301 4.2 27.1 1.0 CA A:ASP303 4.2 26.7 1.0 N A:TYR302 4.3 24.7 1.0 N A:ASP303 4.3 27.6 1.0 CD1 A:TRP403 4.4 43.3 1.0 N A:SER301 4.4 25.0 1.0 CB A:TRP403 4.5 32.5 1.0 OD2 A:ASP404 4.5 18.0 1.0 CA A:TRP403 4.5 30.9 1.0 CA A:TYR302 4.6 25.1 1.0 CA A:SER301 4.6 24.4 1.0 CG A:MET304 4.7 25.6 1.0 C A:ASP303 4.8 25.4 1.0 CG A:TRP403 4.8 39.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of AMYK38 with Lithium Ion


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 AMYK38 with Lithium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:31.3 occ:0.92 OD1 A:ASN289 2.7 29.3 1.0 O A:SER337 2.7 28.6 1.0 O A:ASN289 2.8 25.8 1.0 OD1 A:ASP325 2.8 20.4 1.0 O A:VAL324 3.0 9.4 1.0 CG A:ASN289 3.0 28.2 1.0 ND2 A:ASN289 3.2 24.4 1.0 CG2 A:VAL339 3.5 12.3 1.0 C A:ASN289 3.6 25.9 1.0 CG A:ASP325 3.7 21.1 1.0 C A:SER337 3.9 30.1 1.0 CA A:ASN289 4.0 25.3 1.0 CB A:TYR293 4.0 20.8 1.0 CB A:ASN289 4.1 26.3 1.0 OG A:SER337 4.1 34.1 1.0 OD2 A:ASP325 4.1 22.6 1.0 C A:VAL324 4.2 13.1 1.0 CB A:SER337 4.2 32.4 1.0 N A:TYR293 4.3 21.6 1.0 CA A:TYR293 4.5 21.2 1.0 N A:VAL339 4.5 21.0 1.0 CB A:PHE292 4.7 13.3 1.0 N A:TYR290 4.7 24.6 1.0 CA A:SER337 4.7 33.3 1.0 CB A:VAL339 4.8 18.8 1.0 N A:TRP338 4.8 26.7 1.0 CG A:TYR293 4.9 21.9 1.0 CD1 A:TYR293 4.9 20.6 1.0 CA A:ASP325 4.9 18.9 1.0 C A:TRP338 4.9 23.3 1.0 CB A:ASP325 4.9 17.1 1.0 CA A:TRP338 5.0 22.5 1.0

T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki. Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) and Its Sodium Ion Binding Sites J.Biol.Chem. V. 278 24818 2003.
ISSN: ISSN 0021-9258
PubMed: 12719434
DOI: 10.1074/JBC.M212763200