Potassium in PDB 1ud6: Crystal Structure of AMYK38 with Potassium Ion

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

The structure of Crystal Structure of AMYK38 with Potassium Ion, PDB code: 1ud6 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)	44.18 / 2.50
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	132.525, 132.525, 132.525, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25

The binding sites of Potassium atom in the Crystal Structure of AMYK38 with Potassium Ion (pdb code 1ud6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of AMYK38 with Potassium Ion, PDB code: 1ud6:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of AMYK38 with Potassium Ion


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of AMYK38 with Potassium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:K1001 b:42.0 occ:1.00 O A:ASP194 2.4 22.4 1.0 O A:HIS235 2.4 25.4 1.0 OD1 A:ASP194 2.5 22.6 1.0 O A:HOH2014 2.5 19.7 1.0 OD1 A:ASN104 2.7 18.2 1.0 OD1 A:ASN200 2.7 28.3 1.0 C A:ASP194 3.2 22.9 1.0 ND2 A:ASN200 3.3 25.6 1.0 C A:HIS235 3.4 23.6 1.0 CG A:ASN200 3.4 26.7 1.0 CG A:ASP194 3.5 23.5 1.0 CA A:ASP194 3.6 23.5 1.0 CG A:ASN104 3.7 18.4 1.0 CB A:HIS235 3.9 24.1 1.0 ND2 A:ASN183 4.1 23.1 1.0 CB A:ASP194 4.1 24.1 1.0 CA A:HIS235 4.1 23.5 1.0 ND2 A:ASN104 4.2 16.6 1.0 N A:ILE236 4.2 22.1 1.0 OD2 A:ASP194 4.3 26.2 1.0 O A:ASN104 4.4 19.7 1.0 N A:TYR195 4.4 21.8 1.0 CA A:ILE236 4.4 21.8 1.0 O A:HOH2025 4.5 23.3 1.0 O A:ILE201 4.8 24.5 1.0 CA A:TYR195 4.8 21.4 1.0 CB A:ASN200 4.9 24.1 1.0 O A:TYR193 4.9 30.2 1.0 CB A:ASN104 5.0 18.1 1.0 N A:ASP194 5.0 26.8 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of AMYK38 with Potassium Ion


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of AMYK38 with Potassium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:K1002 b:30.6 occ:1.00 O A:GLY300 2.5 25.6 1.0 O A:TYR302 2.6 28.2 1.0 OD1 A:ASP404 2.6 28.8 1.0 O A:HOH2110 2.6 20.0 1.0 O A:TRP403 2.9 33.1 1.0 OD1 A:ASN427 3.1 26.1 1.0 C A:GLY300 3.6 25.6 1.0 C A:TRP403 3.6 32.5 1.0 ND2 A:ASN427 3.6 21.9 1.0 C A:TYR302 3.6 28.7 1.0 CG A:ASN427 3.7 23.7 1.0 CG A:ASP404 3.8 27.4 1.0 CA A:ASP404 3.8 27.7 1.0 O A:HOH2064 3.9 35.0 1.0 N A:ASP404 4.0 30.0 1.0 N A:TYR302 4.2 26.9 1.0 C A:SER301 4.2 28.0 1.0 CB A:ASP404 4.4 26.9 1.0 CA A:GLY300 4.4 24.9 1.0 CD1 A:TRP403 4.4 40.1 1.0 N A:ASP303 4.4 29.5 1.0 CA A:ASP303 4.4 28.2 1.0 CB A:TRP403 4.5 35.1 1.0 N A:MET304 4.5 26.0 1.0 N A:SER301 4.5 27.0 1.0 CA A:TYR302 4.6 27.5 1.0 CA A:SER301 4.6 27.5 1.0 O A:SER301 4.6 29.7 1.0 CA A:TRP403 4.6 33.0 1.0 OD2 A:ASP404 4.8 28.4 1.0 CG A:MET304 4.9 24.3 1.0 CG A:TRP403 4.9 38.3 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of AMYK38 with Potassium Ion


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of AMYK38 with Potassium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:K1003 b:20.1 occ:1.00 O A:SER337 2.5 21.1 1.0 O A:VAL324 2.6 12.4 1.0 OD1 A:ASP325 2.6 20.8 1.0 OD1 A:ASN289 2.7 22.4 1.0 CG2 A:VAL339 3.3 14.5 1.0 CG A:ASP325 3.3 19.3 1.0 O A:ASN289 3.4 20.2 1.0 CG A:ASN289 3.4 20.6 1.0 C A:SER337 3.7 21.7 1.0 OD2 A:ASP325 3.7 16.9 1.0 ND2 A:ASN289 3.8 17.0 1.0 C A:VAL324 3.8 14.9 1.0 OG A:SER337 4.1 20.5 1.0 N A:VAL339 4.2 16.2 1.0 C A:ASN289 4.2 19.6 1.0 CA A:ASP325 4.3 17.6 1.0 CB A:ASP325 4.4 16.3 1.0 OG1 A:THR329 4.4 24.2 1.0 CB A:SER337 4.4 21.8 1.0 CB A:THR329 4.5 20.9 1.0 N A:ASP325 4.5 16.2 1.0 N A:TRP338 4.5 19.1 1.0 CB A:VAL339 4.5 15.4 1.0 CA A:TRP338 4.5 18.3 1.0 CB A:ASN289 4.6 20.0 1.0 CB A:TYR293 4.6 18.7 1.0 CA A:ASN289 4.6 20.2 1.0 C A:TRP338 4.7 17.6 1.0 CG2 A:THR329 4.7 20.9 1.0 CA A:SER337 4.7 23.1 1.0 N A:TYR293 4.8 19.7 1.0 CA A:VAL324 4.9 15.3 1.0 CA A:VAL339 4.9 15.2 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of AMYK38 with Potassium Ion


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of AMYK38 with Potassium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:K1004 b:26.3 occ:1.00 OD1 A:ASN452 2.6 20.9 1.0 O A:HOH2009 2.7 6.5 1.0 O A:HOH2165 3.4 19.7 1.0 CG A:ASN452 3.7 21.4 1.0 O A:HOH2183 4.1 28.5 1.0 ND2 A:ASN452 4.4 19.1 1.0 CB A:ASN452 4.7 20.7 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