Calcium in PDB 2dck: A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1

All present enzymatic activity of A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1:
3.2.1.8;

The structure of A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1, PDB code: 2dck was solved by G.Fibriansah, Ihsanawati, N.Tanaka, S.Nakamura, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	116.579, 116.579, 45.909, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.8

The binding sites of Calcium atom in the A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 (pdb code 2dck). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1, PDB code: 2dck:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:24.7 occ:1.00 O A:ASN232 2.1 19.6 1.0 OE2 A:GLU213 2.2 31.2 1.0 OD1 A:ASP322 2.4 23.7 1.0 O A:HOH2199 2.4 31.4 1.0 OE1 A:GLU215 2.4 31.7 1.0 OE2 A:GLU215 2.5 29.4 1.0 O A:ASP322 2.7 21.9 1.0 CD A:GLU215 2.9 35.5 1.0 C A:ASN232 3.4 21.8 1.0 C A:ASP322 3.4 23.2 1.0 CD A:GLU213 3.5 32.2 1.0 CG A:ASP322 3.6 24.6 1.0 CA A:ASP322 3.7 22.9 1.0 CA A:GLY233 4.1 22.4 1.0 N A:GLY233 4.2 21.4 1.0 CB A:ASP322 4.2 23.8 1.0 CB A:ASN232 4.3 25.1 1.0 CB A:GLU213 4.3 29.8 1.0 CA A:ASN232 4.3 24.2 1.0 OE1 A:GLU213 4.4 35.8 1.0 CG A:GLU213 4.4 30.2 1.0 CG A:GLU215 4.4 31.1 1.0 N A:TYR323 4.5 23.1 1.0 OD2 A:ASP322 4.5 25.6 1.0 N A:ALA214 4.6 28.1 1.0 O A:HOH2164 4.6 47.9 1.0 CA A:GLU213 4.6 28.8 1.0 N A:ASN232 4.7 23.7 1.0 CB A:TYR323 4.8 23.2 1.0 O A:HOH2088 4.8 31.6 1.0 O A:HOH2158 4.8 40.9 1.0 CA A:TYR323 5.0 24.0 1.0

Calcium binding site 2 out of 2 in the A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Tetragonal-Lattice Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:37.2 occ:1.00 O A:TYR237 2.2 23.5 1.0 OD1 A:ASP313 2.4 28.3 1.0 OD2 A:ASP318 2.4 23.5 1.0 O A:TRP317 2.5 24.8 1.0 O A:HOH2279 2.5 42.0 1.0 O A:HOH2267 2.7 54.2 1.0 O A:HOH2180 2.8 38.1 1.0 CG A:ASP313 3.3 27.4 1.0 C A:TYR237 3.4 23.1 1.0 C A:TRP317 3.5 23.6 1.0 CG A:ASP318 3.6 22.8 1.0 OD2 A:ASP313 3.7 29.0 1.0 CA A:TYR237 3.9 20.9 1.0 CA A:ASP318 4.1 20.7 1.0 N A:ASP318 4.1 22.3 1.0 O A:HOH2005 4.2 20.1 1.0 CB A:ASP318 4.4 21.6 1.0 OD1 A:ASP318 4.4 26.4 1.0 O A:HOH2152 4.4 46.2 1.0 N A:TRP317 4.5 25.7 1.0 CB A:ASP313 4.5 24.6 1.0 CB A:TYR237 4.5 23.6 1.0 N A:ALA238 4.5 23.4 1.0 CA A:TRP317 4.6 24.0 1.0 CA A:GLY315 4.6 29.5 1.0 N A:GLY315 4.7 29.7 1.0 CA A:ALA238 4.9 24.0 1.0 O A:HOH2263 4.9 35.8 1.0 C A:GLY315 5.0 29.5 1.0

Ihsanawati, N.Tanaka, S.Nakamura, T.Kumasaka. A Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 To Be Published.