Calcium in PDB 2dcj: A Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1

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

The structure of A Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1, PDB code: 2dcj was solved by 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)	49.39 / 2.24
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.927, 122.927, 331.943, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 19.1

The binding sites of Calcium atom in the A Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 (pdb code 2dcj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1, PDB code: 2dcj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the A Two-Domain 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 Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:50.2 occ:1.00 OD1 A:ASP322 2.5 30.9 1.0 O A:ASP322 2.5 27.7 1.0 O A:ASN232 2.5 33.0 1.0 OE1 A:GLU213 2.5 39.1 1.0 OE2 A:GLU215 2.6 33.8 1.0 O A:HOH3145 2.9 39.6 1.0 OE1 A:GLU215 3.1 35.2 1.0 CD A:GLU215 3.2 35.6 1.0 C A:ASP322 3.2 28.5 1.0 C A:ASN232 3.5 33.3 1.0 CG A:ASP322 3.6 27.9 1.0 CA A:ASP322 3.7 26.8 1.0 CD A:GLU213 3.7 37.7 1.0 CA A:GLY233 3.9 31.4 1.0 N A:ALA214 4.1 32.1 1.0 CB A:GLU213 4.1 33.6 1.0 N A:GLY233 4.1 32.8 1.0 O2 A:GOL3005 4.2 68.1 1.0 CB A:ASP322 4.2 26.5 1.0 N A:TYR323 4.3 29.0 1.0 CA A:GLU213 4.3 33.4 1.0 CG A:GLU213 4.4 34.2 1.0 CB A:ASN232 4.5 37.8 1.0 CA A:ASN232 4.5 35.9 1.0 OD2 A:ASP322 4.6 29.6 1.0 OE2 A:GLU213 4.6 42.7 1.0 C A:GLU213 4.6 32.5 1.0 CB A:TYR323 4.6 28.7 1.0 CG A:GLU215 4.7 35.5 1.0 CA A:TYR323 4.7 28.8 1.0 N A:GLU215 4.8 32.1 1.0 O A:LEU321 4.9 26.1 1.0 N A:ASP322 4.9 25.8 1.0 C3 A:GOL3005 4.9 65.5 1.0 CB A:ALA214 5.0 32.2 1.0 N A:ASN232 5.0 35.2 1.0

Calcium binding site 2 out of 4 in the A Two-Domain 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 Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:55.3 occ:1.00 O A:TYR237 2.3 33.1 1.0 OD1 A:ASP313 2.3 32.5 1.0 O A:TRP317 2.3 27.1 1.0 OD2 A:ASP318 2.5 31.0 1.0 O A:HOH3159 2.7 35.2 1.0 O A:HOH3425 2.7 47.9 1.0 CG A:ASP313 3.3 32.5 1.0 C A:TYR237 3.3 32.5 1.0 C A:TRP317 3.3 27.2 1.0 CG A:ASP318 3.7 27.2 1.0 CA A:TYR237 3.7 31.3 1.0 OD2 A:ASP313 3.7 34.7 1.0 CA A:ASP318 3.8 26.3 1.0 O A:HOH3161 3.9 44.5 1.0 N A:ASP318 3.9 27.0 1.0 O2 A:GOL3006 3.9 68.8 1.0 O A:HOH3083 4.0 30.6 1.0 CB A:ASP313 4.2 30.3 1.0 CB A:ASP318 4.3 26.4 1.0 N A:ALA238 4.4 32.6 1.0 N A:TRP317 4.5 28.2 1.0 CB A:TYR237 4.5 31.4 1.0 CA A:TRP317 4.6 26.7 1.0 O A:LEU236 4.6 32.9 1.0 OD1 A:ASP318 4.7 31.1 1.0 CA A:GLY315 4.7 32.8 1.0 N A:GLY315 4.8 32.9 1.0 CA A:ALA238 4.8 32.9 1.0 N A:TYR237 4.9 31.6 1.0 CE3 A:TRP317 4.9 27.9 1.0 C2 A:GOL3006 5.0 69.5 1.0

Calcium binding site 3 out of 4 in the A Two-Domain 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 3 of A Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:57.5 occ:1.00 O B:ASP322 2.5 30.3 1.0 OD1 B:ASP322 2.5 33.7 1.0 O B:ASN232 2.5 33.3 1.0 OE1 B:GLU213 2.6 42.2 1.0 OE1 B:GLU215 2.7 40.7 1.0 O B:HOH3377 2.9 49.9 1.0 OE2 B:GLU215 3.1 37.8 1.0 C B:ASP322 3.2 31.1 1.0 CD B:GLU215 3.3 39.8 1.0 C B:ASN232 3.6 34.6 1.0 CA B:ASP322 3.6 30.2 1.0 CG B:ASP322 3.7 31.7 1.0 O3 B:GOL3012 3.7 79.2 1.0 CD B:GLU213 3.8 39.5 1.0 CB B:GLU213 4.0 36.9 1.0 CA B:GLY233 4.0 33.5 1.0 N B:ALA214 4.1 35.1 1.0 N B:TYR323 4.2 31.8 1.0 N B:GLY233 4.2 34.5 1.0 CA B:GLU213 4.2 36.2 1.0 CB B:ASP322 4.3 30.6 1.0 C3 B:GOL3012 4.3 79.4 1.0 CG B:GLU213 4.4 37.7 1.0 CB B:ASN232 4.5 38.8 1.0 CA B:ASN232 4.6 36.5 1.0 C B:GLU213 4.6 35.2 1.0 CB B:TYR323 4.6 30.9 1.0 OD2 B:ASP322 4.6 31.8 1.0 CA B:TYR323 4.7 31.4 1.0 OE2 B:GLU213 4.8 44.1 1.0 CG B:GLU215 4.8 38.0 1.0 N B:GLU215 4.9 38.3 1.0 N B:ASP322 4.9 28.9 1.0 O B:LEU321 4.9 28.9 1.0

Calcium binding site 4 out of 4 in the A Two-Domain 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 4 of A Two-Domain Structure of Alkaliphilic Xynj From Bacillus Sp. 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:54.0 occ:1.00 OD1 B:ASP313 2.3 29.9 1.0 O B:TRP317 2.3 28.8 1.0 O B:TYR237 2.5 32.0 1.0 OD1 B:ASP318 2.5 29.9 1.0 O B:HOH3190 2.5 47.6 1.0 O B:HOH3059 2.7 30.8 1.0 CG B:ASP313 3.2 32.5 1.0 C B:TYR237 3.3 30.3 1.0 C B:TRP317 3.4 27.1 1.0 CG B:ASP318 3.7 28.4 1.0 CA B:TYR237 3.7 29.9 1.0 CA B:ASP318 3.8 26.4 1.0 OD2 B:ASP313 3.8 30.2 1.0 N B:ASP318 3.9 25.2 1.0 O B:HOH3062 3.9 29.4 1.0 O B:HOH3164 4.0 45.9 1.0 CB B:ASP313 4.1 29.8 1.0 CB B:ASP318 4.2 27.5 1.0 O B:HOH3338 4.3 63.1 1.0 N B:ALA238 4.4 30.8 1.0 O B:HOH3403 4.5 62.6 1.0 N B:TRP317 4.5 26.9 1.0 CA B:TRP317 4.6 26.2 1.0 O B:LEU236 4.6 31.9 1.0 CB B:TYR237 4.6 30.6 1.0 OD2 B:ASP318 4.7 32.5 1.0 N B:GLY315 4.8 31.6 1.0 CE3 B:TRP317 4.8 27.4 1.0 CA B:GLY315 4.8 30.7 1.0 CA B:ALA238 4.8 30.4 1.0 N B:TYR237 4.9 29.2 1.0

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