Calcium in PDB 6kjl: Xylanase J From Bacillus Sp. Strain 41M-1

All present enzymatic activity of Xylanase J From Bacillus Sp. Strain 41M-1:
3.2.1.8;

The structure of Xylanase J From Bacillus Sp. Strain 41M-1, PDB code: 6kjl was solved by S.Manami, T.Teisuke, K.Nakatani, K.Katano, K.Kojima, N.Saka, B.Mikami, R.Yatsunami, S.Nakamura, K.Yasukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.45
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	125.940, 125.940, 318.570, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.8

The binding sites of Calcium atom in the Xylanase J From Bacillus Sp. Strain 41M-1 (pdb code 6kjl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Xylanase J From Bacillus Sp. Strain 41M-1, PDB code: 6kjl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Xylanase J From Bacillus Sp. Strain 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xylanase J From Bacillus Sp. Strain 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:45.4 occ:1.00 OD1 A:ASP322 2.3 45.1 1.0 OE2 A:GLU213 2.3 44.7 1.0 O A:ASN232 2.4 40.9 1.0 O A:HOH608 2.5 48.0 1.0 OE1 A:GLU215 2.6 46.6 1.0 OE2 A:GLU215 2.6 42.5 1.0 O A:ASP322 2.7 43.8 1.0 CD A:GLU215 2.9 48.4 1.0 C A:ASP322 3.4 40.6 1.0 C A:ASN232 3.4 44.7 1.0 CG A:ASP322 3.5 38.2 1.0 CD A:GLU213 3.5 43.5 1.0 CA A:ASP322 3.9 36.4 1.0 CB A:GLU213 4.0 39.3 1.0 CB A:ASN232 4.1 47.1 1.0 N A:GLY233 4.3 40.9 1.0 CA A:GLY233 4.3 37.1 1.0 CB A:ASP322 4.3 35.7 1.0 CA A:ASN232 4.3 41.5 1.0 CG A:GLU213 4.3 37.9 1.0 OD2 A:ASP322 4.4 42.2 1.0 N A:TYR323 4.4 37.5 1.0 N A:ALA214 4.4 36.8 1.0 CG A:GLU215 4.5 34.9 1.0 OE1 A:GLU213 4.5 44.2 1.0 CA A:GLU213 4.5 44.5 1.0 CB A:TYR323 4.6 42.8 1.0 N A:ASN232 4.8 42.0 1.0 CA A:TYR323 4.9 43.4 1.0 C A:GLU213 4.9 42.6 1.0 O A:HOH590 4.9 49.1 1.0 N A:GLU215 4.9 36.2 1.0

Calcium binding site 2 out of 4 in the Xylanase J From Bacillus Sp. Strain 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xylanase J From Bacillus Sp. Strain 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:70.4 occ:1.00 O A:TYR237 2.3 55.2 1.0 OD1 A:ASP313 2.3 49.0 1.0 O A:TRP317 2.5 46.6 1.0 OD1 A:ASP318 2.6 51.4 1.0 C5 A:MPD406 3.0 65.6 1.0 CG A:ASP313 3.2 51.4 1.0 C A:TYR237 3.3 45.5 1.0 C A:TRP317 3.5 42.8 1.0 OD2 A:ASP313 3.7 48.3 1.0 CG A:ASP318 3.8 50.3 1.0 CA A:TYR237 3.8 45.2 1.0 O A:HOH555 3.8 73.0 1.0 CA A:ASP318 4.0 44.2 1.0 N A:ASP318 4.1 37.2 1.0 O A:HOH540 4.1 44.8 1.0 CB A:ASP313 4.1 48.1 1.0 C4 A:MPD406 4.2 78.5 1.0 CB A:ASP318 4.4 41.1 1.0 C3 A:MPD406 4.4 62.5 1.0 N A:ALA238 4.5 48.5 1.0 N A:TRP317 4.5 43.7 1.0 CB A:TYR237 4.5 49.0 1.0 CA A:GLY315 4.6 49.1 1.0 N A:GLY315 4.6 48.8 1.0 O4 A:MPD406 4.6 85.2 1.0 CA A:TRP317 4.7 45.7 1.0 O A:LEU236 4.7 43.4 1.0 OD2 A:ASP318 4.8 51.3 1.0 CA A:ALA238 4.9 48.2 1.0 C A:GLY315 5.0 58.1 1.0

Calcium binding site 3 out of 4 in the Xylanase J From Bacillus Sp. Strain 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xylanase J From Bacillus Sp. Strain 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:73.7 occ:1.00 O B:TYR237 2.3 55.9 1.0 OD1 B:ASP313 2.4 46.6 1.0 OD1 B:ASP318 2.4 43.6 1.0 O B:TRP317 2.4 43.1 1.0 O B:HOH624 3.2 57.7 1.0 C B:TRP317 3.4 40.4 1.0 CG B:ASP313 3.4 48.3 1.0 C B:TYR237 3.4 41.0 1.0 CG B:ASP318 3.6 43.8 1.0 O B:HOH630 3.6 46.2 1.0 CA B:ASP318 3.9 37.7 1.0 OD2 B:ASP313 3.9 48.4 1.0 N B:ASP318 3.9 34.6 1.0 CA B:TYR237 3.9 39.8 1.0 O B:HOH511 4.0 42.1 1.0 CB B:ASP318 4.2 40.1 1.0 N B:TRP317 4.4 34.9 1.0 CB B:ASP313 4.4 42.2 1.0 CA B:TRP317 4.5 41.4 1.0 CA B:GLY315 4.5 43.2 1.0 OD2 B:ASP318 4.6 50.9 1.0 N B:ALA238 4.6 40.9 1.0 N B:GLY315 4.6 45.7 1.0 CB B:TYR237 4.6 41.6 1.0 O B:LEU236 4.9 42.7 1.0 CA B:ALA238 4.9 39.7 1.0 C B:GLY315 4.9 46.6 1.0

Calcium binding site 4 out of 4 in the Xylanase J From Bacillus Sp. Strain 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xylanase J From Bacillus Sp. Strain 41M-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:43.3 occ:1.00 OD1 B:ASP322 2.3 39.1 1.0 O B:ASN232 2.3 42.0 1.0 OE2 B:GLU213 2.3 45.0 1.0 O B:HOH606 2.4 47.6 1.0 OE2 B:GLU215 2.5 41.3 1.0 O B:ASP322 2.5 41.1 1.0 OE1 B:GLU215 2.6 45.3 1.0 CD B:GLU215 2.9 44.8 1.0 C B:ASP322 3.3 36.9 1.0 C B:ASN232 3.4 45.5 1.0 CG B:ASP322 3.5 39.2 1.0 CD B:GLU213 3.5 44.6 1.0 CA B:ASP322 3.8 36.8 1.0 CB B:GLU213 4.1 39.4 1.0 CA B:GLY233 4.2 36.2 1.0 N B:GLY233 4.2 37.2 1.0 CB B:ASP322 4.3 37.1 1.0 CG B:GLU213 4.3 33.8 1.0 N B:TYR323 4.4 37.1 1.0 CB B:ASN232 4.4 47.1 1.0 N B:ALA214 4.4 37.5 1.0 CA B:ASN232 4.4 45.6 1.0 OE1 B:GLU213 4.4 48.6 1.0 CG B:GLU215 4.4 31.3 1.0 CA B:GLU213 4.5 38.9 1.0 OD2 B:ASP322 4.5 44.5 1.0 CB B:TYR323 4.6 43.0 1.0 CA B:TYR323 4.8 37.8 1.0 C B:GLU213 4.9 35.8 1.0 N B:ASN232 4.9 44.2 1.0 N B:GLU215 4.9 39.0 1.0

T.Takita, K.Nakatani, Y.Katano, M.Suzuki, K.Kojima, N.Saka, B.Mikami, R.Yatsunami, S.Nakamura, K.Yasukawa. Increase in the Thermostability of GH11 Xylanase Xynj From Bacillus Sp. Strain 41M-1 Using Site Saturation Mutagenesis. Enzyme.Microb.Technol. V. 130 09363 2019.
ISSN: ISSN 0141-0229
PubMed: 31421720
DOI: 10.1016/J.ENZMICTEC.2019.109363