Calcium in PDB 5xqj: Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose

The structure of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose, PDB code: 5xqj was solved by Y.Kunishige, M.Iwai, T.Tada, S.Nishimura, T.Sakamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	171.17 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	167.616, 171.800, 342.337, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.2

The binding sites of Calcium atom in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose (pdb code 5xqj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose, PDB code: 5xqj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:15.1 occ:1.00 OD2 A:ASP562 2.0 27.3 1.0 OD2 A:ASP621 2.1 20.3 1.0 OD1 A:ASP621 2.2 21.3 1.0 NE2 A:HIS616 2.2 25.1 1.0 ND2 A:ASN585 2.3 25.8 1.0 ND1 A:HIS639 2.3 25.1 1.0 CG A:ASP621 2.5 21.7 1.0 CE1 A:HIS639 2.9 26.1 1.0 CD2 A:HIS616 3.1 25.7 1.0 CG A:ASP562 3.2 27.5 1.0 CG A:ASN585 3.2 26.6 1.0 CE1 A:HIS616 3.3 27.6 1.0 CG A:HIS639 3.4 26.1 1.0 OD1 A:ASN585 3.7 26.7 1.0 CB A:HIS639 3.9 24.1 1.0 CB A:ASP562 3.9 25.9 1.0 CB A:ASP621 4.0 22.3 1.0 NE2 A:HIS639 4.1 26.7 1.0 OD1 A:ASP562 4.1 26.5 1.0 CA A:ASN585 4.1 26.0 1.0 CB A:ASN585 4.2 26.7 1.0 CG A:HIS616 4.3 25.1 1.0 N A:ASN585 4.3 25.5 1.0 CD2 A:HIS639 4.3 27.6 1.0 ND1 A:HIS616 4.3 28.8 1.0 CB A:TRP583 4.3 26.4 1.0 CA A:HIS639 4.6 24.7 1.0 CA A:ASP621 4.9 23.2 1.0 CG A:TRP583 4.9 28.2 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:16.7 occ:1.00 OD2 B:ASP562 2.0 30.5 1.0 OD1 B:ASP621 2.1 24.6 1.0 OD2 B:ASP621 2.1 22.7 1.0 ND1 B:HIS639 2.4 26.5 1.0 ND2 B:ASN585 2.4 27.9 1.0 CG B:ASP621 2.4 24.2 1.0 NE2 B:HIS616 2.4 23.5 1.0 CE1 B:HIS639 3.1 27.2 1.0 CG B:ASN585 3.2 26.8 1.0 CD2 B:HIS616 3.2 25.6 1.0 CG B:ASP562 3.2 27.7 1.0 CG B:HIS639 3.5 24.6 1.0 CE1 B:HIS616 3.5 25.9 1.0 OD1 B:ASN585 3.7 27.4 1.0 CB B:HIS639 3.9 23.2 1.0 CB B:ASP621 3.9 24.8 1.0 CB B:ASP562 4.0 25.4 1.0 CA B:ASN585 4.0 24.8 1.0 OD1 B:ASP562 4.1 30.6 1.0 CB B:ASN585 4.2 26.5 1.0 N B:ASN585 4.2 23.8 1.0 CB B:TRP583 4.3 31.7 1.0 NE2 B:HIS639 4.3 26.6 1.0 CG B:HIS616 4.4 25.4 1.0 CD2 B:HIS639 4.5 26.4 1.0 CA B:HIS639 4.5 23.8 1.0 ND1 B:HIS616 4.6 26.5 1.0 CA B:ASP621 4.8 24.3 1.0 CG B:TRP583 4.9 31.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1004 b:16.9 occ:1.00 OD2 C:ASP562 2.0 31.0 1.0 OD1 C:ASP621 2.1 32.7 1.0 ND1 C:HIS639 2.2 27.4 1.0 OD2 C:ASP621 2.2 27.1 1.0 ND2 C:ASN585 2.2 33.7 1.0 NE2 C:HIS616 2.3 29.1 1.0 CG C:ASP621 2.5 28.5 1.0 CE1 C:HIS639 2.9 27.4 1.0 CG C:ASN585 3.1 32.6 1.0 CD2 C:HIS616 3.1 30.3 1.0 CG C:ASP562 3.2 31.2 1.0 CG C:HIS639 3.3 27.2 1.0 CE1 C:HIS616 3.4 31.0 1.0 OD1 C:ASN585 3.5 34.2 1.0 CB C:HIS639 3.9 26.8 1.0 CB C:ASP621 4.0 27.5 1.0 CB C:ASP562 4.0 30.9 1.0 NE2 C:HIS639 4.1 27.2 1.0 CA C:ASN585 4.1 30.9 1.0 CB C:ASN585 4.1 30.6 1.0 OD1 C:ASP562 4.2 29.9 1.0 CB C:TRP583 4.3 31.6 1.0 N C:ASN585 4.3 32.1 1.0 CD2 C:HIS639 4.3 26.6 1.0 CG C:HIS616 4.4 28.9 1.0 ND1 C:HIS616 4.4 30.9 1.0 CA C:HIS639 4.5 27.9 1.0 CA C:ASP621 4.8 28.6 1.0 CG C:TRP583 4.9 33.5 1.0 N C:ASP621 4.9 29.3 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1003 b:24.1 occ:1.00 OD2 D:ASP562 2.1 29.7 1.0 OD2 D:ASP621 2.1 28.5 1.0 OD1 D:ASP621 2.2 33.3 1.0 ND2 D:ASN585 2.2 35.0 1.0 NE2 D:HIS616 2.2 25.0 1.0 ND1 D:HIS639 2.3 38.7 1.0 CG D:ASP621 2.5 32.3 1.0 CD2 D:HIS616 3.1 25.8 1.0 CG D:ASN585 3.1 35.0 1.0 CE1 D:HIS639 3.2 39.5 1.0 CG D:ASP562 3.2 30.4 1.0 CE1 D:HIS616 3.3 27.1 1.0 CG D:HIS639 3.4 36.3 1.0 OD1 D:ASN585 3.7 36.7 1.0 CB D:HIS639 3.7 33.9 1.0 CB D:ASP562 3.9 31.2 1.0 CB D:ASP621 4.0 31.9 1.0 OD1 D:ASP562 4.2 30.3 1.0 CA D:ASN585 4.2 33.3 1.0 CB D:ASN585 4.2 32.7 1.0 CG D:HIS616 4.3 26.2 1.0 NE2 D:HIS639 4.3 39.0 1.0 CB D:TRP583 4.3 28.3 1.0 ND1 D:HIS616 4.4 26.5 1.0 N D:ASN585 4.4 33.9 1.0 CD2 D:HIS639 4.4 39.5 1.0 CA D:HIS639 4.5 31.8 1.0 CA D:ASP621 4.8 32.5 1.0 CG D:TRP583 4.9 29.3 1.0 N D:ASP621 4.9 33.1 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1004 b:20.0 occ:1.00 OD1 E:ASP621 2.1 31.0 1.0 OD2 E:ASP562 2.1 27.7 1.0 ND1 E:HIS639 2.2 26.1 1.0 ND2 E:ASN585 2.2 28.9 1.0 OD2 E:ASP621 2.3 34.5 1.0 NE2 E:HIS616 2.3 25.0 1.0 CG E:ASP621 2.5 29.9 1.0 CE1 E:HIS639 2.9 28.0 1.0 CG E:ASN585 3.0 31.5 1.0 CD2 E:HIS616 3.3 26.2 1.0 CE1 E:HIS616 3.3 26.2 1.0 CG E:ASP562 3.3 27.7 1.0 CG E:HIS639 3.3 28.9 1.0 OD1 E:ASN585 3.5 34.9 1.0 CB E:HIS639 3.8 27.6 1.0 CB E:ASP621 4.0 28.2 1.0 CB E:ASP562 4.0 27.3 1.0 NE2 E:HIS639 4.1 28.6 1.0 OD1 E:ASP562 4.2 30.7 1.0 CB E:ASN585 4.2 31.4 1.0 CA E:ASN585 4.3 29.0 1.0 CD2 E:HIS639 4.3 29.7 1.0 CB E:TRP583 4.3 24.0 1.0 ND1 E:HIS616 4.4 26.1 1.0 CG E:HIS616 4.4 26.2 1.0 N E:ASN585 4.5 27.8 1.0 CA E:HIS639 4.5 26.7 1.0 OG1 E:THR617 4.8 38.1 1.0 CA E:ASP621 4.8 27.5 1.0 CG E:TRP583 4.9 24.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1004 b:20.0 occ:1.00 OD2 F:ASP562 2.0 31.7 1.0 OD1 F:ASP621 2.1 25.8 1.0 OD2 F:ASP621 2.2 25.6 1.0 ND2 F:ASN585 2.2 25.1 1.0 ND1 F:HIS639 2.3 24.9 1.0 NE2 F:HIS616 2.3 26.1 1.0 CG F:ASP621 2.5 25.6 1.0 CE1 F:HIS639 3.0 26.3 1.0 CG F:ASN585 3.1 26.1 1.0 CD2 F:HIS616 3.2 25.3 1.0 CG F:ASP562 3.2 27.9 1.0 CE1 F:HIS616 3.3 30.3 1.0 CG F:HIS639 3.4 27.0 1.0 OD1 F:ASN585 3.6 30.7 1.0 CB F:HIS639 3.9 26.4 1.0 CB F:ASP562 4.0 27.9 1.0 OD1 F:ASP562 4.0 29.2 1.0 CB F:ASP621 4.1 26.2 1.0 NE2 F:HIS639 4.1 27.0 1.0 CA F:ASN585 4.2 26.0 1.0 CB F:ASN585 4.3 26.2 1.0 CB F:TRP583 4.3 24.5 1.0 CG F:HIS616 4.4 26.3 1.0 CD2 F:HIS639 4.4 27.3 1.0 ND1 F:HIS616 4.4 28.7 1.0 N F:ASN585 4.4 26.2 1.0 CA F:HIS639 4.5 28.1 1.0 CG F:TRP583 4.8 24.8 1.0 CA F:ASP621 4.9 26.4 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1004 b:23.8 occ:1.00 OD2 G:ASP562 2.0 27.9 1.0 OD1 G:ASP621 2.0 27.5 1.0 ND1 G:HIS639 2.3 30.9 1.0 ND2 G:ASN585 2.3 42.6 1.0 OD2 G:ASP621 2.4 24.8 1.0 NE2 G:HIS616 2.4 34.4 1.0 CG G:ASP621 2.5 28.0 1.0 CE1 G:HIS639 3.1 30.9 1.0 CG G:ASP562 3.1 30.6 1.0 CG G:ASN585 3.2 39.0 1.0 CG G:HIS639 3.2 34.0 1.0 CE1 G:HIS616 3.3 35.5 1.0 CD2 G:HIS616 3.4 33.9 1.0 CB G:HIS639 3.6 35.2 1.0 OD1 G:ASN585 3.6 37.6 1.0 CB G:ASP562 3.9 30.1 1.0 CB G:ASP621 4.0 29.2 1.0 OD1 G:ASP562 4.1 29.6 1.0 NE2 G:HIS639 4.2 30.6 1.0 CD2 G:HIS639 4.3 32.6 1.0 CB G:TRP583 4.3 31.8 1.0 CB G:ASN585 4.4 36.1 1.0 CA G:HIS639 4.4 35.6 1.0 CA G:ASN585 4.4 36.5 1.0 ND1 G:HIS616 4.5 35.0 1.0 N G:ASN585 4.5 35.2 1.0 CG G:HIS616 4.5 33.9 1.0 CA G:ASP621 4.8 31.1 1.0 CG G:TRP583 4.8 31.2 1.0 N G:ASP621 4.9 30.1 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose Substituted with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca1003 b:22.8 occ:1.00 OD1 H:ASP621 2.1 34.8 1.0 OD2 H:ASP562 2.1 34.0 1.0 ND1 H:HIS639 2.3 29.3 1.0 ND2 H:ASN585 2.3 37.0 1.0 NE2 H:HIS616 2.4 33.2 1.0 OD2 H:ASP621 2.4 29.4 1.0 CG H:ASP621 2.6 33.2 1.0 CE1 H:HIS639 3.0 28.8 1.0 CD2 H:HIS616 3.0 31.7 1.0 CG H:ASP562 3.2 35.5 1.0 CG H:ASN585 3.2 36.2 1.0 CG H:HIS639 3.4 32.0 1.0 CE1 H:HIS616 3.5 34.3 1.0 OD1 H:ASN585 3.7 38.0 1.0 CB H:ASP562 3.8 33.7 1.0 CB H:HIS639 3.9 33.5 1.0 CB H:ASP621 4.1 32.2 1.0 NE2 H:HIS639 4.1 30.3 1.0 OD1 H:ASP562 4.2 35.0 1.0 CA H:ASN585 4.3 34.8 1.0 CG H:HIS616 4.3 32.5 1.0 CB H:ASN585 4.3 35.2 1.0 CD2 H:HIS639 4.3 31.8 1.0 N H:ASN585 4.3 35.6 1.0 CB H:TRP583 4.4 31.9 1.0 ND1 H:HIS616 4.5 34.4 1.0 CA H:HIS639 4.6 33.1 1.0 CA H:ASP621 4.9 33.1 1.0 CG H:TRP583 4.9 30.8 1.0

Y.Kunishige, M.Iwai, M.Nakazawa, M.Ueda, T.Tada, S.Nishimura, T.Sakamoto. Crystal Structure of Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum As A Member of Polysaccharide Lyase Family 26 Febs Lett. V. 592 1378 2018.
ISSN: ISSN 1873-3468
PubMed: 29574769
DOI: 10.1002/1873-3468.13034