Calcium in PDB 5xqo: Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Tetrameric Substrate

The structure of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Tetrameric Substrate, PDB code: 5xqo 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)	119.58 / 3.20
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	166.437, 166.437, 171.932, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 26.4

The binding sites of Calcium atom in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Tetrameric Substrate (pdb code 5xqo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Tetrameric Substrate, PDB code: 5xqo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Tetrameric Substrate


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 Tetrameric Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:44.8 occ:1.00 OD2 A:ASP562 2.0 71.1 1.0 OD2 A:ASP621 2.2 83.1 1.0 NE2 A:HIS616 2.5 69.5 1.0 ND1 A:HIS639 2.5 79.9 1.0 OD1 A:ASP621 2.6 74.7 1.0 ND2 A:ASN585 2.7 87.2 1.0 CG A:ASP621 2.8 81.8 1.0 CE1 A:HIS639 3.0 78.2 1.0 CG A:ASN585 3.2 81.5 1.0 CD2 A:HIS616 3.2 67.5 1.0 CG A:ASP562 3.2 76.4 1.0 CE1 A:HIS616 3.5 70.5 1.0 CG A:HIS639 3.5 80.7 1.0 OD1 A:ASN585 3.6 76.9 1.0 CA A:ASN585 4.0 81.5 1.0 CB A:ASP562 4.0 76.3 1.0 CB A:HIS639 4.0 75.4 1.0 N A:ASN585 4.1 76.8 1.0 NE2 A:HIS639 4.1 80.2 1.0 OD1 A:ASP562 4.1 80.2 1.0 CB A:ASN585 4.2 84.2 1.0 CB A:ASP621 4.3 80.1 1.0 CB A:TRP583 4.3 69.6 1.0 CD2 A:HIS639 4.4 87.8 1.0 CG A:HIS616 4.4 69.0 1.0 ND1 A:HIS616 4.5 72.1 1.0 CA A:HIS639 4.7 72.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Tetrameric Substrate


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 Tetrameric Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:57.2 occ:1.00 OD1 B:ASP621 2.0 85.0 1.0 OD1 B:ASN585 2.3 95.8 1.0 OD2 B:ASP562 2.3 88.4 1.0 ND1 B:HIS639 2.3 80.0 1.0 OD2 B:ASP621 2.4 84.0 1.0 NE2 B:HIS616 2.4 82.8 1.0 CG B:ASP621 2.5 93.6 1.0 CE1 B:HIS639 3.1 77.4 1.0 CG B:ASN585 3.1 88.9 1.0 CD2 B:HIS616 3.3 79.9 1.0 CG B:HIS639 3.3 84.2 1.0 CE1 B:HIS616 3.3 84.0 1.0 CG B:ASP562 3.4 92.3 1.0 ND2 B:ASN585 3.7 86.5 1.0 CB B:HIS639 3.8 89.5 1.0 CB B:ASP621 4.0 95.0 1.0 CB B:ASN585 4.1 79.9 1.0 CA B:ASN585 4.1 77.0 1.0 NE2 B:HIS639 4.1 79.0 1.0 CB B:ASP562 4.2 91.0 1.0 CG2 B:VAL620 4.3 85.6 1.0 CD2 B:HIS639 4.3 82.8 1.0 N B:ASN585 4.3 71.9 1.0 OD1 B:ASP562 4.4 91.0 1.0 ND1 B:HIS616 4.4 86.2 1.0 CG B:HIS616 4.4 84.3 1.0 CA B:HIS639 4.5 88.5 1.0 CB B:TRP583 4.5 74.0 1.0 CA B:ASP621 4.8 92.6 1.0 N B:ASP621 4.9 84.1 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