Calcium in PDB 5xq3: Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum

The structure of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum, PDB code: 5xq3 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)	120.09 / 2.85
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	167.471, 167.471, 172.289, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 23.7

The binding sites of Calcium atom in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum (pdb code 5xq3). 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, PDB code: 5xq3:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:30.3 occ:1.00 OD2 A:ASP562 2.1 49.8 1.0 OD1 A:ASP621 2.2 45.7 1.0 OD2 A:ASP621 2.2 52.1 1.0 NE2 A:HIS616 2.3 42.7 1.0 ND1 A:HIS639 2.3 51.4 1.0 ND2 A:ASN585 2.5 69.0 1.0 CG A:ASP621 2.5 49.4 1.0 CG A:ASN585 2.9 61.7 1.0 CE1 A:HIS639 3.1 54.4 1.0 CD2 A:HIS616 3.2 46.0 1.0 OD1 A:ASN585 3.2 62.9 1.0 CG A:ASP562 3.2 46.5 1.0 CE1 A:HIS616 3.3 50.7 1.0 CG A:HIS639 3.4 49.8 1.0 CB A:HIS639 3.8 51.9 1.0 CA A:ASN585 3.9 60.7 1.0 CB A:ASN585 4.0 64.3 1.0 CB A:ASP621 4.0 46.6 1.0 OD1 A:ASP562 4.1 52.1 1.0 CB A:ASP562 4.1 43.6 1.0 N A:ASN585 4.1 53.2 1.0 NE2 A:HIS639 4.2 54.8 1.0 CB A:TRP583 4.3 51.0 1.0 CG A:HIS616 4.3 49.9 1.0 CD2 A:HIS639 4.4 50.8 1.0 ND1 A:HIS616 4.4 51.3 1.0 CA A:HIS639 4.4 49.8 1.0 CA A:ASP621 4.9 49.1 1.0 CG A:TRP583 4.9 50.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:37.1 occ:1.00 OD1 B:ASN585 2.0 53.6 1.0 OD1 B:ASP621 2.2 49.0 1.0 ND1 B:HIS639 2.2 51.2 1.0 NE2 B:HIS616 2.2 44.0 1.0 OD2 B:ASP562 2.3 58.5 1.0 OD2 B:ASP621 2.3 47.7 1.0 CG B:ASP621 2.6 56.4 1.0 CE1 B:HIS639 3.0 52.1 1.0 CG B:ASN585 3.0 50.8 1.0 CD2 B:HIS616 3.1 45.0 1.0 CG B:HIS639 3.3 54.5 1.0 CE1 B:HIS616 3.3 46.5 1.0 CG B:ASP562 3.4 54.6 1.0 ND2 B:ASN585 3.7 50.1 1.0 CB B:HIS639 3.8 56.5 1.0 CB B:ASP562 4.0 51.7 1.0 CA B:ASN585 4.0 54.8 1.0 CB B:ASN585 4.1 50.7 1.0 NE2 B:HIS639 4.1 52.7 1.0 CB B:ASP621 4.1 59.7 1.0 N B:ASN585 4.2 53.2 1.0 CD2 B:HIS639 4.3 56.0 1.0 CG B:HIS616 4.3 48.6 1.0 OD1 B:ASP562 4.3 54.5 1.0 ND1 B:HIS616 4.4 46.8 1.0 CB B:TRP583 4.4 47.4 1.0 CA B:HIS639 4.5 57.1 1.0 CG2 B:VAL620 4.6 48.5 1.0 CA B:ASP621 4.9 60.2 1.0 CG B:TRP583 5.0 49.6 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