Calcium in PDB 6jwf: Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea

The structure of Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea, PDB code: 6jwf was solved by K.Takeda, T.Ishida, M.Yoshida, M.Samejima, H.Ohno, K.Igarashi, N.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.07 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.330, 95.638, 106.204, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 17.7

The binding sites of Calcium atom in the Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea (pdb code 6jwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea, PDB code: 6jwf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:10.3 occ:1.00 OD1 A:ASP451 2.3 12.5 1.0 O A:HOH845 2.4 11.7 1.0 O5 A:PQQ702 2.4 10.0 1.0 O A:HOH1093 2.5 11.0 1.0 O7A A:PQQ702 2.5 9.9 1.0 N6 A:PQQ702 2.5 9.2 1.0 O A:SER449 2.6 10.4 1.0 C5 A:PQQ702 3.3 9.7 1.0 C6A A:PQQ702 3.3 9.3 1.0 C7X A:PQQ702 3.4 9.4 1.0 C7 A:PQQ702 3.4 9.3 1.0 CG A:ASP451 3.5 12.3 1.0 C A:SER449 3.7 10.8 1.0 OD2 A:ASP451 4.1 13.9 1.0 NH1 A:ARG430 4.2 11.5 1.0 N A:SER449 4.2 10.7 1.0 O A:LEU450 4.3 11.6 1.0 C A:LEU450 4.3 11.3 1.0 ND1 A:HIS539 4.4 10.1 1.0 O2 A:EDO704 4.4 19.0 1.0 N A:ASP451 4.4 11.5 1.0 NH2 A:ARG430 4.5 12.4 1.0 CZ A:ARG430 4.5 11.4 1.0 CA A:SER449 4.6 11.0 1.0 O7B A:PQQ702 4.6 9.6 1.0 N A:LEU450 4.6 11.3 1.0 C A:ASN448 4.6 10.8 1.0 C4 A:PQQ702 4.7 10.1 1.0 CB A:ASP451 4.7 12.2 1.0 CA A:ASP451 4.7 11.8 1.0 OE2 A:GLU471 4.7 12.5 1.0 C8 A:PQQ702 4.7 9.4 1.0 OD1 A:ASN448 4.8 13.4 1.0 C9A A:PQQ702 4.8 9.4 1.0 CB A:ASN448 4.8 11.5 1.0 O A:HOH913 4.8 12.5 1.0 CA A:LEU450 4.9 11.8 1.0 OE1 A:GLU471 5.0 11.5 1.0

Calcium binding site 2 out of 2 in the Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:9.7 occ:1.00 OD1 B:ASP451 2.3 10.6 1.0 O B:HOH824 2.4 11.1 1.0 O5 B:PQQ703 2.4 9.8 1.0 O B:HOH1090 2.5 10.2 1.0 O7B B:PQQ703 2.5 9.9 1.0 N6 B:PQQ703 2.5 9.3 1.0 O B:SER449 2.6 10.3 1.0 C5 B:PQQ703 3.3 9.6 1.0 C6A B:PQQ703 3.3 9.2 1.0 C7X B:PQQ703 3.4 9.2 1.0 C7 B:PQQ703 3.4 9.3 1.0 CG B:ASP451 3.5 11.0 1.0 C B:SER449 3.7 10.2 1.0 OD2 B:ASP451 4.0 11.6 1.0 NH1 B:ARG430 4.1 11.2 1.0 N B:SER449 4.2 10.1 1.0 O B:LEU450 4.3 10.3 1.0 C B:LEU450 4.3 10.5 1.0 O1 B:EDO705 4.4 17.5 1.0 ND1 B:HIS539 4.4 9.7 1.0 NH2 B:ARG430 4.5 11.3 1.0 N B:ASP451 4.5 10.4 1.0 CZ B:ARG430 4.5 10.5 1.0 CA B:SER449 4.6 10.1 1.0 O7A B:PQQ703 4.6 9.4 1.0 C B:ASN448 4.6 10.1 1.0 N B:LEU450 4.6 10.3 1.0 C4 B:PQQ703 4.6 9.5 1.0 OE2 B:GLU471 4.7 11.7 1.0 CB B:ASP451 4.7 11.0 1.0 C8 B:PQQ703 4.7 9.2 1.0 OD1 B:ASN448 4.7 13.4 1.0 C9A B:PQQ703 4.7 9.3 1.0 CA B:ASP451 4.8 11.1 1.0 CB B:ASN448 4.8 11.1 1.0 O B:HOH920 4.8 11.7 1.0 CA B:LEU450 4.9 10.8 1.0 OE1 B:GLU471 5.0 11.7 1.0 CE1 B:HIS539 5.0 10.0 1.0

K.Takeda, T.Ishida, M.Yoshida, M.Samejima, H.Ohno, K.Igarashi, N.Nakamura. The Holo Form Structure of the Catalytic Domain of A Eukaryotic Pqq-Dependent Dehydrogenase To Be Published.