Calcium in PDB 1sio: Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf

The structure of Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf, PDB code: 1sio was solved by M.Li, A.Wlodawer, A.Gustchina, N.Tsuruoka, M.Ashida, H.Minakata, H.Oyama, K.Oda, T.Nishino, T.Nakayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.370, 238.730, 49.250, 90.00, 113.70, 90.00
R / Rfree (%)	17.3 / 24.3

The binding sites of Calcium atom in the Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf (pdb code 1sio). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf, PDB code: 1sio:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:18.1 occ:1.00 OD2 A:ASP338 2.3 14.9 1.0 OD1 A:ASP316 2.3 22.1 1.0 O A:GLY334 2.3 20.6 1.0 O A:GLY336 2.3 14.7 1.0 O A:HOH1501 2.3 14.4 1.0 O A:ILE317 2.4 15.0 1.0 CG A:ASP338 3.4 20.4 1.0 CG A:ASP316 3.5 18.2 1.0 C A:ILE317 3.5 13.8 1.0 C A:GLY336 3.5 11.7 1.0 C A:GLY334 3.6 22.7 1.0 N A:ILE317 3.8 17.2 1.0 N A:GLY336 3.9 20.8 1.0 N A:GLY334 4.0 18.3 1.0 OD2 A:ASP316 4.1 24.8 1.0 C A:PRO335 4.1 24.4 1.0 OG1 A:THR341 4.2 15.7 1.0 CB A:ASP338 4.2 14.9 1.0 O A:GLY342 4.2 18.6 1.0 CA A:GLY336 4.2 16.7 1.0 CA A:ILE317 4.3 11.7 1.0 OD1 A:ASP338 4.3 14.7 1.0 N A:ASP338 4.3 12.3 1.0 CA A:GLY334 4.4 20.4 1.0 N A:PRO335 4.5 24.5 1.0 CA A:PRO335 4.5 19.6 1.0 N A:THR318 4.5 14.2 1.0 C A:ASP316 4.5 23.8 1.0 C A:TRP337 4.5 20.1 1.0 O A:PRO335 4.5 18.6 1.0 CA A:THR318 4.5 17.5 1.0 N A:TRP337 4.6 14.4 1.0 CB A:ASP316 4.6 13.4 1.0 CA A:ASP316 4.7 18.2 1.0 CG2 A:THR318 4.7 22.2 1.0 CA A:TRP337 4.8 11.7 1.0 CB A:ILE317 4.9 13.3 1.0 CA A:ASP338 5.0 13.8 1.0

Calcium binding site 2 out of 3 in the Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:18.2 occ:1.00 O B:GLY336 2.3 15.6 1.0 O B:GLY334 2.3 21.1 1.0 O B:ILE317 2.3 15.7 1.0 OD2 B:ASP338 2.3 18.1 1.0 OD1 B:ASP316 2.3 17.9 1.0 O B:HOH2501 2.4 15.7 1.0 C B:ILE317 3.4 13.5 1.0 C B:GLY336 3.5 13.3 1.0 CG B:ASP338 3.5 20.9 1.0 CG B:ASP316 3.5 22.2 1.0 C B:GLY334 3.5 27.2 1.0 N B:ILE317 3.8 16.8 1.0 N B:GLY336 3.8 17.8 1.0 N B:GLY334 3.9 23.3 1.0 C B:PRO335 4.1 15.9 1.0 OD2 B:ASP316 4.1 18.3 1.0 OG1 B:THR341 4.2 13.3 1.0 CA B:ILE317 4.2 12.4 1.0 O B:GLY342 4.2 12.6 1.0 CA B:GLY336 4.2 16.8 1.0 CB B:ASP338 4.2 13.2 1.0 N B:ASP338 4.3 12.0 1.0 CA B:GLY334 4.4 25.6 1.0 OD1 B:ASP338 4.4 19.7 1.0 N B:THR318 4.4 17.8 1.0 CA B:PRO335 4.4 20.3 1.0 N B:PRO335 4.4 25.5 1.0 C B:TRP337 4.4 18.2 1.0 CA B:THR318 4.5 15.1 1.0 N B:TRP337 4.6 13.8 1.0 O B:PRO335 4.6 21.4 1.0 C B:ASP316 4.6 16.7 1.0 CG2 B:THR318 4.7 24.6 1.0 CB B:ASP316 4.7 15.1 1.0 CA B:TRP337 4.7 8.2 1.0 CA B:ASP316 4.8 13.9 1.0 CB B:ILE317 4.8 13.8 1.0 O B:TRP337 4.9 12.7 1.0 CA B:ASP338 4.9 10.4 1.0 C B:ALA333 5.0 21.4 1.0

Calcium binding site 3 out of 3 in the Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Kumamolisin-As Complexed with A Covalently-Bound Inhibitor, Acipf within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:41.4 occ:1.00 O C:GLY334 2.3 45.5 1.0 OD1 C:ASP316 2.3 48.7 1.0 O C:HOH3501 2.3 31.3 1.0 O C:ILE317 2.3 39.4 1.0 OD2 C:ASP338 2.3 29.2 1.0 O C:GLY336 2.3 31.5 1.0 C C:ILE317 3.5 37.7 1.0 CG C:ASP316 3.5 51.8 1.0 CG C:ASP338 3.5 33.2 1.0 C C:GLY334 3.5 41.3 1.0 C C:GLY336 3.5 39.4 1.0 N C:ILE317 3.9 28.5 1.0 N C:GLY334 3.9 32.0 1.0 N C:GLY336 3.9 34.9 1.0 O C:GLY342 4.0 31.6 1.0 OD2 C:ASP316 4.0 51.0 1.0 OG1 C:THR341 4.0 31.5 1.0 C C:PRO335 4.1 32.5 1.0 CA C:GLY336 4.3 41.4 1.0 CA C:ILE317 4.3 26.3 1.0 OD1 C:ASP338 4.3 30.7 1.0 CB C:ASP338 4.3 25.1 1.0 CA C:GLY334 4.3 34.9 1.0 CA C:PRO335 4.4 43.3 1.0 N C:PRO335 4.4 48.5 1.0 N C:ASP338 4.4 23.9 1.0 C C:ASP316 4.4 31.9 1.0 N C:THR318 4.4 35.4 1.0 CA C:THR318 4.5 37.2 1.0 CG2 C:THR318 4.5 44.6 1.0 C C:TRP337 4.5 30.5 1.0 N C:TRP337 4.6 35.9 1.0 O C:PRO335 4.6 38.5 1.0 CB C:ASP316 4.6 44.4 1.0 CA C:ASP316 4.7 37.0 1.0 CA C:TRP337 4.8 31.9 1.0 CB C:ILE317 4.9 32.4 1.0 C C:ALA333 5.0 28.9 1.0

A.Wlodawer, M.Li, A.Gustchina, N.Tsuruoka, M.Ashida, H.Minakata, H.Oyama, K.Oda, T.Nishino, T.Nakayama. Crystallographic and Biochemical Investigations of Kumamolisin-As, A Serine-Carboxyl Peptidase with Collagenase Activity J.Biol.Chem. V. 279 21500 2004.
ISSN: ISSN 0021-9258
PubMed: 15014068
DOI: 10.1074/JBC.M401141200