Calcium in PDB 1zvk: Structure of Double Mutant, D164N, E78H of Kumamolisin-As

The structure of Structure of Double Mutant, D164N, E78H of Kumamolisin-As, PDB code: 1zvk was solved by M.Li, A.Wlodawer, A.Gustchina, T.Nakayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.050, 74.810, 78.380, 90.00, 103.08, 90.00
R / Rfree (%)	18.9 / 29.2

The binding sites of Calcium atom in the Structure of Double Mutant, D164N, E78H of Kumamolisin-As (pdb code 1zvk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Double Mutant, D164N, E78H of Kumamolisin-As, PDB code: 1zvk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Double Mutant, D164N, E78H of Kumamolisin-As


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Double Mutant, D164N, E78H of Kumamolisin-As within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:24.1 occ:1.00 OD1 A:ASP316 2.3 24.7 1.0 O A:GLY336 2.3 21.0 1.0 O A:GLY334 2.3 26.3 1.0 O A:HOH1001 2.3 22.0 1.0 OD2 A:ASP338 2.3 28.6 1.0 O A:ILE317 2.4 19.9 1.0 C A:GLY336 3.5 23.6 1.0 CG A:ASP316 3.5 26.3 1.0 C A:ILE317 3.5 18.4 1.0 CG A:ASP338 3.5 25.8 1.0 C A:GLY334 3.5 27.5 1.0 N A:ILE317 3.7 21.6 1.0 N A:GLY336 3.9 20.6 1.0 OG1 A:THR341 4.0 23.4 1.0 OD2 A:ASP316 4.0 23.2 1.0 N A:GLY334 4.0 31.6 1.0 C A:PRO335 4.1 19.0 1.0 CA A:ILE317 4.2 21.2 1.0 CA A:GLY336 4.2 22.0 1.0 O A:GLY342 4.3 19.6 1.0 CB A:ASP338 4.3 29.9 1.0 OD1 A:ASP338 4.3 19.8 1.0 N A:ASP338 4.3 31.1 1.0 CA A:GLY334 4.4 24.9 1.0 N A:PRO335 4.5 30.8 1.0 N A:THR318 4.5 14.1 1.0 CA A:PRO335 4.5 21.4 1.0 C A:TRP337 4.5 35.2 1.0 CA A:THR318 4.5 17.9 1.0 N A:TRP337 4.5 26.2 1.0 C A:ASP316 4.5 21.3 1.0 CG2 A:THR318 4.5 24.4 1.0 O A:PRO335 4.6 46.9 1.0 CB A:ASP316 4.7 25.6 1.0 CB A:ILE317 4.8 19.7 1.0 CA A:ASP316 4.8 18.7 1.0 CA A:TRP337 4.8 28.0 1.0 CA A:ASP338 5.0 31.0 1.0

Calcium binding site 2 out of 2 in the Structure of Double Mutant, D164N, E78H of Kumamolisin-As


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Double Mutant, D164N, E78H of Kumamolisin-As within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:22.3 occ:1.00 O B:GLY336 2.3 21.1 1.0 OD2 B:ASP338 2.3 21.5 1.0 OD1 B:ASP316 2.3 26.9 1.0 O B:GLY334 2.3 22.1 1.0 O B:HOH2001 2.3 24.1 1.0 O B:ILE317 2.4 19.9 1.0 C B:GLY336 3.4 20.6 1.0 CG B:ASP338 3.5 26.7 1.0 CG B:ASP316 3.5 29.5 1.0 C B:ILE317 3.5 18.4 1.0 C B:GLY334 3.5 25.6 1.0 N B:ILE317 3.9 15.9 1.0 N B:GLY336 3.9 21.4 1.0 OD2 B:ASP316 4.0 16.2 1.0 N B:GLY334 4.0 28.4 1.0 O B:GLY342 4.1 21.7 1.0 OG1 B:THR341 4.2 20.8 1.0 C B:PRO335 4.2 24.0 1.0 CA B:GLY336 4.2 24.9 1.0 OD1 B:ASP338 4.2 17.6 1.0 CA B:ILE317 4.3 19.7 1.0 CB B:ASP338 4.3 23.4 1.0 CA B:GLY334 4.4 22.1 1.0 N B:ASP338 4.4 16.4 1.0 C B:TRP337 4.4 28.3 1.0 N B:PRO335 4.5 27.3 1.0 N B:THR318 4.5 15.7 1.0 N B:TRP337 4.5 24.7 1.0 CA B:PRO335 4.5 27.3 1.0 CA B:THR318 4.6 24.7 1.0 C B:ASP316 4.6 19.4 1.0 CB B:ASP316 4.7 27.1 1.0 O B:PRO335 4.8 24.2 1.0 O B:TRP337 4.8 18.3 1.0 CA B:TRP337 4.8 20.9 1.0 CG2 B:THR318 4.8 19.3 1.0 CA B:ASP316 4.8 22.6 1.0 CB B:ILE317 4.9 29.0 1.0 CB B:ALA333 4.9 22.4 1.0 CA B:ASP338 5.0 16.4 1.0

A.Okubo, M.Li, M.Ashida, H.Oyama, A.Gustchina, K.Oda, B.M.Dunn, A.Wlodawer, T.Nakayama. Processing, Catalytic Activity and Crystal Structures of Kumamolisin-As with An Engineered Active Site. Febs J. V. 273 2563 2006.
ISSN: ISSN 1742-464X
PubMed: 16704427
DOI: 10.1111/J.1742-4658.2006.05266.X