Calcium in PDB 2nqa: Catalytic Domain of Human Calpain 8

All present enzymatic activity of Catalytic Domain of Human Calpain 8:
3.4.22.53;

The structure of Catalytic Domain of Human Calpain 8, PDB code: 2nqa was solved by T.L.Davis, R.Paramanathan, C.Butler-Cole, P.J.Finerty Jr., J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.95 / 2.20
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	91.794, 91.794, 194.592, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 26.8

The binding sites of Calcium atom in the Catalytic Domain of Human Calpain 8 (pdb code 2nqa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Catalytic Domain of Human Calpain 8, PDB code: 2nqa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Catalytic Domain of Human Calpain 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Human Calpain 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:33.4 occ:1.00 O A:VAL319 2.3 19.7 1.0 OD2 A:ASP299 2.4 12.8 1.0 O A:GLU323 2.5 18.2 1.0 OE1 A:GLU292 2.7 19.0 1.0 OE2 A:GLU292 2.8 17.6 1.0 OD1 A:ASP321 2.8 18.0 1.0 CD A:GLU292 3.0 18.0 1.0 CG A:ASP299 3.1 17.0 1.0 OD1 A:ASP299 3.1 15.9 1.0 C A:VAL319 3.5 19.4 1.0 C A:GLU323 3.7 18.7 1.0 CG A:ASP321 3.7 17.8 1.0 N A:VAL319 4.1 20.2 1.0 N A:ASP321 4.1 18.2 1.0 O A:HOH938 4.1 22.7 1.0 O A:LYS317 4.2 19.3 1.0 OD2 A:ASP321 4.2 16.4 1.0 N A:GLU323 4.3 18.2 1.0 CA A:VAL319 4.3 19.9 1.0 CG A:GLU292 4.4 19.4 1.0 N A:GLU320 4.5 19.3 1.0 CA A:GLU323 4.5 18.6 1.0 CB A:ASP299 4.5 17.0 1.0 CA A:GLU320 4.6 18.7 1.0 N A:PHE324 4.6 20.2 1.0 O A:HOH958 4.6 19.2 1.0 O A:HOH993 4.7 22.2 1.0 CA A:PHE324 4.8 21.2 1.0 CB A:VAL319 4.8 19.4 1.0 CB A:ASP321 4.8 17.7 1.0 N A:GLY322 4.9 16.8 1.0 O A:HOH976 4.9 29.5 1.0 CB A:PHE324 4.9 20.8 1.0 CA A:ASP321 4.9 17.7 1.0 C A:GLU320 4.9 18.4 1.0

Calcium binding site 2 out of 5 in the Catalytic Domain of Human Calpain 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Human Calpain 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:35.5 occ:1.00 O A:GLY91 2.4 14.6 1.0 O A:HOH1060 2.5 24.2 1.0 O A:VAL89 2.5 15.1 1.0 OD2 A:ASP96 2.6 19.3 1.0 OD1 A:ASP96 2.6 20.5 1.0 OE2 A:GLU175 2.7 18.1 1.0 CG A:ASP96 2.9 20.0 1.0 OE1 A:GLU175 2.9 19.9 1.0 CD A:GLU175 3.2 18.5 1.0 C A:GLY91 3.6 15.3 1.0 C A:VAL89 3.7 16.3 1.0 OG1 A:THR93 4.0 14.8 1.0 O A:GLY90 4.1 16.3 1.0 C A:GLY90 4.2 16.4 1.0 O A:HOH1030 4.3 27.0 1.0 CB A:ASP96 4.3 20.5 1.0 N A:GLY91 4.4 15.8 1.0 N A:VAL89 4.4 16.1 1.0 N A:THR93 4.4 16.6 1.0 NE1 A:TRP177 4.5 13.2 1.0 CA A:VAL89 4.5 16.1 1.0 N A:ALA92 4.6 15.1 1.0 CA A:GLY91 4.6 15.8 1.0 CA A:ALA92 4.6 15.4 1.0 N A:GLY90 4.6 16.4 1.0 CG A:GLU175 4.7 18.6 1.0 CA A:GLY90 4.7 16.5 1.0 OG A:SER170 4.8 15.7 1.0 CB A:VAL89 4.9 16.2 1.0

Calcium binding site 3 out of 5 in the Catalytic Domain of Human Calpain 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Human Calpain 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:38.7 occ:1.00 OE1 A:GLU320 3.3 18.2 1.0 O A:GLU292 3.7 19.6 1.0 N A:GLU292 4.0 19.2 1.0 CD A:GLU320 4.2 19.7 1.0 CB A:GLU292 4.4 19.6 1.0 OE2 A:GLU320 4.4 20.6 1.0 CA A:GLU292 4.4 19.5 1.0 C A:GLU292 4.5 18.7 1.0 CG A:LYS257 4.9 21.0 1.0 CB A:LYS257 5.0 19.7 1.0

Calcium binding site 4 out of 5 in the Catalytic Domain of Human Calpain 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catalytic Domain of Human Calpain 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:34.3 occ:1.00 O B:VAL319 2.3 26.9 1.0 O B:GLU323 2.4 19.6 1.0 OE2 B:GLU292 2.5 24.5 1.0 OD2 B:ASP299 2.6 19.3 1.0 OE1 B:GLU292 2.6 24.9 1.0 OD1 B:ASP321 2.7 19.3 1.0 CD B:GLU292 2.9 23.6 1.0 OD1 B:ASP299 3.0 19.0 1.0 CG B:ASP299 3.1 21.0 1.0 C B:VAL319 3.6 27.1 1.0 C B:GLU323 3.6 20.3 1.0 CG B:ASP321 3.7 21.9 1.0 N B:GLU323 4.0 20.1 1.0 N B:ASP321 4.1 23.7 1.0 O B:LYS317 4.2 24.8 1.0 N B:VAL319 4.2 28.0 1.0 OD2 B:ASP321 4.3 22.5 1.0 CA B:GLU323 4.4 19.6 1.0 CG B:GLU292 4.4 21.7 1.0 CA B:VAL319 4.4 27.5 1.0 N B:GLU320 4.5 26.5 1.0 O B:HOH940 4.5 21.3 1.0 CB B:ASP299 4.6 22.0 1.0 N B:PHE324 4.6 21.6 1.0 CA B:GLU320 4.6 26.1 1.0 N B:GLY322 4.7 20.9 1.0 CA B:PHE324 4.7 22.8 1.0 CB B:VAL319 4.7 27.4 1.0 CB B:ASP321 4.8 23.0 1.0 CB B:GLU323 4.9 19.2 1.0 CA B:ASP321 4.9 22.9 1.0 CB B:PHE324 4.9 22.2 1.0 C B:GLU320 4.9 25.1 1.0 O B:HOH908 4.9 31.4 1.0

Calcium binding site 5 out of 5 in the Catalytic Domain of Human Calpain 8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Catalytic Domain of Human Calpain 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca904 b:38.1 occ:1.00 OE2 B:GLU175 2.4 14.4 1.0 OD2 B:ASP96 2.5 18.1 1.0 O B:GLY91 2.6 19.2 1.0 O B:VAL89 2.6 21.8 1.0 OD1 B:ASP96 2.7 21.1 1.0 OE1 B:GLU175 2.8 18.5 1.0 O B:HOH996 2.8 20.9 1.0 CG B:ASP96 2.9 20.4 1.0 CD B:GLU175 2.9 17.0 1.0 C B:VAL89 3.6 22.1 1.0 C B:GLY91 3.8 19.5 1.0 N B:VAL89 4.0 21.2 1.0 O B:GLY90 4.2 21.5 1.0 C B:GLY90 4.3 21.6 1.0 NE1 B:TRP177 4.3 18.4 1.0 CB B:ASP96 4.3 21.1 1.0 CA B:VAL89 4.3 21.9 1.0 CG B:GLU175 4.4 19.3 1.0 N B:GLY91 4.4 20.7 1.0 OG1 B:THR93 4.4 19.5 1.0 CB B:VAL89 4.5 21.9 1.0 OG B:SER170 4.6 16.8 1.0 N B:THR93 4.6 19.4 1.0 N B:GLY90 4.6 22.2 1.0 CA B:GLY91 4.7 20.2 1.0 N B:ALA92 4.7 19.4 1.0 CA B:ALA92 4.8 19.3 1.0 CA B:GLY90 4.8 22.2 1.0 CD1 B:TRP177 5.0 17.9 1.0

T.L.Davis, R.Paramanathan, C.Butler-Cole, P.J.Finerty Jr., J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon. Structure of Human Calpain 8 To Be Published.