Cadmium in PDB 1np8: 18-K C-Terminally Trunucated Small Subunit of Calpain

The structure of 18-K C-Terminally Trunucated Small Subunit of Calpain, PDB code: 1np8 was solved by E.K.Leinala, J.S.Arthur, P.Grochulski, P.L.Davies, J.S.Elce, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.040, 67.570, 75.070, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the 18-K C-Terminally Trunucated Small Subunit of Calpain (pdb code 1np8). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the 18-K C-Terminally Trunucated Small Subunit of Calpain, PDB code: 1np8:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd700 b:18.3 occ:1.00 OE1 A:GLU79 2.1 20.0 1.0 O A:LYS74 2.3 21.2 1.0 OD1 A:ASP68 2.3 17.7 1.0 OD1 A:ASP70 2.3 27.6 1.0 O A:HOH778 2.4 17.2 1.0 OG1 A:THR72 2.5 25.5 1.0 CD A:GLU79 2.8 20.7 1.0 OE2 A:GLU79 2.9 22.5 1.0 CG A:ASP70 3.2 26.1 1.0 CG A:ASP68 3.4 21.6 1.0 OD2 A:ASP70 3.4 26.9 1.0 C A:LYS74 3.5 19.9 1.0 CB A:THR72 3.7 23.8 1.0 N A:THR72 3.8 24.0 1.0 CG2 A:THR72 3.9 24.4 1.0 N A:GLY76 4.1 18.9 1.0 CA A:ASP68 4.2 20.6 1.0 CA A:LEU75 4.2 19.6 1.0 CB A:ASP68 4.2 19.5 1.0 N A:LEU75 4.2 19.2 1.0 OE2 A:GLU30 4.3 27.4 1.0 OE1 A:GLU30 4.3 22.5 1.0 CG A:GLU79 4.3 21.1 1.0 CA A:THR72 4.3 24.1 1.0 OD2 A:ASP68 4.3 24.8 1.0 N A:LYS74 4.3 18.8 1.0 N A:ASP70 4.4 24.9 1.0 C A:ASP68 4.5 22.2 1.0 CB A:ASP70 4.5 25.6 1.0 CA A:LYS74 4.5 19.7 1.0 N A:THR71 4.6 23.8 1.0 C A:LEU75 4.6 19.0 1.0 CD A:GLU30 4.6 22.9 1.0 N A:GLY73 4.6 22.8 1.0 C A:ASP70 4.7 24.9 1.0 CA A:ASP70 4.7 24.7 1.0 O A:ASP68 4.8 22.6 1.0 C A:THR72 4.8 23.4 1.0 N A:SER69 4.9 22.6 1.0 C A:THR71 5.0 25.5 1.0 CB A:GLU79 5.0 19.0 1.0 CD1 A:LEU75 5.0 20.3 1.0

Cadmium binding site 2 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd701 b:18.2 occ:1.00 OD2 A:ASP100 2.3 17.1 1.0 O A:HOH774 2.4 14.1 1.0 O A:HOH771 2.4 18.0 1.0 O A:HOH769 2.4 1.0 1.0 CG A:ASP100 3.2 18.8 1.0 CB A:ASP100 3.6 16.7 1.0 OE2 A:GLU109 4.1 11.7 1.0 OD1 A:ASP100 4.2 14.0 1.0 O A:HOH805 4.3 19.1 1.0 O A:HOH720 4.3 12.8 1.0 CD A:GLU109 4.4 10.7 1.0 ND2 A:ASN108 4.5 18.9 1.0 CG A:GLU109 4.6 13.7 1.0 O A:HOH723 4.6 16.3 1.0 CB A:ASN108 4.7 18.3 1.0 CA A:ASP100 5.0 18.0 1.0 OE1 A:GLU109 5.0 13.9 1.0

Cadmium binding site 3 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd702 b:15.9 occ:1.00 OD1 A:ASP98 2.1 14.5 1.0 OD1 A:ASP100 2.2 14.0 1.0 O A:HOH720 2.2 12.8 1.0 OE1 A:GLU109 2.3 13.9 1.0 OG A:SER102 2.3 15.7 1.0 O A:THR104 2.4 13.8 1.0 OE2 A:GLU109 2.7 11.7 1.0 CD A:GLU109 2.8 10.7 1.0 CG A:ASP100 3.2 18.8 1.0 CG A:ASP98 3.2 17.2 1.0 OD2 A:ASP100 3.5 17.1 1.0 CB A:SER102 3.5 19.4 1.0 C A:THR104 3.5 14.7 1.0 CA A:ASP98 3.8 17.0 1.0 CB A:ASP98 3.9 17.0 1.0 N A:SER102 3.9 18.8 1.0 OG1 A:THR104 4.1 14.2 1.0 N A:GLY106 4.2 13.1 1.0 OD2 A:ASP98 4.2 17.7 1.0 CA A:ILE105 4.3 15.5 1.0 C A:ASP98 4.3 17.4 1.0 CA A:SER102 4.3 18.2 1.0 N A:ILE105 4.3 12.2 1.0 N A:THR104 4.3 15.0 1.0 CG A:GLU109 4.3 13.7 1.0 N A:ASP100 4.4 18.0 1.0 CA A:THR104 4.5 13.3 1.0 OD1 A:ASN139 4.5 24.5 1.0 CB A:ASP100 4.5 16.7 1.0 N A:ARG101 4.6 19.1 1.0 C A:ILE105 4.7 13.7 1.0 N A:THR99 4.7 18.3 1.0 C A:ASP100 4.7 19.4 1.0 N A:GLY103 4.8 17.7 1.0 CA A:ASP100 4.8 18.0 1.0 O A:ASP98 4.8 17.9 1.0 C A:SER102 4.9 17.9 1.0 CB A:THR104 4.9 15.6 1.0 O A:HOH774 4.9 14.1 1.0

Cadmium binding site 4 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd703 b:17.6 occ:1.00 O A:ALA25 2.2 18.3 1.0 OD1 A:ASP28 2.2 22.5 1.0 O A:HOH772 2.2 16.3 1.0 OE2 A:GLU35 2.4 17.2 1.0 O A:GLU30 2.4 16.1 1.0 OE1 A:GLU35 2.4 15.4 1.0 O A:HOH726 2.5 19.3 1.0 CD A:GLU35 2.7 16.7 1.0 CG A:ASP28 3.1 25.9 1.0 C A:ALA25 3.2 19.6 1.0 OD2 A:ASP28 3.3 26.9 1.0 C A:GLU30 3.6 16.3 1.0 CA A:ALA25 3.8 18.1 1.0 CG A:GLU35 4.2 16.3 1.0 N A:GLU30 4.3 19.2 1.0 N A:GLY26 4.3 21.1 1.0 N A:SER32 4.3 16.0 1.0 O A:HOH732 4.4 26.3 1.0 CA A:VAL31 4.5 14.5 1.0 CB A:ALA25 4.5 19.3 1.0 N A:VAL31 4.5 16.4 1.0 CB A:ASP28 4.5 24.4 1.0 O A:LEU24 4.5 18.2 1.0 N A:ASP28 4.6 25.6 1.0 O A:HOH817 4.6 36.2 1.0 CA A:GLY26 4.6 22.1 1.0 CA A:GLU30 4.6 18.5 1.0 O A:HOH810 4.7 24.4 1.0 N A:MET29 4.8 23.2 1.0 OG A:SER32 4.8 14.2 1.0 C A:GLY26 4.8 23.1 1.0 CB A:SER32 4.8 16.3 1.0 C A:VAL31 4.8 15.8 1.0 CA A:ASP28 4.9 23.9 1.0

Cadmium binding site 5 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd704 b:14.9 occ:1.00 OD2 A:ASP143 2.1 10.4 1.0 OD1 A:ASP53 2.1 15.7 1.0 OD1 A:ASP141 2.2 19.0 1.0 O A:HOH729 2.3 16.0 1.0 O A:HOH773 2.3 17.1 1.0 OD1 A:ASN144 2.5 15.3 1.0 OD2 A:ASP141 2.5 12.7 1.0 CG A:ASP141 2.7 15.0 1.0 CG A:ASP143 2.9 14.0 1.0 OD1 A:ASP143 3.1 15.5 1.0 CG A:ASP53 3.2 16.8 1.0 O A:HOH725 3.3 19.3 1.0 CG A:ASN144 3.3 13.2 1.0 OD2 A:ASP53 3.5 23.7 1.0 O A:HOH717 3.7 12.9 1.0 ND2 A:ASN144 4.0 13.1 1.0 N A:ASN144 4.1 11.9 1.0 CB A:ASP141 4.2 15.4 1.0 N A:ASP53 4.3 13.4 1.0 CB A:ASP143 4.3 13.9 1.0 CB A:ASN144 4.3 11.5 1.0 O A:HOH757 4.4 23.4 1.0 O B:HOH239 4.5 35.6 1.0 CB A:ASP53 4.5 15.8 1.0 O A:HOH755 4.5 29.7 1.0 O A:HOH713 4.5 52.1 1.0 CA A:ASN144 4.7 11.9 1.0 C A:ASP143 4.8 13.7 1.0 CA A:ASP53 4.9 14.4 1.0 CA A:ASP143 4.9 12.8 1.0 O A:GLY54 4.9 15.0 1.0 N A:ASP143 4.9 12.9 1.0 O A:HOH765 5.0 34.9 1.0

Cadmium binding site 6 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd705 b:16.8 occ:1.00 O A:HOH776 2.2 16.8 1.0 OD1 A:ASP27 2.3 27.2 1.0 O A:HOH768 2.4 1.0 1.0 CG A:ASP27 3.0 28.7 1.0 OD2 A:ASP27 3.1 29.3 1.0 O A:HOH791 4.3 36.4 1.0 CB A:ASP27 4.5 27.6 1.0

Cadmium binding site 7 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd711 b:29.6 occ:1.00 OD2 A:ASP49 2.2 22.1 1.0 ND1 A:HIS47 2.3 19.3 1.0 OD1 A:ASP49 2.5 21.4 1.0 O A:HOH777 2.7 10.0 1.0 CG A:ASP49 2.7 22.6 1.0 O B:HOH140 3.2 20.0 1.0 CG A:HIS47 3.2 19.2 1.0 CB A:HIS47 3.3 18.2 1.0 CE1 A:HIS47 3.4 21.2 1.0 CA A:HIS47 4.1 17.5 1.0 CB A:ASP49 4.2 19.4 1.0 NZ A:LYS95 4.2 36.3 1.0 NE2 B:HIS624 4.3 42.3 1.0 CD2 A:HIS47 4.4 18.0 1.0 NE2 A:HIS47 4.4 19.9 1.0 CE A:LYS95 4.6 35.5 1.0 CE1 B:HIS624 4.6 43.2 1.0 CD A:LYS95 4.7 33.0 1.0 C A:HIS47 4.7 17.3 1.0 NE2 A:GLN91 4.8 18.7 1.0 N A:ASP49 4.9 18.1 1.0

Cadmium binding site 8 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd707 b:17.6 occ:1.00 OG1 B:THR572 2.1 20.1 1.0 OE1 B:GLU579 2.2 22.0 1.0 OD1 B:ASP570 2.2 21.0 1.0 O B:HOH112 2.2 15.8 1.0 OD1 B:ASP568 2.3 13.9 1.0 O B:LYS574 2.4 15.2 1.0 CD B:GLU579 3.0 20.9 1.0 OE2 B:GLU579 3.1 20.5 1.0 CG B:ASP570 3.1 21.3 1.0 CG B:ASP568 3.4 18.5 1.0 OD2 B:ASP570 3.4 19.4 1.0 CB B:THR572 3.4 19.9 1.0 C B:LYS574 3.6 16.9 1.0 N B:THR572 3.7 19.9 1.0 CG2 B:THR572 3.8 20.9 1.0 N B:GLY576 4.0 18.6 1.0 OE1 B:GLU530 4.1 22.9 1.0 CB B:ASP568 4.1 16.5 1.0 CA B:ASP568 4.1 18.0 1.0 CA B:THR572 4.1 20.3 1.0 CA B:LEU575 4.2 16.4 1.0 OD2 B:ASP568 4.2 16.8 1.0 OE2 B:GLU530 4.3 24.8 1.0 N B:LYS574 4.3 17.7 1.0 N B:LEU575 4.4 15.5 1.0 CG B:GLU579 4.4 17.9 1.0 CB B:ASP570 4.4 20.1 1.0 N B:ASP570 4.5 22.3 1.0 N B:THR571 4.5 20.7 1.0 N B:GLY573 4.5 17.6 1.0 C B:ASP568 4.5 19.6 1.0 CD B:GLU530 4.6 24.4 1.0 C B:LEU575 4.6 17.8 1.0 CA B:LYS574 4.6 17.6 1.0 C B:ASP570 4.7 21.0 1.0 C B:THR572 4.7 18.5 1.0 CA B:ASP570 4.8 21.0 1.0 C B:THR571 4.8 22.2 1.0 O B:ASP568 4.9 19.2 1.0 N B:SER569 5.0 20.2 1.0 CA B:GLY576 5.0 19.1 1.0 CB B:GLU579 5.0 19.3 1.0

Cadmium binding site 9 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd708 b:16.4 occ:1.00 OD1 B:ASP598 2.0 13.2 1.0 O B:HOH138 2.1 12.4 1.0 OE1 B:GLU609 2.1 15.7 1.0 OD1 B:ASP600 2.2 16.6 1.0 OG B:SER602 2.3 18.5 1.0 O B:THR604 2.4 15.9 1.0 OE2 B:GLU609 2.6 10.1 1.0 CD B:GLU609 2.7 14.0 1.0 CG B:ASP598 3.1 17.5 1.0 CG B:ASP600 3.1 20.4 1.0 OD2 B:ASP600 3.4 20.1 1.0 C B:THR604 3.4 17.1 1.0 CB B:SER602 3.5 18.7 1.0 CA B:ASP598 3.9 16.1 1.0 CB B:ASP598 3.9 16.3 1.0 N B:SER602 4.0 20.0 1.0 OD2 B:ASP598 4.0 18.6 1.0 N B:GLY606 4.1 15.3 1.0 CA B:ILE605 4.2 14.3 1.0 CG B:GLU609 4.2 15.3 1.0 OG1 B:THR604 4.2 18.1 1.0 N B:ILE605 4.2 15.5 1.0 CA B:SER602 4.3 19.8 1.0 N B:THR604 4.3 18.5 1.0 C B:ASP598 4.3 18.3 1.0 OD1 B:ASN639 4.4 21.3 1.0 N B:ASP600 4.4 19.0 1.0 CA B:THR604 4.4 17.9 1.0 CB B:ASP600 4.5 18.4 1.0 C B:ILE605 4.6 15.4 1.0 N B:THR599 4.7 18.2 1.0 N B:ARG601 4.7 19.5 1.0 CA B:ASP600 4.8 19.0 1.0 N B:GLY603 4.8 19.1 1.0 C B:ASP600 4.8 19.5 1.0 C B:SER602 4.8 19.1 1.0 O B:ASP598 4.9 17.4 1.0 CB B:THR604 5.0 17.8 1.0

Cadmium binding site 10 out of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd709 b:19.8 occ:1.00 O B:HOH142 2.2 17.4 1.0 O B:ALA525 2.2 20.9 1.0 OE2 B:GLU535 2.3 18.0 1.0 OD1 B:ASP528 2.3 27.6 1.0 O B:GLU530 2.4 18.4 1.0 O B:HOH186 2.5 22.5 1.0 OE1 B:GLU535 2.5 12.2 1.0 CD B:GLU535 2.7 16.3 1.0 CG B:ASP528 3.1 29.9 1.0 OD2 B:ASP528 3.2 32.5 1.0 C B:ALA525 3.3 20.7 1.0 C B:GLU530 3.6 19.9 1.0 CA B:ALA525 3.8 20.5 1.0 CG B:GLU535 4.2 16.7 1.0 N B:GLU530 4.2 21.7 1.0 N B:SER532 4.3 15.0 1.0 N B:GLY526 4.4 22.4 1.0 CB B:ASP528 4.5 30.1 1.0 CA B:VAL531 4.5 16.6 1.0 O B:HOH61 4.5 28.4 1.0 N B:VAL531 4.5 19.7 1.0 N B:ASP528 4.5 30.3 1.0 CA B:GLU530 4.5 21.9 1.0 CB B:ALA525 4.5 20.6 1.0 O B:HOH184 4.6 39.7 1.0 CD B:LYS574 4.7 24.6 1.0 CA B:GLY526 4.7 22.9 1.0 O B:LEU524 4.7 19.8 1.0 OG B:SER532 4.7 15.2 1.0 N B:MET529 4.7 26.1 1.0 C B:GLY526 4.8 23.6 1.0 CB B:SER532 4.8 15.2 1.0 C B:VAL531 4.8 17.4 1.0 CA B:ASP528 4.8 29.4 1.0 O B:HOH187 5.0 42.5 1.0

E.K.Leinala, J.S.Arthur, P.Grochulski, P.L.Davies, J.S.Elce, Z.Jia. A Second Binding Site Revealed By C-Terminal Truncation of Calpain Small Subunit, A Penta-Ef-Hand Protein Proteins: V. 53 649 2003STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 14579356
DOI: 10.1002/PROT.10453