Calcium in PDB 4d5a: Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage

All present enzymatic activity of Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage:
3.4.22.15;

The structure of Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage, PDB code: 4d5a was solved by W.J.Bradshaw, A.K.Roberts, C.C.Shone, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.38 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.094, 70.152, 78.852, 65.22, 89.89, 80.18
R / Rfree (%)	18.112 / 21.055

The binding sites of Calcium atom in the Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage (pdb code 4d5a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage, PDB code: 4d5a:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1498 b:12.2 occ:1.00 O A:LEU339 2.2 10.2 1.0 OD1 A:ASN487 2.3 9.9 1.0 O A:LYS460 2.3 12.1 1.0 O1 A:GOL1506 2.4 18.8 1.0 O2 A:GOL1506 2.5 14.7 1.0 OE1 A:GLU448 2.6 11.3 1.0 O A:HOH2279 2.6 19.7 1.0 C2 A:GOL1506 3.4 18.7 1.0 CG A:ASN487 3.4 9.9 1.0 C1 A:GOL1506 3.4 18.5 1.0 C A:LEU339 3.5 10.8 1.0 C A:LYS460 3.5 13.4 1.0 CD A:GLU448 3.5 10.8 1.0 OE2 A:GLU448 3.7 10.5 1.0 O A:HOH2390 4.0 24.4 1.0 CB A:ASN487 4.1 9.7 1.0 N A:LYS460 4.2 12.4 1.0 CA A:LEU339 4.3 11.1 1.0 CB A:LEU339 4.4 11.5 1.0 N A:GLU340 4.4 10.3 1.0 CA A:LYS460 4.4 13.8 1.0 N A:ALA461 4.4 14.0 1.0 ND2 A:ASN487 4.4 9.7 1.0 CA A:ALA461 4.4 14.9 1.0 CA A:GLU340 4.5 10.7 1.0 CB A:ALA461 4.6 14.8 1.0 CB A:GLU340 4.7 10.9 1.0 C3 A:GOL1506 4.7 19.7 1.0 OE1 A:GLU465 4.8 14.8 1.0 CB A:LYS460 4.9 15.7 1.0 CG A:GLU448 4.9 10.7 1.0

Calcium binding site 2 out of 4 in the Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1499 b:8.2 occ:1.00 O A:LEU139 2.2 8.4 1.0 OD1 A:ASP138 2.3 7.8 1.0 O A:HOH2024 2.3 9.3 1.0 OE1 A:GLU141 2.3 7.8 1.0 OE1 A:GLU181 2.4 10.0 1.0 O A:HOH2064 2.5 10.7 1.0 O A:HOH2074 2.5 22.2 1.0 CD A:GLU141 3.3 8.2 1.0 CD A:GLU181 3.3 10.8 1.0 OE2 A:GLU141 3.4 9.3 1.0 C A:LEU139 3.5 7.7 1.0 O A:HOH2073 3.5 15.0 0.5 CG A:ASP138 3.5 8.5 1.0 CG A:GLU181 3.9 10.4 1.0 O4 A:PGE1504 3.9 19.1 0.5 N A:LEU139 4.0 8.3 1.0 CB A:GLU181 4.0 10.1 1.0 OD2 A:ASP138 4.2 9.2 1.0 C A:ASP138 4.2 8.6 1.0 OE2 A:GLU181 4.2 10.3 1.0 O A:HOH2063 4.3 14.1 1.0 CE A:LYS108 4.3 11.1 1.0 CA A:LEU139 4.3 8.2 1.0 N A:GLU141 4.4 7.1 1.0 OE2 A:GLU126 4.4 10.3 1.0 N A:SER140 4.4 7.9 1.0 CG A:LYS108 4.6 11.0 1.0 CA A:SER140 4.6 7.4 1.0 CA A:ASP138 4.6 8.7 1.0 O A:HOH2070 4.6 8.4 1.0 CB A:ASP138 4.7 8.5 1.0 O A:ASP138 4.7 8.2 1.0 CG A:GLU141 4.7 7.7 1.0 CD A:LYS108 4.8 10.9 1.0 CA A:GLU181 4.9 9.9 1.0 NZ A:LYS108 5.0 11.4 1.0

Calcium binding site 3 out of 4 in the Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1498 b:11.6 occ:1.00 OD1 B:ASN487 2.2 9.2 1.0 O B:LYS460 2.3 12.7 1.0 O B:LEU339 2.3 11.4 1.0 O B:HOH2243 2.4 14.7 1.0 OE1 B:GLU448 2.5 11.0 1.0 O3 B:GOL1501 2.5 19.4 1.0 O2 B:GOL1501 2.5 14.7 1.0 CG B:ASN487 3.3 9.8 1.0 C2 B:GOL1501 3.4 18.3 1.0 C B:LYS460 3.5 14.1 1.0 C B:LEU339 3.5 11.0 1.0 C3 B:GOL1501 3.5 18.7 1.0 CD B:GLU448 3.5 10.6 1.0 OE2 B:GLU448 3.7 10.4 1.0 O B:HOH2325 3.8 18.1 1.0 CB B:ASN487 4.0 9.9 1.0 N B:LYS460 4.2 13.4 1.0 CA B:LEU339 4.4 11.3 1.0 O B:HOH2366 4.4 38.1 1.0 ND2 B:ASN487 4.4 9.7 1.0 N B:ALA461 4.4 14.3 1.0 CA B:LYS460 4.4 14.2 1.0 CA B:ALA461 4.4 15.1 1.0 N B:GLU340 4.4 10.5 1.0 CB B:LEU339 4.4 11.9 1.0 CA B:GLU340 4.5 10.8 1.0 CB B:GLU340 4.6 11.2 1.0 CB B:ALA461 4.7 14.9 1.0 C1 B:GOL1501 4.8 18.3 1.0 OE1 B:GLU465 4.8 16.4 1.0 CB B:LYS460 4.9 16.3 1.0 CG B:GLU448 4.9 10.3 1.0

Calcium binding site 4 out of 4 in the Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Clostridial Cysteine Protease CWP84 C116A After Propeptide Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1499 b:7.6 occ:1.00 OD1 B:ASP138 2.3 7.4 1.0 OE1 B:GLU141 2.3 9.0 1.0 O B:HOH2022 2.3 11.1 1.0 O B:LEU139 2.4 8.8 1.0 OE1 B:GLU181 2.4 11.7 1.0 O B:HOH2063 2.4 11.0 1.0 O B:HOH2069 2.6 18.9 1.0 CD B:GLU141 3.3 9.3 1.0 CD B:GLU181 3.3 10.9 1.0 CG B:ASP138 3.5 8.2 1.0 OE2 B:GLU141 3.5 9.8 1.0 C B:LEU139 3.6 8.5 1.0 O B:HOH2068 3.6 22.2 1.0 CB B:GLU181 3.9 10.2 1.0 CG B:GLU181 3.9 10.9 1.0 N B:LEU139 4.0 8.4 1.0 OD2 B:ASP138 4.1 8.8 1.0 C B:ASP138 4.2 8.2 1.0 OE2 B:GLU181 4.2 11.7 1.0 O B:HOH2064 4.4 11.6 1.0 CE B:LYS108 4.4 10.4 1.0 OE2 B:GLU126 4.4 9.8 1.0 CA B:LEU139 4.4 8.5 1.0 N B:GLU141 4.4 8.0 1.0 CG B:LYS108 4.5 9.9 1.0 N B:SER140 4.5 8.2 1.0 O B:HOH2066 4.6 9.7 1.0 CA B:ASP138 4.6 8.6 1.0 CA B:SER140 4.6 8.1 1.0 CB B:ASP138 4.6 8.5 1.0 O B:ASP138 4.7 7.5 1.0 CD B:LYS108 4.7 10.1 1.0 CG B:GLU141 4.7 8.9 1.0 CA B:GLU181 4.9 9.7 1.0

W.J.Bradshaw, A.K.Roberts, C.C.Shone, K.R.Acharya. CWP84, A Clostridium Difficile Cysteine Protease, Exhibits Conformational Flexibility in the Absence of Its Propeptide Acta Crystallogr.,Sect.F 2015.
ISSN: ESSN 1744-3091
DOI: 10.1107/S2053230X15001065