Cobalt in PDB 5imh: D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis

The structure of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis, PDB code: 5imh was solved by R.Kono, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.24 / 2.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.337, 137.088, 101.297, 90.00, 100.75, 90.00
R / Rfree (%)	18.8 / 24.1

The binding sites of Cobalt atom in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis (pdb code 5imh). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis, PDB code: 5imh:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:85.4 occ:1.00 OE2 A:GLU334 2.3 47.8 1.0 CD A:GLU334 3.1 26.6 1.0 OE1 A:GLU334 3.3 25.9 1.0 O A:HOH612 3.9 27.8 1.0 O A:HOH718 4.2 29.6 1.0 CG A:GLU334 4.5 31.4 1.0

Cobalt binding site 2 out of 7 in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ A:Co502 b:50.6 occ:1.00 O A:HOH660 2.1 40.4 1.0 OD2 A:ASP201 2.3 51.3 1.0 CG A:ASP201 3.3 47.2 1.0 CB A:ASP201 3.9 48.6 1.0 O A:HOH603 4.1 37.2 1.0 OD1 A:ASP201 4.2 57.8 1.0

Cobalt binding site 3 out of 7 in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ B:Co501 b:81.6 occ:1.00 OD1 B:ASP184 2.3 30.9 1.0 NE2 B:HIS274 2.7 35.5 1.0 OD2 B:ASP184 2.7 43.2 1.0 CG B:ASP184 2.9 37.5 1.0 CD2 B:HIS274 3.4 34.9 1.0 CE1 B:HIS274 3.8 33.7 1.0 CB B:PRO182 4.3 24.2 1.0 CB B:ASP184 4.4 22.8 1.0 CG B:HIS274 4.6 35.5 1.0 ND1 B:HIS274 4.8 33.0 1.0 CG B:PRO182 5.0 22.9 1.0

Cobalt binding site 4 out of 7 in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ C:Co501 b:90.5 occ:1.00 O C:HOH651 3.0 37.2 1.0 OE2 C:GLU266 4.3 36.2 1.0 OE1 C:GLU266 4.4 39.0 1.0 OD1 A:ASP258 4.4 35.6 1.0 OD2 A:ASP258 4.6 44.2 1.0 OD2 C:ASP268 4.7 37.3 1.0 CD C:GLU266 4.8 34.3 1.0 CG A:ASP258 5.0 37.6 1.0

Cobalt binding site 5 out of 7 in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ C:Co502 b:70.3 occ:1.00 NE2 C:HIS274 2.6 43.7 1.0 OD2 C:ASP184 2.6 41.6 1.0 OD1 C:ASP184 2.7 34.7 1.0 CG C:ASP184 3.0 39.2 1.0 CD2 C:HIS274 3.3 35.3 1.0 CE1 C:HIS274 3.6 40.9 1.0 O C:HOH694 4.3 47.8 1.0 CG C:HIS274 4.4 37.4 1.0 ND1 C:HIS274 4.5 37.2 1.0 CB C:ASP184 4.6 33.7 1.0 CB C:PRO182 4.8 30.7 1.0 O C:HOH621 4.9 42.5 1.0

Cobalt binding site 6 out of 7 in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ D:Co501 b:91.7 occ:1.00 O D:HOH689 2.7 55.3 1.0 OE2 D:GLU266 3.9 38.1 1.0 OE1 D:GLU266 4.1 43.0 1.0 OD2 D:ASP268 4.2 41.9 1.0 O D:HOH612 4.3 50.5 1.0 CD D:GLU266 4.4 39.5 1.0 OD1 C:ASP258 4.8 46.2 1.0 OD2 C:ASP258 5.0 50.7 1.0 CB D:ASP268 5.0 26.2 1.0

Cobalt binding site 7 out of 7 in the D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of D31P Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ E:Co501 b:60.0 occ:1.00 O E:HOH601 2.4 38.1 1.0 OD2 E:ASP183 3.7 37.4 1.0 NZ E:LYS16 3.7 48.8 1.0 OD1 E:ASP183 4.1 42.3 1.0 OE1 E:GLU163 4.3 48.3 1.0 CG E:ASP183 4.3 42.5 1.0 NH1 E:ARG180 4.4 39.0 1.0 CZ E:ARG180 4.8 45.1 1.0 O E:GLU163 4.8 37.0 1.0 NH2 E:ARG180 5.0 41.9 1.0

R.Kono, K.Watanabe. A C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis; Substrate Recognition Mechanism and Autoproteolytic Mechanism in Enzyme Maturation To Be Published.