Cobalt in PDB 5img: C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis

The structure of C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis, PDB code: 5img 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)	40.53 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.944, 182.788, 158.523, 90.00, 102.19, 90.00
R / Rfree (%)	13.8 / 16.9

Pages:

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

Binding sites:

The binding sites of Cobalt atom in the C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis (pdb code 5img). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 11 binding sites of Cobalt where determined in the C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis, PDB code: 5img:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 11 in the C9A 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 C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ C:Co503 b:27.6 occ:1.00 OD1 C:ASP184 2.2 11.5 1.0 NE2 C:HIS274 2.2 16.1 1.0 OD2 C:ASP184 2.4 13.6 1.0 CG C:ASP184 2.6 12.7 1.0 CD2 C:HIS274 3.1 16.0 1.0 CE1 C:HIS274 3.3 15.2 1.0 CB C:PRO182 4.1 11.7 1.0 CB C:ASP184 4.2 9.2 1.0 CG C:HIS274 4.3 16.3 1.0 ND1 C:HIS274 4.3 16.1 1.0 CG C:PRO182 4.7 8.8 1.0 C C:ASP184 4.9 9.8 1.0 CA C:ASP184 4.9 11.2 1.0

Cobalt binding site 2 out of 11 in the C9A 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 C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ C:Co504 b:21.0 occ:1.00 OD2 C:ASP66 2.1 17.3 1.0 O C:HOH614 2.3 20.6 1.0 O C:HOH925 2.3 16.0 1.0 CG C:ASP66 3.0 16.6 1.0 OD1 C:ASP66 3.2 20.5 1.0 O C:HOH862 4.1 19.6 1.0 O C:HOH1220 4.2 28.4 1.0 CB C:ASP66 4.4 15.7 1.0 O C:LEU64 4.6 14.2 1.0 N C:ASP66 4.8 13.9 1.0

Cobalt binding site 3 out of 11 in the C9A 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 C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ D:Co501 b:20.5 occ:1.00 O D:HOH775 2.0 17.3 1.0 OE2 D:GLU428 2.1 13.3 1.0 O D:HOH731 2.1 17.0 1.0 CD D:GLU428 3.1 16.6 1.0 OE1 D:GLU428 3.4 15.3 1.0 NH1 D:ARG70 4.2 14.2 1.0 OD1 D:ASN357 4.2 10.6 1.0 O D:HOH666 4.2 26.6 1.0 O D:HOH994 4.3 18.4 1.0 O D:HOH859 4.3 25.8 1.0 O D:HOH1105 4.4 34.9 1.0 CG D:GLU428 4.4 12.4 1.0 CG2 D:ILE427 4.5 16.5 1.0 NH2 D:ARG70 4.7 14.1 1.0 CZ D:ARG70 4.8 14.0 1.0

Cobalt binding site 4 out of 11 in the C9A 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 C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ E:Co502 b:33.3 occ:1.00 O E:HOH915 2.2 25.2 1.0 OD1 E:ASP203 2.2 25.9 1.0 OD2 E:ASP204 2.7 37.3 1.0 OD1 E:ASP204 3.1 30.0 1.0 CG E:ASP204 3.1 28.0 1.0 CG E:ASP203 3.1 26.9 1.0 OD2 E:ASP203 3.4 21.8 1.0 O E:HOH679 3.9 30.8 1.0 NH2 E:ARG180 4.1 32.8 1.0 CB E:ASP204 4.4 20.5 1.0 CB E:ASP203 4.4 23.4 1.0 N E:ASP204 4.6 15.2 1.0 C E:ASP203 4.8 21.0 1.0 O E:HOH1078 5.0 29.7 1.0

Cobalt binding site 5 out of 11 in the C9A 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 C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ F:Co501 b:24.6 occ:1.00 O F:HOH618 2.2 23.2 1.0 O F:HOH652 2.3 17.2 1.0 OE1 F:GLU163 4.1 21.9 1.0 OD2 F:ASP183 4.1 17.6 1.0 OD1 F:ASP183 4.3 13.4 1.0 OE2 F:GLU164 4.5 19.0 1.0 NH1 F:ARG180 4.5 17.1 1.0 O F:GLU163 4.6 10.6 1.0 CG F:GLU164 4.6 11.8 1.0 CG F:ASP183 4.6 16.9 1.0 NZ F:LYS16 4.8 18.7 1.0 CE F:LYS16 4.9 19.2 1.0 CZ F:ARG180 4.9 21.8 1.0

Cobalt binding site 6 out of 11 in the C9A 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 C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ F:Co502 b:34.7 occ:1.00 O F:HOH630 2.6 26.9 1.0 OD1 F:ASP201 4.1 14.6 1.0

Cobalt binding site 7 out of 11 in the C9A 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 C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ F:Co503 b:59.7 occ:1.00 O G:HOH1131 1.9 36.2 1.0 O G:HOH725 2.2 29.7 1.0 O F:HOH767 2.5 31.6 1.0 O F:HOH646 2.6 20.6 1.0 O G:HOH1058 2.7 33.8 1.0 OE2 F:GLU266 4.2 13.2 1.0 O F:HOH806 4.2 35.2 1.0 O F:HOH1159 4.2 45.7 1.0 OD2 G:ASP258 4.3 28.3 1.0 OD2 F:ASP268 4.4 14.1 1.0 OE1 F:GLU266 4.6 16.2 1.0 OD1 G:ASP258 4.6 28.6 1.0 CD F:GLU266 4.8 13.0 1.0 O G:HOH961 4.9 18.9 1.0 CG G:ASP258 4.9 21.2 1.0

Cobalt binding site 8 out of 11 in the C9A 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 8 of C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ G:Co502 b:21.1 occ:1.00 O G:HOH649 2.1 13.3 1.0 OD2 G:ASP184 2.1 15.8 1.0 O G:HOH927 2.2 18.2 1.0 NE2 G:HIS274 2.3 18.7 1.0 CG G:ASP184 3.0 14.4 1.0 CD2 G:HIS274 3.1 21.2 1.0 OD1 G:ASP184 3.2 13.1 1.0 CE1 G:HIS274 3.4 20.2 1.0 O G:HOH1097 4.2 35.6 1.0 CG G:HIS274 4.3 11.6 1.0 ND1 G:HIS274 4.4 14.2 1.0 CB G:ASP184 4.4 9.2 1.0 O G:HOH1087 4.6 35.5 1.0

Cobalt binding site 9 out of 11 in the C9A 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 9 of C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ H:Co503 b:57.6 occ:1.00 O I:HOH1000 2.1 39.0 1.0 O I:HOH754 2.3 40.4 1.0 O I:HOH531 2.5 28.9 1.0 O H:HOH1076 2.5 39.6 1.0 O H:HOH684 2.6 43.1 1.0 O H:HOH1156 2.6 44.5 1.0 O I:HOH779 3.8 35.7 1.0 OE2 I:GLU266 4.2 12.5 1.0 OD2 H:ASP258 4.3 27.7 1.0 OD1 H:ASP258 4.4 29.9 1.0 OE1 I:GLU266 4.6 15.7 1.0 OD2 I:ASP268 4.6 19.7 1.0 O H:HOH991 4.7 20.0 1.0 CG H:ASP258 4.7 19.8 1.0 CG H:PRO257 4.8 14.6 1.0 CD I:GLU266 4.8 14.7 1.0 O I:HOH814 4.9 14.9 1.0

Cobalt binding site 10 out of 11 in the C9A 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 10 of C9A Mutant of C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis within 5.0Å range: probe atom residue distance (Å) B Occ H:Co504 b:39.5 occ:1.00 OD1 H:ASP199 2.0 20.0 1.0 O H:HOH621 2.3 19.5 1.0 CG H:ASP199 2.9 24.3 1.0 CB H:ASP201 3.0 21.3 1.0 OD2 H:ASP199 3.2 25.9 1.0 OD2 H:ASP201 3.3 24.4 1.0 CG H:ASP201 3.5 25.8 1.0 N H:ASP201 3.8 15.6 1.0 CA H:ASP201 3.9 19.4 1.0 O H:HOH1007 4.2 19.2 1.0 CB H:ASP199 4.3 13.9 1.0 O H:HOH1122 4.3 26.9 1.0 C H:ASP201 4.5 18.3 1.0 OD1 H:ASP201 4.6 28.7 1.0 N H:SER202 4.6 14.4 1.0 CA H:ASP199 4.6 15.4 1.0 N H:PHE200 4.7 15.1 1.0 C H:ASP199 4.7 13.9 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.