Atomistry » Cobalt » PDB 5img-5np4 » 5img
Atomistry »
  Cobalt »
    PDB 5img-5np4 »
      5img »

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

Protein crystallography data

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

Cobalt Binding Sites:

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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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 5img

Go back to Cobalt Binding Sites List in 5img
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

Reference:

R.Kono, K.Watanabe. A C69-Family Cysteine Dipeptidase From Lactobacillus Farciminis; Substrate Recognition Mechanism and Autoproteolytic Mechanism in Enzyme Maturation To Be Published.
Page generated: Sun Dec 13 10:47:45 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy