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Cobalt in PDB 2dxc: Recombinant Thiocyanate Hydrolase, Fully-Matured Form

Enzymatic activity of Recombinant Thiocyanate Hydrolase, Fully-Matured Form

All present enzymatic activity of Recombinant Thiocyanate Hydrolase, Fully-Matured Form:
3.5.5.8;

Protein crystallography data

The structure of Recombinant Thiocyanate Hydrolase, Fully-Matured Form, PDB code: 2dxc was solved by T.Arakawa, Y.Kawano, Y.Katayama, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.85 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.874, 170.531, 175.152, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.3

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Recombinant Thiocyanate Hydrolase, Fully-Matured Form (pdb code 2dxc). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Recombinant Thiocyanate Hydrolase, Fully-Matured Form, PDB code: 2dxc:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2dxc

Go back to Cobalt Binding Sites List in 2dxc
Cobalt binding site 1 out of 4 in the Recombinant Thiocyanate Hydrolase, Fully-Matured Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Recombinant Thiocyanate Hydrolase, Fully-Matured Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co301

b:6.0
occ:0.61
 N C:CSO133 1.9 11.6 1.0
N C:SER132 2.1 10.6 1.0
SG C:CSD131 2.2 13.6 1.0
SG C:CYS128 2.4 15.4 1.0
O2 C:TLA3001 2.4 31.1 1.0
SG C:CSO133 2.4 17.1 1.0
C C:SER132 2.8 13.0 1.0
OD C:CSO133 2.9 14.6 0.8
CA C:CSO133 2.9 11.6 1.0
CA C:SER132 2.9 12.0 1.0
C C:CSD131 3.1 10.7 1.0
OD1 C:CSD131 3.1 12.0 0.7
CB C:CSO133 3.1 12.5 1.0
CB C:CSD131 3.1 11.1 1.0
OD2 C:CSD131 3.1 13.9 0.7
CA C:CSD131 3.3 10.5 1.0
CB C:CYS128 3.4 9.6 1.0
N C:CSD131 3.8 9.6 1.0
C2 C:TLA3001 3.9 31.9 1.0
O C:SER132 3.9 13.6 1.0
OG C:SER132 4.1 15.7 1.0
CB C:SER132 4.1 12.4 1.0
O C:CSD131 4.2 12.8 1.0
C C:CSO133 4.3 12.0 1.0
O11 C:TLA3001 4.3 31.7 1.0
C1 C:TLA3001 4.6 29.0 1.0
O C:CSO133 4.7 10.3 1.0
O41 C:TLA3001 4.7 27.1 1.0
C3 C:TLA3001 4.7 31.7 1.0
C C:LEU130 4.8 9.2 1.0
C4 C:TLA3001 4.8 30.7 1.0
O C:CYS128 4.8 8.3 1.0
O3 C:TLA3001 4.8 35.5 1.0
CA C:CYS128 4.8 10.1 1.0
NH2 A:ARG55 4.9 7.2 1.0
O C:SER181 5.0 14.1 1.0

Cobalt binding site 2 out of 4 in 2dxc

Go back to Cobalt Binding Sites List in 2dxc
Cobalt binding site 2 out of 4 in the Recombinant Thiocyanate Hydrolase, Fully-Matured Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Recombinant Thiocyanate Hydrolase, Fully-Matured Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co301

b:14.8
occ:0.60
 N F:CSO133 1.9 13.1 1.0
N F:SER132 2.2 13.1 1.0
SG F:CSD131 2.3 15.4 1.0
SG F:CSO133 2.4 17.7 1.0
SG F:CYS128 2.5 14.2 1.0
OD F:CSO133 2.8 16.7 0.9
C F:SER132 2.8 13.4 1.0
CA F:CSO133 2.9 13.3 1.0
CA F:SER132 3.0 12.8 1.0
O2 E:TLA3002 3.0 41.4 1.0
OD1 F:CSD131 3.0 13.7 0.9
CB F:CSO133 3.1 14.5 1.0
C F:CSD131 3.1 13.6 1.0
CB F:CSD131 3.2 13.0 1.0
CA F:CSD131 3.3 12.3 1.0
OD2 F:CSD131 3.4 14.6 0.7
CB F:CYS128 3.4 10.8 1.0
N F:CSD131 3.8 11.1 1.0
O F:SER132 4.0 13.3 1.0
OG F:SER132 4.1 16.7 1.0
CB F:SER132 4.1 13.8 1.0
O F:CSD131 4.2 14.7 1.0
C F:CSO133 4.2 13.0 1.0
C2 E:TLA3002 4.4 39.7 1.0
O11 E:TLA3002 4.6 34.1 1.0
O3 E:TLA3002 4.6 44.8 1.0
O F:CSO133 4.7 11.9 1.0
C F:LEU130 4.8 11.2 1.0
O41 E:TLA3002 4.8 46.6 1.0
CA F:CYS128 4.8 9.8 1.0
O F:CYS128 4.8 9.5 1.0
C1 E:TLA3002 4.9 34.7 1.0
O F:SER181 4.9 17.9 1.0
C3 E:TLA3002 4.9 42.4 1.0
NH2 D:ARG55 5.0 11.0 1.0

Cobalt binding site 3 out of 4 in 2dxc

Go back to Cobalt Binding Sites List in 2dxc
Cobalt binding site 3 out of 4 in the Recombinant Thiocyanate Hydrolase, Fully-Matured Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Recombinant Thiocyanate Hydrolase, Fully-Matured Form within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co301

b:7.8
occ:0.58
 N I:CSO133 1.9 11.7 1.0
N I:SER132 2.1 12.1 1.0
SG I:CSD131 2.2 12.9 1.0
SG I:CYS128 2.4 12.7 1.0
SG I:CSO133 2.5 17.6 1.0
O2 I:TLA3003 2.5 45.1 1.0
C I:SER132 2.8 12.1 1.0
OD I:CSO133 2.8 13.9 0.8
CA I:SER132 2.9 11.8 1.0
CA I:CSO133 2.9 11.6 1.0
OD1 I:CSD131 3.1 13.5 0.9
C I:CSD131 3.1 12.7 1.0
CB I:CSO133 3.1 13.1 1.0
OD2 I:CSD131 3.2 13.4 0.6
CB I:CSD131 3.2 11.9 1.0
CA I:CSD131 3.4 12.2 1.0
CB I:CYS128 3.4 11.1 1.0
N I:CSD131 3.8 10.5 1.0
C2 I:TLA3003 3.8 46.5 1.0
O I:SER132 3.9 11.3 1.0
CB I:SER132 4.1 12.3 1.0
OG I:SER132 4.1 13.4 1.0
O I:CSD131 4.2 14.8 1.0
O11 I:TLA3003 4.3 45.6 1.0
C I:CSO133 4.3 12.1 1.0
C1 I:TLA3003 4.7 44.7 1.0
O I:CSO133 4.7 11.7 1.0
C I:LEU130 4.8 9.0 1.0
O I:CYS128 4.8 8.1 1.0
CA I:CYS128 4.8 10.4 1.0
C4 I:TLA3003 4.8 49.0 1.0
C3 I:TLA3003 4.8 47.9 1.0
O41 I:TLA3003 4.9 51.3 1.0
O I:SER181 5.0 16.9 1.0
NH2 G:ARG55 5.0 7.5 1.0
NE H:ARG91 5.0 9.7 1.0
O I:HOH3159 5.0 32.9 1.0

Cobalt binding site 4 out of 4 in 2dxc

Go back to Cobalt Binding Sites List in 2dxc
Cobalt binding site 4 out of 4 in the Recombinant Thiocyanate Hydrolase, Fully-Matured Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Recombinant Thiocyanate Hydrolase, Fully-Matured Form within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co301

b:9.6
occ:0.60
 N L:CSO133 1.9 10.4 1.0
N L:SER132 2.2 10.5 1.0
SG L:CSD131 2.2 12.6 1.0
SG L:CSO133 2.4 14.5 1.0
SG L:CYS128 2.4 10.8 1.0
O2 L:TLA3004 2.5 35.9 1.0
C L:SER132 2.8 11.4 1.0
CA L:CSO133 2.9 9.5 1.0
OD L:CSO133 2.9 14.4 0.7
OD2 L:CSD131 3.0 14.7 0.8
CA L:SER132 3.0 10.4 1.0
CB L:CSO133 3.1 11.1 1.0
C L:CSD131 3.1 11.2 1.0
CB L:CSD131 3.1 11.1 1.0
OD1 L:CSD131 3.2 15.1 0.9
CA L:CSD131 3.4 10.2 1.0
CB L:CYS128 3.5 8.8 1.0
N L:CSD131 3.8 9.1 1.0
C2 L:TLA3004 3.9 36.5 1.0
O L:SER132 3.9 10.6 1.0
OG L:SER132 4.1 13.5 1.0
CB L:SER132 4.2 11.8 1.0
O L:CSD131 4.2 13.1 1.0
C L:CSO133 4.2 10.5 1.0
O11 L:TLA3004 4.5 34.5 1.0
O41 L:TLA3004 4.6 39.0 1.0
O L:CSO133 4.7 9.7 1.0
C4 L:TLA3004 4.7 37.5 1.0
C3 L:TLA3004 4.8 37.8 1.0
C L:LEU130 4.8 9.0 1.0
C1 L:TLA3004 4.8 32.6 1.0
CA L:CYS128 4.9 8.6 1.0
O L:CYS128 4.9 7.5 1.0
NE K:ARG91 4.9 10.4 1.0
NH2 J:ARG55 4.9 7.0 1.0
O L:SER181 5.0 16.1 1.0

Reference:

T.Arakawa, Y.Kawano, Y.Katayama, H.Nakayama, N.Dohmae, M.Yohda, M.Odaka. Structural Basis For Catalytic Activation of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification J.Am.Chem.Soc. V. 131 14838 2009.
ISSN: ISSN 0002-7863
PubMed: 19785438
DOI: 10.1021/JA903979S
Page generated: Sun Jul 13 18:08:22 2025

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