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Cobalt in PDB 2dd5: Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme

Enzymatic activity of Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme

All present enzymatic activity of Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme:
3.5.5.8;

Protein crystallography data

The structure of Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme, PDB code: 2dd5 was solved by T.Arakawa, Y.Kawano, S.Kataoka, Y.Katayama, N.Kamiya, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.80 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 170.187, 170.187, 282.469, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme (pdb code 2dd5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme, PDB code: 2dd5:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2dd5

Go back to Cobalt Binding Sites List in 2dd5
Cobalt binding site 1 out of 4 in the Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co301

b:14.3
occ:0.00
 N C:CSO133 2.0 16.0 1.0
N C:SER132 2.2 14.5 1.0
SG C:CSD131 2.3 13.5 1.0
SG C:CSO133 2.4 16.3 1.0
SG C:CYS128 2.5 13.6 1.0
O3 C:SO43001 2.8 32.8 1.0
C C:SER132 2.9 12.3 1.0
CA C:CSO133 2.9 9.4 1.0
CB C:CSO133 3.0 9.8 1.0
CA C:SER132 3.0 12.3 1.0
CB C:CSD131 3.1 8.8 1.0
C C:CSD131 3.1 11.5 1.0
OD C:CSO133 3.2 13.6 0.0
OD1 C:CSD131 3.2 11.7 0.0
CA C:CSD131 3.3 11.1 1.0
OD2 C:CSD131 3.3 11.6 0.0
CB C:CYS128 3.4 12.7 1.0
N C:CSD131 3.7 11.0 1.0
OG C:SER132 4.0 16.0 1.0
O C:SER132 4.0 16.9 1.0
CB C:SER132 4.1 14.1 1.0
S C:SO43001 4.2 34.7 1.0
O C:CSD131 4.3 15.8 1.0
C C:CSO133 4.3 13.2 1.0
O2 C:SO43001 4.7 37.4 1.0
O C:CSO133 4.7 11.9 1.0
C C:LEU130 4.7 9.9 1.0
CA C:CYS128 4.8 12.9 1.0
O C:CYS128 4.8 12.0 1.0
O4 C:SO43001 4.8 34.8 1.0
O C:HOH3015 4.9 12.0 1.0
O C:HOH3071 4.9 27.5 1.0
O C:SER181 5.0 18.1 1.0

Cobalt binding site 2 out of 4 in 2dd5

Go back to Cobalt Binding Sites List in 2dd5
Cobalt binding site 2 out of 4 in the Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co301

b:18.1
occ:0.00
 N F:CSO133 2.0 19.3 1.0
N F:SER132 2.2 17.9 1.0
SG F:CSD131 2.4 15.8 1.0
SG F:CSO133 2.4 18.9 1.0
SG F:CYS128 2.4 19.3 1.0
C F:SER132 2.9 16.5 1.0
CA F:CSO133 2.9 14.3 1.0
CB F:CSO133 3.0 13.2 1.0
CA F:SER132 3.0 15.5 1.0
CB F:CSD131 3.1 11.8 1.0
C F:CSD131 3.1 15.0 1.0
O4 F:SO43002 3.1 37.2 1.0
OD F:CSO133 3.2 16.2 0.0
OD1 F:CSD131 3.2 14.2 0.0
CA F:CSD131 3.3 14.5 1.0
OD2 F:CSD131 3.3 13.9 0.0
CB F:CYS128 3.4 16.4 1.0
N F:CSD131 3.7 14.7 1.0
OG F:SER132 4.0 18.2 1.0
O F:SER132 4.0 18.8 1.0
CB F:SER132 4.1 18.2 1.0
O F:CSD131 4.3 17.3 1.0
C F:CSO133 4.3 16.1 1.0
S F:SO43002 4.3 37.8 1.0
O1 F:SO43002 4.7 40.1 1.0
C F:LEU130 4.7 16.1 1.0
O2 F:SO43002 4.7 39.3 1.0
O F:CSO133 4.8 14.8 1.0
O F:CYS128 4.8 14.7 1.0
CA F:CYS128 4.8 16.5 1.0
O F:HOH3006 4.9 17.0 1.0
NH2 D:ARG55 5.0 14.2 1.0
O F:SER181 5.0 22.1 1.0
O F:HOH3076 5.0 28.5 1.0
NE E:ARG91 5.0 18.3 1.0

Cobalt binding site 3 out of 4 in 2dd5

Go back to Cobalt Binding Sites List in 2dd5
Cobalt binding site 3 out of 4 in the Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co301

b:13.8
occ:0.00
 N I:CSO133 2.0 17.7 1.0
N I:SER132 2.2 13.8 1.0
SG I:CSD131 2.3 14.3 1.0
SG I:CSO133 2.4 18.3 1.0
SG I:CYS128 2.5 11.9 1.0
C I:SER132 2.8 13.4 1.0
CA I:CSO133 2.9 12.2 1.0
O4 I:SO43003 3.0 33.1 1.0
CA I:SER132 3.0 12.4 1.0
CB I:CSO133 3.0 11.9 1.0
CB I:CSD131 3.1 8.1 1.0
C I:CSD131 3.1 10.1 1.0
OD1 I:CSD131 3.1 12.1 0.0
OD I:CSO133 3.1 15.6 0.0
CA I:CSD131 3.2 9.6 1.0
CB I:CYS128 3.4 9.9 1.0
OD2 I:CSD131 3.4 11.7 0.0
N I:CSD131 3.7 10.2 1.0
O I:SER132 4.0 17.4 1.0
OG I:SER132 4.0 16.1 1.0
CB I:SER132 4.1 13.7 1.0
O I:CSD131 4.2 13.9 1.0
S I:SO43003 4.3 34.1 1.0
C I:CSO133 4.3 14.0 1.0
O1 I:SO43003 4.6 35.1 1.0
O3 I:SO43003 4.7 35.2 1.0
C I:LEU130 4.7 11.4 1.0
O I:CSO133 4.7 10.8 1.0
CA I:CYS128 4.8 10.3 1.0
O I:CYS128 4.8 10.5 1.0
O I:HOH3043 4.9 13.4 1.0
O I:HOH3095 5.0 25.3 1.0
NE H:ARG91 5.0 10.8 1.0

Cobalt binding site 4 out of 4 in 2dd5

Go back to Cobalt Binding Sites List in 2dd5
Cobalt binding site 4 out of 4 in the Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus Native Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co301

b:12.8
occ:0.00
 N L:CSO133 2.0 13.6 1.0
N L:SER132 2.2 11.0 1.0
SG L:CSD131 2.4 12.1 1.0
SG L:CSO133 2.4 15.2 1.0
SG L:CYS128 2.5 9.6 1.0
C L:SER132 2.9 8.1 1.0
CA L:CSO133 2.9 9.0 1.0
O2 L:SO43004 3.0 30.6 1.0
CB L:CSO133 3.0 6.7 1.0
CA L:SER132 3.0 7.6 1.0
CB L:CSD131 3.1 5.2 1.0
C L:CSD131 3.1 6.8 1.0
OD L:CSO133 3.1 11.4 0.0
OD1 L:CSD131 3.2 9.3 0.0
CA L:CSD131 3.2 8.1 1.0
CB L:CYS128 3.3 8.4 1.0
OD2 L:CSD131 3.4 9.2 0.0
N L:CSD131 3.7 9.0 1.0
OG L:SER132 4.0 10.8 1.0
O L:SER132 4.0 12.5 1.0
CB L:SER132 4.1 10.9 1.0
S L:SO43004 4.2 34.3 1.0
O L:CSD131 4.3 10.7 1.0
C L:CSO133 4.3 12.0 1.0
O3 L:SO43004 4.6 37.4 1.0
O1 L:SO43004 4.7 36.0 1.0
C L:LEU130 4.7 9.8 1.0
CA L:CYS128 4.7 8.7 1.0
O L:CSO133 4.7 9.7 1.0
O L:CYS128 4.8 9.0 1.0
O J:HOH3021 4.9 20.6 1.0
O L:HOH3057 4.9 13.6 1.0

Reference:

T.Arakawa, Y.Kawano, S.Kataoka, Y.Katayama, N.Kamiya, M.Yohda, M.Odaka. Structure of Thiocyanate Hydrolase: A New Nitrile Hydratase Family Protein with A Novel Five-Coordinate Cobalt(III) Center. J.Mol.Biol. V. 366 1497 2007.
ISSN: ISSN 0022-2836
PubMed: 17222425
DOI: 10.1016/J.JMB.2006.12.011
Page generated: Sun Dec 13 10:37:24 2020

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