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Cobalt in PDB 2dxb: Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers

Enzymatic activity of Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers

All present enzymatic activity of Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers:
3.5.5.8;

Protein crystallography data

The structure of Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers, PDB code: 2dxb 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) 49.41 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.874, 245.141, 244.653, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.8

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers (pdb code 2dxb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers, PDB code: 2dxb:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 2dxb

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Cobalt binding site 1 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


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 Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co301

b:15.2
occ:0.59
 N C:CSO133 1.9 17.9 1.0
N C:SER132 2.1 17.2 1.0
SG C:CSD131 2.2 19.2 1.0
SG C:CYS128 2.5 17.4 1.0
SG C:CSO133 2.5 19.9 1.0
C C:SER132 2.7 18.0 1.0
CA C:SER132 2.9 17.1 1.0
CA C:CSO133 2.9 17.2 1.0
OD1 C:CSD131 3.0 19.1 0.8
OD2 C:CSD131 3.0 19.2 0.8
C C:CSD131 3.1 17.7 1.0
CB C:CSO133 3.1 16.9 1.0
CB C:CSD131 3.2 18.0 1.0
OD C:CSO133 3.2 18.3 0.3
CA C:CSD131 3.4 17.4 1.0
CB C:CYS128 3.5 13.1 1.0
O1 C:PO44001 3.6 43.7 1.0
N C:CSD131 3.8 16.2 1.0
O C:SER132 3.9 18.4 1.0
OG C:SER132 4.0 17.1 1.0
CB C:SER132 4.0 15.0 1.0
O C:CSD131 4.2 19.2 1.0
C C:CSO133 4.2 16.9 1.0
O2 C:PO44001 4.3 43.8 1.0
P C:PO44001 4.3 43.5 1.0
O3 C:PO44001 4.3 42.3 1.0
O C:CSO133 4.7 17.0 1.0
O C:CYS128 4.8 13.2 1.0
C C:LEU130 4.8 15.6 1.0
O C:HOH4098 4.8 22.8 1.0
CA C:CYS128 4.9 12.3 1.0
O C:HOH4099 4.9 25.6 1.0

Cobalt binding site 2 out of 8 in 2dxb

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Cobalt binding site 2 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


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 Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co301

b:13.4
occ:0.59
 N F:CSO133 1.9 15.1 1.0
N F:SER132 2.1 16.9 1.0
SG F:CSD131 2.2 19.7 1.0
SG F:CYS128 2.4 18.4 1.0
SG F:CSO133 2.5 21.2 1.0
C F:SER132 2.7 16.5 1.0
CA F:CSO133 2.8 15.1 1.0
CA F:SER132 2.9 17.4 1.0
OD1 F:CSD131 3.0 20.4 0.7
CB F:CSO133 3.0 16.4 1.0
C F:CSD131 3.1 17.8 1.0
CB F:CSD131 3.2 18.7 1.0
OD F:CSO133 3.2 17.8 0.2
OD2 F:CSD131 3.3 20.9 0.8
CA F:CSD131 3.4 17.6 1.0
CB F:CYS128 3.5 13.1 1.0
O1 F:PO44002 3.5 44.8 1.0
N F:CSD131 3.8 15.0 1.0
O F:SER132 3.9 14.4 1.0
OG F:SER132 4.0 20.6 1.0
CB F:SER132 4.0 17.8 1.0
O F:CSD131 4.2 20.5 1.0
C F:CSO133 4.2 14.9 1.0
P F:PO44002 4.3 44.6 1.0
O3 F:PO44002 4.3 47.4 1.0
O2 F:PO44002 4.4 44.4 1.0
O F:CSO133 4.6 14.3 1.0
C F:LEU130 4.9 15.2 1.0
CA F:CYS128 4.9 13.1 1.0
O F:CYS128 4.9 11.7 1.0

Cobalt binding site 3 out of 8 in 2dxb

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Cobalt binding site 3 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


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 Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co301

b:14.0
occ:0.58
 N I:CSO133 1.9 16.7 1.0
N I:SER132 2.1 18.4 1.0
SG I:CSD131 2.2 21.7 1.0
SG I:CYS128 2.4 18.4 1.0
SG I:CSO133 2.5 19.6 1.0
C I:SER132 2.7 17.9 1.0
CA I:CSO133 2.9 15.7 1.0
CA I:SER132 2.9 18.9 1.0
C I:CSD131 3.0 18.5 1.0
OD1 I:CSD131 3.1 21.9 0.8
OD2 I:CSD131 3.1 20.6 0.9
CB I:CSO133 3.1 14.9 1.0
CB I:CSD131 3.2 19.5 1.0
OD I:CSO133 3.2 17.6 0.2
CA I:CSD131 3.3 18.7 1.0
CB I:CYS128 3.5 14.9 1.0
O1 I:PO44003 3.6 43.7 1.0
N I:CSD131 3.8 17.1 1.0
O I:SER132 3.9 17.2 1.0
OG I:SER132 4.0 20.1 1.0
CB I:SER132 4.0 18.1 1.0
O I:CSD131 4.1 22.3 1.0
C I:CSO133 4.2 15.6 1.0
P I:PO44003 4.4 44.5 1.0
O3 I:PO44003 4.5 41.9 1.0
O2 I:PO44003 4.6 45.3 1.0
O I:CSO133 4.7 16.1 1.0
O I:CYS128 4.8 12.9 1.0
C I:LEU130 4.8 15.8 1.0
CA I:CYS128 4.9 13.7 1.0
O I:HOH4106 4.9 19.7 1.0

Cobalt binding site 4 out of 8 in 2dxb

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Cobalt binding site 4 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


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 Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co301

b:14.1
occ:0.58
 N L:CSO133 1.9 15.8 1.0
N L:SER132 2.1 18.5 1.0
SG L:CSD131 2.3 19.2 1.0
SG L:CYS128 2.5 18.6 1.0
SG L:CSO133 2.6 24.5 1.0
C L:SER132 2.7 17.3 1.0
CA L:SER132 2.9 18.0 1.0
CA L:CSO133 2.9 15.8 1.0
OD1 L:CSD131 3.0 21.1 0.6
C L:CSD131 3.1 19.4 1.0
O1 L:PO44004 3.1 46.3 1.0
CB L:CSO133 3.1 17.7 1.0
CB L:CSD131 3.2 18.7 1.0
OD2 L:CSD131 3.3 22.1 0.8
CA L:CSD131 3.4 18.5 1.0
OD L:CSO133 3.4 21.9 0.0
CB L:CYS128 3.5 12.7 1.0
N L:CSD131 3.8 15.1 1.0
O L:SER132 3.8 17.9 1.0
OG L:SER132 4.0 18.3 1.0
CB L:SER132 4.0 16.4 1.0
O L:CSD131 4.2 22.2 1.0
P L:PO44004 4.3 44.2 1.0
C L:CSO133 4.3 15.6 1.0
O2 L:PO44004 4.5 44.5 1.0
O3 L:PO44004 4.6 44.6 1.0
O L:CSO133 4.7 14.7 1.0
C L:LEU130 4.8 14.2 1.0
O L:CYS128 4.8 9.7 1.0
CA L:CYS128 4.9 12.2 1.0

Cobalt binding site 5 out of 8 in 2dxb

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Cobalt binding site 5 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Co301

b:15.1
occ:0.59
 N O:CSO133 1.9 16.0 1.0
N O:SER132 2.1 16.1 1.0
SG O:CSD131 2.2 18.7 1.0
SG O:CYS128 2.4 15.1 1.0
SG O:CSO133 2.4 19.8 1.0
C O:SER132 2.8 16.7 1.0
CA O:CSO133 2.9 15.5 1.0
CA O:SER132 2.9 16.7 1.0
OD1 O:CSD131 3.0 20.2 0.7
CB O:CSO133 3.1 15.1 1.0
C O:CSD131 3.1 17.0 1.0
CB O:CSD131 3.2 16.1 1.0
OD2 O:CSD131 3.2 18.0 0.8
OD O:CSO133 3.3 17.2 0.2
CA O:CSD131 3.4 16.4 1.0
CB O:CYS128 3.4 12.9 1.0
N O:CSD131 3.8 15.5 1.0
O1 O:PO44005 3.9 43.3 1.0
O O:SER132 3.9 16.7 1.0
O4 O:PO44005 4.0 42.1 1.0
OG O:SER132 4.1 19.2 1.0
CB O:SER132 4.1 16.3 1.0
O O:CSD131 4.2 19.9 1.0
C O:CSO133 4.2 15.3 1.0
P O:PO44005 4.4 43.4 1.0
O O:CSO133 4.6 15.7 1.0
O3 O:PO44005 4.6 44.4 1.0
O O:CYS128 4.8 14.0 1.0
O M:HOH156 4.8 26.1 1.0
C O:LEU130 4.8 14.4 1.0
CA O:CYS128 4.8 12.5 1.0
O O:HOH4032 5.0 19.0 1.0

Cobalt binding site 6 out of 8 in 2dxb

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Cobalt binding site 6 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Co301

b:16.7
occ:0.58
 N R:CSO133 1.9 16.9 1.0
N R:SER132 2.1 17.9 1.0
SG R:CSD131 2.3 18.6 1.0
SG R:CSO133 2.5 22.0 1.0
SG R:CYS128 2.5 16.7 1.0
C R:SER132 2.7 18.3 1.0
CA R:CSO133 2.9 16.7 1.0
CA R:SER132 2.9 18.6 1.0
OD1 R:CSD131 3.0 20.3 0.7
CB R:CSO133 3.1 18.0 1.0
C R:CSD131 3.1 18.2 1.0
CB R:CSD131 3.2 16.6 1.0
OD R:CSO133 3.3 20.0 0.1
OD2 R:CSD131 3.3 19.2 0.8
CA R:CSD131 3.4 16.9 1.0
CB R:CYS128 3.5 12.8 1.0
O1 R:PO44006 3.6 49.5 1.0
O R:SER132 3.8 17.0 1.0
N R:CSD131 3.8 14.4 1.0
OG R:SER132 4.0 22.6 1.0
CB R:SER132 4.0 18.5 1.0
O3 R:PO44006 4.2 49.5 1.0
O R:CSD131 4.2 21.1 1.0
C R:CSO133 4.2 16.9 1.0
P R:PO44006 4.4 49.8 1.0
O2 R:PO44006 4.7 50.6 1.0
O R:CSO133 4.7 17.6 1.0
C R:LEU130 4.9 13.7 1.0
O R:CYS128 4.9 10.6 1.0
CA R:CYS128 4.9 11.1 1.0
O R:HOH4047 5.0 24.7 1.0
O R:HOH4021 5.0 25.6 1.0
NH2 P:ARG55 5.0 12.2 1.0

Cobalt binding site 7 out of 8 in 2dxb

Go back to Cobalt Binding Sites List in 2dxb
Cobalt binding site 7 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Co301

b:14.0
occ:0.58
 N U:CSO133 1.9 14.4 1.0
SG U:CSD131 2.1 17.1 1.0
N U:SER132 2.1 16.1 1.0
SG U:CYS128 2.5 16.1 1.0
SG U:CSO133 2.5 21.0 1.0
C U:SER132 2.8 15.6 1.0
CA U:CSO133 2.9 14.2 1.0
OD1 U:CSD131 2.9 20.1 0.7
CA U:SER132 3.0 14.9 1.0
CB U:CSO133 3.1 15.0 1.0
C U:CSD131 3.1 15.5 1.0
CB U:CSD131 3.1 16.9 1.0
OD2 U:CSD131 3.2 18.5 0.8
OD U:CSO133 3.2 17.9 0.2
CA U:CSD131 3.4 15.0 1.0
CB U:CYS128 3.5 10.8 1.0
O1 U:PO44007 3.5 44.1 1.0
N U:CSD131 3.8 15.1 1.0
O U:SER132 3.9 16.6 1.0
OG U:SER132 4.1 17.1 1.0
CB U:SER132 4.1 15.0 1.0
O U:CSD131 4.2 17.6 1.0
C U:CSO133 4.2 13.6 1.0
P U:PO44007 4.3 43.1 1.0
O2 U:PO44007 4.3 41.7 1.0
O4 U:PO44007 4.5 42.7 1.0
O U:CSO133 4.7 14.8 1.0
C U:LEU130 4.8 14.3 1.0
O U:CYS128 4.8 12.0 1.0
CA U:CYS128 4.9 12.9 1.0
O U:HOH4120 5.0 24.0 1.0
NH2 S:ARG55 5.0 9.8 1.0

Cobalt binding site 8 out of 8 in 2dxb

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Cobalt binding site 8 out of 8 in the Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Recombinant Thiocyanate Hydrolase Comprising Partially-Modified Cobalt Centers within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Co301

b:16.9
occ:0.59
 N X:CSO133 1.9 16.8 1.0
N X:SER132 2.1 17.0 1.0
SG X:CSD131 2.3 19.1 1.0
SG X:CYS128 2.5 18.4 1.0
SG X:CSO133 2.6 21.6 1.0
C X:SER132 2.7 16.8 1.0
CA X:SER132 2.9 17.3 1.0
CA X:CSO133 2.9 16.8 1.0
C X:CSD131 3.1 18.2 1.0
OD1 X:CSD131 3.1 19.2 0.6
CB X:CSO133 3.1 17.1 1.0
OD2 X:CSD131 3.2 18.6 0.9
CB X:CSD131 3.2 17.9 1.0
OD X:CSO133 3.3 19.2 0.3
CA X:CSD131 3.4 17.5 1.0
O1 X:PO44008 3.4 45.8 1.0
CB X:CYS128 3.5 11.6 1.0
N X:CSD131 3.8 15.6 1.0
O X:SER132 3.8 18.0 1.0
OG X:SER132 4.0 19.3 1.0
CB X:SER132 4.1 15.9 1.0
O X:CSD131 4.2 21.5 1.0
C X:CSO133 4.2 17.1 1.0
P X:PO44008 4.4 47.0 1.0
O4 X:PO44008 4.4 45.2 1.0
O3 X:PO44008 4.7 48.4 1.0
O X:CSO133 4.7 16.2 1.0
C X:LEU130 4.8 14.8 1.0
O X:HOH4032 4.9 22.7 1.0
O X:CYS128 4.9 10.2 1.0
O X:HOH4087 4.9 27.8 1.0
CA X:CYS128 4.9 11.7 1.0
NH2 V:ARG55 4.9 8.0 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 Dec 13 10:37:35 2020

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