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Cobalt in PDB 3vyg: Crystal Structure of Thiocyanate Hydrolase Mutant R136W

Enzymatic activity of Crystal Structure of Thiocyanate Hydrolase Mutant R136W

All present enzymatic activity of Crystal Structure of Thiocyanate Hydrolase Mutant R136W:
3.5.5.8;

Protein crystallography data

The structure of Crystal Structure of Thiocyanate Hydrolase Mutant R136W, PDB code: 3vyg was solved by Y.Yamanaka, M.Sato, T.Arakawa, S.Namima, S.Hori, A.Ohtaki, K.Noguchi, 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) 33.96 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.448, 172.398, 172.531, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.8

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Thiocyanate Hydrolase Mutant R136W (pdb code 3vyg). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Thiocyanate Hydrolase Mutant R136W, PDB code: 3vyg:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 3vyg

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Cobalt binding site 1 out of 4 in the Crystal Structure of Thiocyanate Hydrolase Mutant R136W


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Thiocyanate Hydrolase Mutant R136W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co301

b:12.5
occ:0.61
 N C:CSO133 1.9 14.5 1.0
N C:SER132 2.0 14.6 1.0
SG C:CSD131 2.1 17.7 1.0
SG C:CSO133 2.3 20.6 1.0
SG C:CYS128 2.4 16.2 1.0
C C:SER132 2.8 14.6 1.0
CA C:CSO133 2.9 13.8 1.0
CA C:SER132 2.9 14.3 1.0
CB C:CSO133 3.0 15.0 1.0
C C:CSD131 3.0 15.9 1.0
OD1 C:CSD131 3.1 13.1 0.7
CB C:CSD131 3.2 15.7 1.0
OD C:CSO133 3.2 29.3 0.8
OD2 C:CSD131 3.2 18.7 0.7
CB C:CYS128 3.4 13.9 1.0
CA C:CSD131 3.4 14.5 1.0
N C:CSD131 3.7 12.7 1.0
OG C:SER132 3.9 18.4 1.0
O C:SER132 4.0 16.7 1.0
CB C:SER132 4.1 18.2 1.0
O C:CSD131 4.1 18.3 1.0
C C:CSO133 4.2 15.0 1.0
O C:CSO133 4.5 15.5 1.0
C C:LEU130 4.7 13.5 1.0
CA C:CYS128 4.8 12.5 1.0
O C:HOH526 4.8 22.0 1.0
O C:HOH454 4.9 18.9 1.0
O C:CYS128 4.9 13.6 1.0
NH2 A:ARG55 5.0 14.0 1.0

Cobalt binding site 2 out of 4 in 3vyg

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Cobalt binding site 2 out of 4 in the Crystal Structure of Thiocyanate Hydrolase Mutant R136W


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Thiocyanate Hydrolase Mutant R136W within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co301

b:12.5
occ:0.61
 N F:CSO133 1.9 13.8 1.0
N F:SER132 2.0 14.3 1.0
SG F:CSD131 2.1 17.7 1.0
SG F:CSO133 2.3 20.7 1.0
SG F:CYS128 2.4 16.7 1.0
C F:SER132 2.8 14.7 1.0
CA F:CSO133 2.9 14.0 1.0
CA F:SER132 2.9 14.2 1.0
CB F:CSO133 3.0 15.9 1.0
C F:CSD131 3.0 15.7 1.0
OD1 F:CSD131 3.1 13.6 0.7
OD2 F:CSD131 3.1 19.7 0.7
CB F:CSD131 3.1 15.2 1.0
OD F:CSO133 3.2 31.2 0.8
CB F:CYS128 3.4 15.0 1.0
CA F:CSD131 3.4 14.0 1.0
N F:CSD131 3.8 12.3 1.0
OG F:SER132 3.9 18.6 1.0
O F:SER132 3.9 17.2 1.0
CB F:SER132 4.1 16.9 1.0
O F:CSD131 4.1 18.1 1.0
C F:CSO133 4.2 15.5 1.0
O F:CSO133 4.5 16.8 1.0
CA F:CYS128 4.7 12.9 1.0
C F:LEU130 4.7 12.2 1.0
O F:HOH499 4.8 24.4 1.0
O F:HOH463 4.9 19.1 1.0
O F:CYS128 4.9 14.2 1.0
NH2 D:ARG55 5.0 15.5 1.0

Cobalt binding site 3 out of 4 in 3vyg

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Cobalt binding site 3 out of 4 in the Crystal Structure of Thiocyanate Hydrolase Mutant R136W


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Thiocyanate Hydrolase Mutant R136W within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co301

b:13.4
occ:0.61
 N I:CSO133 1.9 12.2 1.0
N I:SER132 2.0 15.3 1.0
SG I:CSD131 2.1 16.6 1.0
SG I:CSO133 2.3 21.1 1.0
SG I:CYS128 2.4 16.3 1.0
C I:SER132 2.8 16.0 1.0
CA I:CSO133 2.9 15.6 1.0
CA I:SER132 2.9 13.6 1.0
CB I:CSO133 3.0 14.8 1.0
C I:CSD131 3.0 17.5 1.0
OD I:CSO133 3.1 32.9 0.8
CB I:CSD131 3.1 16.2 1.0
OD2 I:CSD131 3.1 17.0 0.7
OD1 I:CSD131 3.2 15.8 0.7
CA I:CSD131 3.3 16.5 1.0
CB I:CYS128 3.4 14.2 1.0
N I:CSD131 3.7 12.6 1.0
OG I:SER132 3.9 21.6 1.0
CB I:SER132 4.0 16.8 1.0
O I:CSD131 4.0 18.2 1.0
O I:SER132 4.1 16.4 1.0
C I:CSO133 4.2 15.9 1.0
O I:CSO133 4.6 14.6 1.0
C I:LEU130 4.7 14.3 1.0
O I:HOH473 4.8 23.1 1.0
CA I:CYS128 4.8 12.0 1.0
O I:CYS128 4.8 13.5 1.0
O I:HOH424 4.9 18.0 1.0
NH2 G:ARG55 5.0 10.8 1.0

Cobalt binding site 4 out of 4 in 3vyg

Go back to Cobalt Binding Sites List in 3vyg
Cobalt binding site 4 out of 4 in the Crystal Structure of Thiocyanate Hydrolase Mutant R136W


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Thiocyanate Hydrolase Mutant R136W within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co301

b:13.1
occ:0.61
 N L:CSO133 1.9 13.2 1.0
N L:SER132 2.0 14.8 1.0
SG L:CSD131 2.2 16.9 1.0
SG L:CSO133 2.3 21.4 1.0
SG L:CYS128 2.4 16.2 1.0
C L:SER132 2.8 16.1 1.0
CA L:SER132 2.9 13.2 1.0
CA L:CSO133 2.9 15.4 1.0
CB L:CSO133 3.0 14.4 1.0
C L:CSD131 3.0 17.1 1.0
OD L:CSO133 3.1 33.3 0.8
CB L:CSD131 3.1 14.3 1.0
OD2 L:CSD131 3.1 17.1 0.7
OD1 L:CSD131 3.2 13.2 0.7
CB L:CYS128 3.3 13.2 1.0
CA L:CSD131 3.3 15.2 1.0
N L:CSD131 3.7 12.8 1.0
O L:SER132 4.0 16.2 1.0
OG L:SER132 4.0 21.2 1.0
O L:CSD131 4.1 17.4 1.0
CB L:SER132 4.1 15.8 1.0
C L:CSO133 4.2 15.6 1.0
O L:CSO133 4.6 14.3 1.0
C L:LEU130 4.7 13.3 1.0
O L:HOH487 4.8 23.3 1.0
CA L:CYS128 4.8 11.4 1.0
O L:HOH441 4.8 18.7 1.0
O L:CYS128 4.8 14.7 1.0
NH2 J:ARG55 5.0 11.2 1.0

Reference:

Y.Yamanaka, M.Sato, T.Arakawa, S.Namima, S.Hori, A.Ohtaki, K.Noguchi, Y.Katayama, M.Yohda, M.Odaka. Effects of Argnine Residue Around the Substrate Pocket on the Substrate Specificity of Thiocyanate Hydrolase To Be Published.
Page generated: Sun Dec 13 10:42:54 2020

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