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Cobalt in PDB 2zzd: Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme

Enzymatic activity of Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme

All present enzymatic activity of Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme:
3.5.5.8;

Protein crystallography data

The structure of Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme, PDB code: 2zzd 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) 40.76 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 115.012, 170.756, 175.176, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 15.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme (pdb code 2zzd). 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, Air-Oxidized Form of Holo-Enzyme, PDB code: 2zzd:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2zzd

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Cobalt binding site 1 out of 4 in the Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme


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, Air-Oxidized Form of Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co301

b:14.7
occ:1.00
 N C:CSD133 1.9 11.5 1.0
O C:HOH244 2.1 24.2 0.9
N C:SER132 2.1 10.7 1.0
SG C:CSD131 2.2 13.2 1.0
SG C:CSD133 2.2 14.2 1.0
SG C:CYS128 2.4 12.8 1.0
C C:SER132 2.8 13.1 1.0
CA C:CSD133 2.9 13.2 1.0
CA C:SER132 3.0 11.5 1.0
OD1 C:CSD133 3.0 15.8 0.9
OD2 C:CSD131 3.0 15.0 1.0
CB C:CSD133 3.0 14.3 1.0
OD1 C:CSD131 3.1 12.6 1.0
C C:CSD131 3.1 11.7 1.0
CB C:CSD131 3.2 12.1 1.0
OD2 C:CSD133 3.3 16.2 0.8
CA C:CSD131 3.4 11.6 1.0
CB C:CYS128 3.4 11.5 1.0
N C:CSD131 3.7 10.4 1.0
O C:SER132 4.0 12.6 1.0
OG C:SER132 4.0 15.7 1.0
CB C:SER132 4.1 12.7 1.0
O C:CSD131 4.2 12.4 1.0
C C:CSD133 4.3 12.8 1.0
O C:CSD133 4.7 12.2 1.0
O C:HOH566 4.7 20.4 1.0
CA C:CYS128 4.8 11.0 1.0
O C:CYS128 4.8 10.6 1.0
C C:LEU130 4.8 11.1 1.0
O C:SER181 5.0 20.1 1.0

Cobalt binding site 2 out of 4 in 2zzd

Go back to Cobalt Binding Sites List in 2zzd
Cobalt binding site 2 out of 4 in the Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme


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, Air-Oxidized Form of Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co301

b:14.6
occ:0.93
 N F:CSD133 2.0 12.9 1.0
O F:HOH244 2.1 37.8 0.9
N F:SER132 2.1 12.8 1.0
SG F:CSD131 2.2 13.4 1.0
SG F:CSD133 2.2 15.4 1.0
SG F:CYS128 2.4 12.6 1.0
C F:SER132 2.8 14.0 1.0
CA F:CSD133 2.9 14.2 1.0
OD1 F:CSD133 2.9 15.9 0.9
CA F:SER132 3.0 12.7 1.0
CB F:CSD133 3.0 14.5 1.0
OD2 F:CSD131 3.1 14.5 1.0
OD1 F:CSD131 3.1 13.9 1.0
C F:CSD131 3.1 12.3 1.0
CB F:CSD131 3.2 12.8 1.0
OD2 F:CSD133 3.3 14.1 0.8
CB F:CYS128 3.3 12.9 1.0
CA F:CSD131 3.4 12.9 1.0
N F:CSD131 3.7 12.1 1.0
O F:SER132 4.0 12.8 1.0
OG F:SER132 4.0 18.0 1.0
CB F:SER132 4.1 14.2 1.0
O F:CSD131 4.2 12.5 1.0
C F:CSD133 4.3 14.0 1.0
O F:CSD133 4.7 13.2 1.0
CA F:CYS128 4.7 11.1 1.0
O F:CYS128 4.8 11.4 1.0
C F:LEU130 4.8 11.5 1.0
O F:HOH412 4.8 20.1 1.0
NH2 D:ARG55 5.0 10.6 1.0

Cobalt binding site 3 out of 4 in 2zzd

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Cobalt binding site 3 out of 4 in the Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme


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, Air-Oxidized Form of Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co301

b:14.3
occ:1.00
 N I:CSD133 1.9 11.1 1.0
N I:SER132 2.1 11.7 1.0
O I:HOH244 2.2 25.5 0.9
SG I:CSD131 2.2 12.9 1.0
SG I:CSD133 2.2 15.6 1.0
SG I:CYS128 2.4 12.8 1.0
C I:SER132 2.8 12.1 1.0
CA I:CSD133 2.9 12.4 1.0
CA I:SER132 2.9 12.4 1.0
OD1 I:CSD133 3.0 14.7 1.0
CB I:CSD133 3.0 13.8 1.0
OD2 I:CSD131 3.1 14.3 1.0
C I:CSD131 3.1 11.9 1.0
OD1 I:CSD131 3.1 13.7 1.0
CB I:CSD131 3.2 12.2 1.0
OD2 I:CSD133 3.3 15.7 0.8
CA I:CSD131 3.4 11.4 1.0
CB I:CYS128 3.4 10.6 1.0
N I:CSD131 3.8 11.1 1.0
O I:SER132 4.0 11.0 1.0
OG I:SER132 4.0 13.7 1.0
CB I:SER132 4.0 12.4 1.0
O I:CSD131 4.2 12.5 1.0
C I:CSD133 4.3 12.4 1.0
O I:CSD133 4.7 12.2 1.0
O I:HOH380 4.7 18.2 1.0
CA I:CYS128 4.8 10.3 1.0
O I:CYS128 4.8 9.7 1.0
C I:LEU130 4.8 11.2 1.0

Cobalt binding site 4 out of 4 in 2zzd

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Cobalt binding site 4 out of 4 in the Recombinant Thiocyanate Hydrolase, Air-Oxidized Form of Holo-Enzyme


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, Air-Oxidized Form of Holo-Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co301

b:13.8
occ:0.98
 N L:CSD133 1.9 10.8 1.0
N L:SER132 2.1 10.7 1.0
O L:HOH244 2.2 28.9 0.9
SG L:CSD131 2.2 12.1 1.0
SG L:CSD133 2.2 12.4 1.0
SG L:CYS128 2.4 11.8 1.0
C L:SER132 2.8 11.3 1.0
CA L:CSD133 2.9 11.3 1.0
OD1 L:CSD133 2.9 14.3 1.0
CA L:SER132 3.0 9.7 1.0
CB L:CSD133 3.0 11.2 1.0
OD2 L:CSD131 3.0 12.9 1.0
OD1 L:CSD131 3.1 12.4 1.0
C L:CSD131 3.1 10.8 1.0
CB L:CSD131 3.2 11.5 1.0
OD2 L:CSD133 3.3 14.7 0.8
CB L:CYS128 3.3 10.9 1.0
CA L:CSD131 3.4 11.2 1.0
N L:CSD131 3.8 11.0 1.0
O L:SER132 4.0 10.6 1.0
OG L:SER132 4.0 13.8 1.0
CB L:SER132 4.1 10.4 1.0
O L:CSD131 4.2 11.6 1.0
C L:CSD133 4.3 11.8 1.0
O L:CSD133 4.7 10.7 1.0
CA L:CYS128 4.7 10.2 1.0
O L:HOH648 4.8 18.4 1.0
O L:CYS128 4.8 9.1 1.0
C L:LEU130 4.8 10.4 1.0
NH2 J:ARG55 5.0 9.1 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: Tue Jul 30 15:43:58 2024

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