Cobalt in PDB 2zzd: 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;

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

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 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 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 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 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

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