Cobalt in PDB 3qz9: Crystal Structure of Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida.

The structure of Crystal Structure of Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida., PDB code: 3qz9 was solved by H.R.Brodkin, W.R.P.Novak, D.Ringe, G.A.Petsko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.80 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.889, 137.203, 86.094, 90.00, 91.77, 90.00
R / Rfree (%)	18.5 / 21.5

The binding sites of Cobalt atom in the Crystal Structure of Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida. (pdb code 3qz9). 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 Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida., PDB code: 3qz9:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida.


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 Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co213 b:14.8 occ:1.00 N A:CSD117 2.0 17.1 1.0 N A:SER116 2.0 10.3 1.0 SG A:CSD115 2.1 11.9 1.0 SG A:CSD117 2.2 12.4 1.0 SG A:CYS112 2.4 13.1 1.0 C A:SER116 2.7 22.2 1.0 OD2 A:CSD117 2.8 11.1 1.0 CA A:SER116 2.8 12.7 1.0 OD1 A:CSD115 2.9 14.0 1.0 CA A:CSD117 3.0 9.0 1.0 C A:CSD115 3.1 9.6 1.0 CB A:CSD117 3.1 9.5 1.0 CB A:CSD115 3.1 5.7 1.0 OD2 A:CSD115 3.3 12.1 1.0 CB A:CYS112 3.4 11.0 1.0 CA A:CSD115 3.4 9.1 1.0 OG A:SER116 3.6 18.8 1.0 O A:HOH244 3.8 24.0 1.0 OD1 A:CSD117 3.8 21.4 1.0 CB A:SER116 3.8 7.9 1.0 N A:CSD115 3.8 14.2 1.0 O A:SER116 3.9 10.0 1.0 O A:CSD115 4.2 12.5 1.0 C A:CSD117 4.3 13.0 1.0 O A:CSD117 4.6 11.6 1.0 CA A:CYS112 4.8 12.7 1.0 O A:CYS112 4.9 12.2 1.0 C A:LEU114 4.9 10.5 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida.


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 Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co213 b:14.1 occ:1.00 N C:SER116 2.0 8.8 1.0 N C:CSD117 2.0 9.6 1.0 SG C:CSD115 2.1 11.5 1.0 SG C:CSD117 2.2 18.5 1.0 SG C:CYS112 2.4 15.5 1.0 C C:SER116 2.8 17.5 1.0 CA C:SER116 2.8 15.7 1.0 C C:CSD115 3.0 13.6 1.0 CB C:CSD115 3.0 11.5 1.0 CA C:CSD117 3.0 12.4 1.0 OD2 C:CSD117 3.1 22.0 1.0 CB C:CSD117 3.1 17.8 1.0 OD1 C:CSD115 3.2 19.6 1.0 CA C:CSD115 3.3 13.8 1.0 CB C:CYS112 3.3 10.8 1.0 OD2 C:CSD115 3.4 25.3 1.0 OG C:SER116 3.4 15.1 1.0 O C:HOH225 3.6 34.0 1.0 OD1 C:CSD117 3.6 25.2 1.0 N C:CSD115 3.7 18.8 1.0 CB C:SER116 3.7 14.3 1.0 O C:SER116 3.9 25.3 1.0 O C:CSD115 4.1 16.6 1.0 C C:CSD117 4.3 20.7 1.0 O C:CSD117 4.7 21.3 1.0 CA C:CYS112 4.8 17.0 1.0 O C:CYS112 4.9 15.9 1.0 C C:LEU114 4.9 10.5 1.0 O C:HOH363 5.0 24.8 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida.


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 Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ E:Co213 b:14.3 occ:1.00 N E:CSD117 2.0 19.4 1.0 N E:SER116 2.0 12.7 1.0 SG E:CSD117 2.2 12.6 1.0 SG E:CSD115 2.2 15.5 1.0 SG E:CYS112 2.4 12.4 1.0 C E:SER116 2.8 10.0 1.0 CA E:SER116 2.9 15.5 1.0 OD2 E:CSD117 3.0 9.9 1.0 C E:CSD115 3.0 10.2 1.0 CA E:CSD117 3.1 15.3 1.0 CB E:CSD117 3.1 16.0 1.0 OD1 E:CSD115 3.2 18.3 1.0 CB E:CSD115 3.2 14.5 1.0 OD2 E:CSD115 3.3 19.6 1.0 CB E:CYS112 3.4 11.3 1.0 CA E:CSD115 3.4 10.3 1.0 O E:HOH228 3.5 34.2 1.0 OD1 E:CSD117 3.6 24.9 1.0 OG E:SER116 3.7 24.3 1.0 N E:CSD115 3.8 11.9 1.0 CB E:SER116 3.9 15.1 1.0 O E:SER116 4.0 17.5 1.0 O E:CSD115 4.2 15.9 1.0 C E:CSD117 4.3 20.5 1.0 O E:CSD117 4.6 14.7 1.0 CA E:CYS112 4.8 11.8 1.0 O E:CYS112 4.8 14.9 1.0 C E:LEU114 4.9 10.2 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida.


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 Co-Type Nitrile Hydratase Beta-Y215F From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ G:Co213 b:16.9 occ:1.00 N G:CSD117 2.0 14.7 1.0 N G:SER116 2.0 9.8 1.0 SG G:CSD115 2.1 15.2 1.0 SG G:CSD117 2.3 16.8 1.0 SG G:CYS112 2.3 15.3 1.0 C G:SER116 2.8 20.1 1.0 CA G:SER116 2.8 9.0 1.0 OD2 G:CSD117 2.9 17.4 1.0 CA G:CSD117 3.0 17.6 1.0 C G:CSD115 3.1 12.7 1.0 CB G:CSD115 3.1 21.1 1.0 OD1 G:CSD115 3.2 22.1 1.0 CB G:CSD117 3.2 18.7 1.0 OD2 G:CSD115 3.3 18.0 1.0 CB G:CYS112 3.3 12.2 1.0 CA G:CSD115 3.4 13.4 1.0 OG G:SER116 3.5 21.9 1.0 O G:HOH222 3.6 35.4 1.0 OD1 G:CSD117 3.7 23.4 1.0 CB G:SER116 3.7 17.6 1.0 N G:CSD115 3.8 15.8 1.0 O G:SER116 3.9 20.0 1.0 O G:CSD115 4.2 19.3 1.0 C G:CSD117 4.3 20.5 1.0 O G:CSD117 4.6 19.4 1.0 O G:HOH426 4.7 26.7 1.0 CA G:CYS112 4.8 13.5 1.0 O G:CYS112 4.9 15.2 1.0 C G:LEU114 4.9 11.1 1.0

H.R.Brodkin, W.R.Novak, A.C.Milne, J.A.D'aquino, N.M.Karabacak, I.G.Goldberg, J.N.Agar, M.S.Payne, G.A.Petsko, M.J.Ondrechen, D.Ringe. Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase From Pseudomonas Putida. Biochemistry V. 50 4923 2011.
ISSN: ISSN 0006-2960
PubMed: 21473592
DOI: 10.1021/BI101761E