Cobalt in PDB 3qyg: Crystal Structure of Co-Type Nitrile Hydratase Beta-E56Q From Pseudomonas Putida.

The structure of Crystal Structure of Co-Type Nitrile Hydratase Beta-E56Q From Pseudomonas Putida., PDB code: 3qyg 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)	45.37 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.962, 137.549, 85.416, 90.00, 92.41, 90.00
R / Rfree (%)	19.6 / 22.4

The binding sites of Cobalt atom in the Crystal Structure of Co-Type Nitrile Hydratase Beta-E56Q From Pseudomonas Putida. (pdb code 3qyg). 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-E56Q From Pseudomonas Putida., PDB code: 3qyg:
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-E56Q 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-E56Q From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co213 b:18.1 occ:1.00 N A:SER116 2.0 18.0 1.0 N A:CSD117 2.0 18.2 1.0 SG A:CSD117 2.2 18.6 1.0 SG A:CSD115 2.3 18.2 1.0 SG A:CYS112 2.4 17.5 1.0 C A:SER116 2.8 18.2 1.0 CA A:SER116 2.8 18.1 1.0 C A:CSD115 3.0 17.9 1.0 OD2 A:CSD117 3.0 19.0 1.0 CA A:CSD117 3.1 18.4 1.0 CB A:CSD117 3.1 18.5 1.0 CB A:CSD115 3.3 18.0 1.0 OD2 A:CSD115 3.3 18.1 1.0 CB A:CYS112 3.4 19.1 1.0 OD1 A:CSD115 3.4 18.5 1.0 CA A:CSD115 3.4 18.0 1.0 OD1 A:CSD117 3.6 18.8 1.0 OG A:SER116 3.7 18.5 1.0 N A:CSD115 3.8 17.9 1.0 CB A:SER116 3.8 18.4 1.0 O A:HOH583 3.9 19.4 1.0 O A:SER116 3.9 18.3 1.0 O A:CSD115 4.1 17.9 1.0 C A:CSD117 4.3 18.3 1.0 O A:CSD117 4.6 18.1 1.0 CA A:CYS112 4.8 16.7 1.0 C A:LEU114 4.9 18.6 1.0 NH2 B:ARG149 5.0 18.3 1.0 O A:CYS112 5.0 17.8 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Co-Type Nitrile Hydratase Beta-E56Q 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-E56Q From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co213 b:18.4 occ:1.00 N C:SER116 2.0 18.3 1.0 N C:CSD117 2.0 18.3 1.0 SG C:CSD117 2.1 18.7 1.0 SG C:CSD115 2.1 18.6 1.0 SG C:CYS112 2.5 18.1 1.0 C C:SER116 2.8 18.3 1.0 CA C:SER116 2.8 18.4 1.0 C C:CSD115 3.0 18.4 1.0 OD2 C:CSD117 3.1 19.0 1.0 CA C:CSD117 3.1 18.4 1.0 CB C:CSD115 3.2 18.7 1.0 CB C:CSD117 3.2 18.6 1.0 OD1 C:CSD115 3.2 19.1 1.0 OD2 C:CSD115 3.3 18.4 1.0 OD1 C:CSD117 3.4 18.9 1.0 CA C:CSD115 3.4 18.4 1.0 CB C:CYS112 3.4 17.1 1.0 OG C:SER116 3.6 18.9 1.0 N C:CSD115 3.8 18.1 1.0 CB C:SER116 3.8 18.7 1.0 O C:SER116 4.0 18.3 1.0 O C:CSD115 4.2 18.3 1.0 C C:CSD117 4.4 18.2 1.0 O C:CSD117 4.6 18.1 1.0 CA C:CYS112 4.9 17.9 1.0 C C:LEU114 4.9 18.2 1.0 O C:CYS112 4.9 17.5 1.0 NH2 D:ARG149 5.0 18.7 1.0 NE D:ARG52 5.0 19.6 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Co-Type Nitrile Hydratase Beta-E56Q 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-E56Q From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ E:Co213 b:18.3 occ:1.00 N E:CSD117 2.0 18.3 1.0 N E:SER116 2.0 18.2 1.0 SG E:CSD115 2.1 18.4 1.0 SG E:CSD117 2.2 18.7 1.0 SG E:CYS112 2.4 18.5 1.0 O E:HOH1049 2.6 18.6 1.0 C E:SER116 2.8 18.2 1.0 CA E:SER116 2.9 18.2 1.0 OD2 E:CSD117 3.0 19.0 1.0 C E:CSD115 3.1 18.2 1.0 CA E:CSD117 3.1 18.5 1.0 OD1 E:CSD115 3.1 18.7 1.0 CB E:CSD117 3.2 18.6 1.0 CB E:CSD115 3.2 18.3 1.0 OD2 E:CSD115 3.3 18.3 1.0 CB E:CYS112 3.4 17.6 1.0 CA E:CSD115 3.4 18.2 1.0 OD1 E:CSD117 3.5 18.9 1.0 OG E:SER116 3.7 18.6 1.0 N E:CSD115 3.8 18.0 1.0 CB E:SER116 3.9 18.5 1.0 O E:SER116 4.0 18.3 1.0 O E:CSD115 4.2 18.1 1.0 C E:CSD117 4.4 18.3 1.0 O E:CSD117 4.6 18.1 1.0 NH2 F:ARG149 4.8 18.4 1.0 CA E:CYS112 4.8 18.2 1.0 C E:LEU114 4.9 17.6 1.0 NE F:ARG52 4.9 19.5 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Co-Type Nitrile Hydratase Beta-E56Q 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-E56Q From Pseudomonas Putida. within 5.0Å range: probe atom residue distance (Å) B Occ G:Co213 b:18.3 occ:1.00 N G:CSD117 1.9 18.3 1.0 N G:SER116 2.0 18.2 1.0 SG G:CSD115 2.2 18.4 1.0 SG G:CSD117 2.2 18.7 1.0 SG G:CYS112 2.4 17.7 1.0 C G:SER116 2.8 18.3 1.0 CA G:SER116 2.8 18.3 1.0 C G:CSD115 3.0 18.2 1.0 CA G:CSD117 3.0 18.4 1.0 CB G:CSD115 3.1 18.5 1.0 OD1 G:CSD115 3.1 18.8 1.0 CB G:CSD117 3.1 18.5 1.0 OD2 G:CSD117 3.1 19.0 1.0 CA G:CSD115 3.4 18.3 1.0 CB G:CYS112 3.4 17.7 1.0 OD2 G:CSD115 3.5 18.4 1.0 OD1 G:CSD117 3.6 18.8 1.0 OG G:SER116 3.7 18.7 1.0 N G:CSD115 3.8 18.1 1.0 CB G:SER116 3.9 18.6 1.0 O G:SER116 3.9 18.3 1.0 O G:CSD115 4.1 18.2 1.0 C G:CSD117 4.3 18.3 1.0 O G:CSD117 4.6 18.1 1.0 CA G:CYS112 4.8 18.1 1.0 C G:LEU114 4.9 17.8 1.0 O G:CYS112 4.9 18.0 1.0 NH2 H:ARG149 5.0 18.4 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