Cobalt in PDB 6icn: Pseudomonas Putida CBB5 Ndma with Caffeine

All present enzymatic activity of Pseudomonas Putida CBB5 Ndma with Caffeine:
1.14.13.178;

The structure of Pseudomonas Putida CBB5 Ndma with Caffeine, PDB code: 6icn was solved by J.H.Kim, B.H.Kim, S.Y.Kang, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.76 / 1.65
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.938, 135.938, 155.430, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.4

The structure of Pseudomonas Putida CBB5 Ndma with Caffeine also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Cobalt atom in the Pseudomonas Putida CBB5 Ndma with Caffeine (pdb code 6icn). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Pseudomonas Putida CBB5 Ndma with Caffeine, PDB code: 6icn:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Pseudomonas Putida CBB5 Ndma with Caffeine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Pseudomonas Putida CBB5 Ndma with Caffeine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:20.1 occ:1.00 NE2 A:HIS178 2.0 21.2 1.0 O A:HOH782 2.1 22.9 1.0 NE2 A:HIS173 2.1 19.3 1.0 OD1 A:ASP289 2.1 20.9 1.0 OD2 A:ASP289 2.2 17.1 1.0 CG A:ASP289 2.5 20.4 1.0 CE1 A:HIS178 3.0 18.9 1.0 CD2 A:HIS173 3.0 22.7 1.0 CD2 A:HIS178 3.0 21.2 1.0 CE1 A:HIS173 3.1 24.9 1.0 ND2 A:ASN167 3.7 20.0 1.0 O A:HOH655 3.8 24.0 1.0 OD1 A:ASN167 3.9 20.1 1.0 CB A:ASP289 4.0 15.6 1.0 ND1 A:HIS178 4.1 20.1 1.0 CG A:ASN167 4.2 21.0 1.0 CG A:HIS178 4.2 23.1 1.0 ND1 A:HIS173 4.2 24.0 1.0 CG A:HIS173 4.2 24.8 1.0 O A:ASN167 4.4 19.9 1.0 CG2 A:ILE177 4.4 20.8 1.0 CG1 A:VAL285 4.7 20.1 1.0 CA A:ASP289 4.8 17.3 1.0

Cobalt binding site 2 out of 3 in the Pseudomonas Putida CBB5 Ndma with Caffeine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Pseudomonas Putida CBB5 Ndma with Caffeine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:20.1 occ:1.00 NE2 B:HIS178 2.0 20.1 1.0 O B:HOH739 2.0 23.0 1.0 NE2 B:HIS173 2.1 18.5 1.0 OD1 B:ASP289 2.1 20.3 1.0 OD2 B:ASP289 2.2 20.4 1.0 CG B:ASP289 2.5 18.6 1.0 CE1 B:HIS178 3.0 20.0 1.0 CD2 B:HIS178 3.0 21.4 1.0 CE1 B:HIS173 3.0 24.1 1.0 CD2 B:HIS173 3.0 22.3 1.0 ND2 B:ASN167 3.6 24.0 1.0 OD1 B:ASN167 3.9 20.1 1.0 O B:HOH652 3.9 23.3 1.0 CB B:ASP289 4.0 14.9 1.0 ND1 B:HIS178 4.1 21.0 1.0 CG B:ASN167 4.1 21.4 1.0 ND1 B:HIS173 4.1 22.7 1.0 CG B:HIS178 4.2 23.1 1.0 CG B:HIS173 4.2 22.5 1.0 CG2 B:ILE177 4.3 18.2 1.0 O B:ASN167 4.3 19.6 1.0 CG1 B:VAL285 4.7 20.8 1.0 CA B:ASP289 4.8 17.1 1.0 CE1 B:PHE174 4.9 30.9 1.0 CB B:ILE177 4.9 21.3 1.0 CD1 B:PHE174 5.0 26.9 1.0

Cobalt binding site 3 out of 3 in the Pseudomonas Putida CBB5 Ndma with Caffeine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Pseudomonas Putida CBB5 Ndma with Caffeine within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:20.1 occ:1.00 NE2 C:HIS178 2.0 19.2 1.0 O C:HOH748 2.0 22.6 1.0 NE2 C:HIS173 2.1 19.0 1.0 OD1 C:ASP289 2.1 18.3 1.0 OD2 C:ASP289 2.2 18.7 1.0 CG C:ASP289 2.5 17.2 1.0 CE1 C:HIS178 3.0 18.5 1.0 CD2 C:HIS178 3.0 21.0 1.0 CE1 C:HIS173 3.1 23.8 1.0 CD2 C:HIS173 3.1 22.4 1.0 ND2 C:ASN167 3.7 20.9 1.0 OD1 C:ASN167 3.8 19.9 1.0 O C:HOH674 3.9 23.9 1.0 CB C:ASP289 4.0 15.2 1.0 ND1 C:HIS178 4.1 20.0 1.0 CG C:ASN167 4.1 19.4 1.0 CG C:HIS178 4.2 19.4 1.0 ND1 C:HIS173 4.2 21.6 1.0 CG C:HIS173 4.2 20.3 1.0 O C:ASN167 4.3 19.5 1.0 CG2 C:ILE177 4.4 19.6 1.0 CG1 C:VAL285 4.8 19.6 1.0 CA C:ASP289 4.8 15.6 1.0 CB C:ILE177 5.0 22.7 1.0

J.H.Kim, B.H.Kim, S.Brooks, S.Y.Kang, R.M.Summers, H.K.Song. Structural and Mechanistic Insights Into Caffeine Degradation By the Bacterial N-Demethylase Complex. J.Mol.Biol. V. 431 3647 2019.
ISSN: ESSN 1089-8638
PubMed: 31412262
DOI: 10.1016/J.JMB.2019.08.004