Iron in PDB 6icl: Pseudomonas Putida CBB5 Ndmb

All present enzymatic activity of Pseudomonas Putida CBB5 Ndmb:
1.14.13.179;

The structure of Pseudomonas Putida CBB5 Ndmb, PDB code: 6icl 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)	41.45 / 2.10
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.553, 98.553, 174.441, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.2

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

Iron binding site 1 out of 3 in the Pseudomonas Putida CBB5 Ndmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pseudomonas Putida CBB5 Ndmb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:47.7 occ:1.00 FE1 A:FES400 0.0 47.7 1.0 S2 A:FES400 2.2 36.6 1.0 S1 A:FES400 2.3 36.1 1.0 ND1 A:HIS66 2.3 36.8 1.0 ND1 A:HIS90 2.4 39.6 1.0 FE2 A:FES400 2.8 33.8 1.0 CG A:HIS66 3.2 34.9 1.0 CG A:HIS90 3.2 38.4 1.0 CE1 A:HIS66 3.3 37.0 1.0 CB A:HIS66 3.4 35.3 1.0 CB A:HIS90 3.4 38.4 1.0 CE1 A:HIS90 3.4 38.8 1.0 N A:HIS90 3.6 36.8 1.0 N A:ARG67 4.0 38.3 1.0 CA A:HIS90 4.0 41.7 1.0 CB A:TYR89 4.1 31.6 1.0 CB A:ARG67 4.2 32.9 1.0 CD2 A:HIS66 4.4 34.3 1.0 NE2 A:HIS66 4.4 37.5 1.0 CD2 A:HIS90 4.4 36.7 1.0 CG A:TYR89 4.4 32.0 1.0 NE2 A:HIS90 4.5 39.8 1.0 CG A:ARG67 4.5 32.8 1.0 SG A:CYS64 4.5 38.8 1.0 CD2 A:TYR89 4.5 37.2 1.0 SG A:CYS87 4.6 33.2 1.0 CA A:HIS66 4.6 38.6 1.0 C A:TYR89 4.6 37.1 1.0 C A:HIS66 4.6 38.7 1.0 CA A:ARG67 4.7 37.0 1.0 C A:HIS90 4.8 38.8 1.0 NE1 A:TRP92 4.8 38.4 1.0 CD1 A:TRP92 4.8 37.7 1.0 CA A:TYR89 4.9 33.4 1.0

Iron binding site 2 out of 3 in the Pseudomonas Putida CBB5 Ndmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pseudomonas Putida CBB5 Ndmb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:33.8 occ:1.00 FE2 A:FES400 0.0 33.8 1.0 S2 A:FES400 2.2 36.6 1.0 S1 A:FES400 2.2 36.1 1.0 SG A:CYS87 2.3 33.2 1.0 SG A:CYS64 2.4 38.8 1.0 FE1 A:FES400 2.8 47.7 1.0 CB A:CYS64 3.1 35.6 1.0 CB A:CYS87 3.1 35.1 1.0 CB A:HIS66 4.1 35.3 1.0 CB A:TYR89 4.3 31.6 1.0 N A:HIS90 4.3 36.8 1.0 CB A:ALA69 4.5 28.8 1.0 CA A:CYS64 4.5 38.7 1.0 N A:ARG67 4.6 38.3 1.0 CA A:CYS87 4.6 36.3 1.0 ND1 A:HIS66 4.6 36.8 1.0 ND1 A:HIS90 4.8 39.6 1.0 N A:TYR89 4.8 29.7 1.0 CB A:TRP92 4.8 36.3 1.0 CG A:HIS66 4.9 34.9 1.0 CG A:TRP92 4.9 37.9 1.0 N A:HIS66 4.9 36.0 1.0 N A:ALA69 4.9 30.0 1.0 CA A:TYR89 5.0 33.4 1.0 N A:TRP92 5.0 38.7 1.0

Iron binding site 3 out of 3 in the Pseudomonas Putida CBB5 Ndmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pseudomonas Putida CBB5 Ndmb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:32.6 occ:1.00 NE2 A:HIS184 1.9 33.5 1.0 O A:HOH632 2.1 39.7 1.0 NE2 A:HIS179 2.1 42.2 1.0 OD2 A:ASP296 2.2 39.0 1.0 OD1 A:ASP296 2.3 40.2 1.0 CG A:ASP296 2.6 38.6 1.0 CE1 A:HIS184 2.9 35.5 1.0 CD2 A:HIS184 2.9 39.6 1.0 CE1 A:HIS179 3.0 42.7 1.0 CD2 A:HIS179 3.1 39.5 1.0 ND2 A:ASN173 3.9 34.0 1.0 ND1 A:HIS184 4.0 33.3 1.0 CG A:HIS184 4.1 38.4 1.0 CB A:ASP296 4.1 35.1 1.0 ND1 A:HIS179 4.2 40.3 1.0 OD1 A:ASN173 4.2 37.9 1.0 CG A:HIS179 4.3 40.4 1.0 CE1 A:PHE180 4.4 44.2 1.0 CG A:ASN173 4.4 35.4 1.0 CG1 A:VAL292 4.5 36.2 1.0 CG1 A:VAL183 4.6 34.3 1.0 O A:ASN173 4.7 36.7 1.0 CD1 A:PHE180 4.7 43.4 1.0 CA A:ASP296 5.0 31.7 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