Iron in PDB 4dcx: X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine

The structure of X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine, PDB code: 4dcx was solved by M.V.Cherrier, E.Girgenti, P.Amara, M.Iannello, C.Marchi-Delapierre, J.C.Fontecilla-Camps, S.Menage, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.82 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.350, 95.640, 125.190, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 20.3

The binding sites of Iron atom in the X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine (pdb code 4dcx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine, PDB code: 4dcx:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe630 b:24.8 occ:1.00 FE A:L2D630 0.0 24.8 1.0 NBD A:L2D630 2.0 23.0 1.0 NAU A:L2D630 2.1 28.4 1.0 OAD A:L2D630 2.1 26.3 1.0 OXT A:L2D630 2.1 19.2 1.0 N A:L2D630 2.1 22.4 1.0 NAV A:L2D630 2.2 30.6 1.0 C A:L2D630 2.8 28.1 1.0 CA A:L2D630 2.8 26.6 1.0 CAX A:L2D630 2.8 35.7 1.0 CBB A:L2D630 2.8 21.6 1.0 CAI A:L2D630 2.9 30.2 1.0 CAR A:L2D630 2.9 21.6 1.0 CAY A:L2D630 2.9 26.0 1.0 CAT A:L2D630 2.9 24.8 1.0 CBA A:L2D630 2.9 21.9 1.0 CAZ A:L2D630 2.9 26.6 1.0 CAS A:L2D630 3.1 22.1 1.0 CAJ A:L2D630 3.2 43.8 1.0 OAB A:L2D630 4.1 37.9 1.0 O A:L2D630 4.1 20.7 1.0 CAE A:L2D630 4.2 32.5 1.0 CAK A:L2D630 4.2 26.4 1.0 CAP A:L2D630 4.2 28.6 1.0 CAL A:L2D630 4.3 36.6 1.0 CAO A:L2D630 4.3 24.7 1.0 NH2 A:ARG137 4.3 18.3 1.0 CAF A:L2D630 4.4 46.4 1.0 CAG A:L2D630 4.7 26.6 1.0 CE1 A:HIS416 4.7 42.7 1.0 CD1 A:TYR22 4.8 21.8 1.0 CAH A:L2D630 4.9 36.2 1.0 C1 A:GOL628 5.0 82.4 1.0

Iron binding site 2 out of 2 in the X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Nika in Complex with Fe(1R,2R)-N,N'-Bis(2- Pyridylmethyl)-N,N'-Dicarboxymethyl-1,2-Cyclohexanediamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe620 b:32.2 occ:1.00 FE B:L2D620 0.0 32.2 1.0 NAU B:L2D620 2.0 39.7 1.0 NBD B:L2D620 2.0 28.7 1.0 OAD B:L2D620 2.1 37.8 1.0 OXT B:L2D620 2.2 27.1 1.0 NAV B:L2D620 2.2 37.2 1.0 N B:L2D620 2.3 32.2 1.0 CAR B:L2D620 2.8 31.1 1.0 CBB B:L2D620 2.8 28.4 1.0 CAX B:L2D620 2.8 37.6 1.0 CAY B:L2D620 2.8 36.2 1.0 CAI B:L2D620 2.9 42.7 1.0 CAZ B:L2D620 2.9 37.7 1.0 CAT B:L2D620 2.9 33.1 1.0 CBA B:L2D620 2.9 28.9 1.0 C B:L2D620 3.0 27.2 1.0 CAS B:L2D620 3.0 34.1 1.0 CA B:L2D620 3.2 29.2 1.0 CAJ B:L2D620 3.3 53.9 1.0 OAB B:L2D620 4.0 45.1 1.0 CAK B:L2D620 4.2 41.0 1.0 CAE B:L2D620 4.2 42.1 1.0 O B:L2D620 4.2 24.7 1.0 CAP B:L2D620 4.2 26.0 1.0 CAL B:L2D620 4.3 48.8 1.0 NH2 B:ARG137 4.3 22.3 1.0 CAO B:L2D620 4.4 25.8 1.0 CAF B:L2D620 4.5 49.0 1.0 CAG B:L2D620 4.7 40.8 1.0 CD2 B:TYR22 4.8 31.0 1.0 CAH B:L2D620 4.9 50.7 1.0

M.V.Cherrier, E.Girgenti, P.Amara, M.Iannello, C.Marchi-Delapierre, J.C.Fontecilla-Camps, S.Menage, C.Cavazza. The Structure of the Periplasmic Nickel-Binding Protein Nika Provides Insights For Artificial Metalloenzyme Design. J.Biol.Inorg.Chem. V. 17 817 2012.
ISSN: ISSN 0949-8257
PubMed: 22526565
DOI: 10.1007/S00775-012-0899-7