Iron in PDB 4dcy: X-Ray Structure of Nika in Complex with Fe(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-1,2-Cyclohexanediamine

The structure of X-Ray Structure of Nika in Complex with Fe(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-1,2-Cyclohexanediamine, PDB code: 4dcy 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)	41.74 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.880, 95.190, 125.150, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 19.6

The binding sites of Iron atom in the X-Ray Structure of Nika in Complex with Fe(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-1,2-Cyclohexanediamine (pdb code 4dcy). 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(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-1,2-Cyclohexanediamine, PDB code: 4dcy:
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(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-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(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-1,2-Cyclohexanediamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe629 b:34.2 occ:1.00 FE1 A:L2M629 0.0 34.2 1.0 N1 A:L2M629 2.0 56.7 1.0 O2 A:L2M629 2.3 20.6 1.0 N4 A:L2M629 2.3 29.6 1.0 N3 A:L2M629 2.4 43.6 1.0 UNK A:UNX631 2.4 30.0 1.0 N2 A:L2M629 2.4 84.8 1.0 UNK A:UNX630 2.4 30.0 1.0 C15 A:L2M629 2.5 65.4 1.0 C18 A:L2M629 2.8 70.1 1.0 C20 A:L2M629 2.9 36.1 1.0 C21 A:L2M629 2.9 24.4 1.0 C1 A:L2M629 3.0 67.1 1.0 C16 A:L2M629 3.0 27.7 1.0 C17 A:L2M629 3.0 19.2 1.0 C19 A:L2M629 3.1 43.0 1.0 C14 A:L2M629 3.1 25.9 1.0 C7 A:L2M629 3.3 52.2 1.0 C6 A:L2M629 3.6 91.2 1.0 C12 A:L2M629 4.2 29.4 1.0 C8 A:L2M629 4.2 70.5 1.0 NH2 A:ARG137 4.2 17.9 1.0 O1 A:L2M629 4.3 19.4 1.0 C13 A:L2M629 4.4 27.1 1.0 C9 A:L2M629 4.4 38.6 1.0 C3 A:L2M629 4.6 49.2 1.0 C2 A:L2M629 4.8 84.8 1.0

Iron binding site 2 out of 2 in the X-Ray Structure of Nika in Complex with Fe(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-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(1S,2S)-N,N-Kappa-Bis(2- Pyridylmethyl)-N-Carboxymethyl-N-Kappa-Methyl-1,2-Cyclohexanediamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe611 b:41.6 occ:1.00 FE1 B:L2M611 0.0 41.6 1.0 N1 B:L2M611 2.1 39.4 1.0 O2 B:L2M611 2.2 22.2 1.0 N4 B:L2M611 2.2 35.6 1.0 N3 B:L2M611 2.3 55.8 1.0 O B:HOH1004 2.5 39.5 1.0 N2 B:L2M611 2.7 50.1 1.0 C1 B:L2M611 2.8 32.1 1.0 C20 B:L2M611 2.9 26.7 1.0 C16 B:L2M611 2.9 41.8 1.0 C21 B:L2M611 2.9 28.1 1.0 C14 B:L2M611 2.9 33.5 1.0 C17 B:L2M611 2.9 22.5 1.0 C19 B:L2M611 2.9 55.2 1.0 C15 B:L2M611 3.0 46.9 1.0 C18 B:L2M611 3.3 50.2 1.0 C7 B:L2M611 3.3 64.1 1.0 C6 B:L2M611 3.7 56.4 1.0 O1 B:L2M611 4.2 23.9 1.0 C12 B:L2M611 4.2 31.9 1.0 NH2 B:ARG137 4.2 21.3 1.0 C9 B:L2M611 4.3 64.3 1.0 C13 B:L2M611 4.3 28.3 1.0 O B:HOH1121 4.5 51.9 0.8 C3 B:L2M611 4.5 67.8 1.0 C8 B:L2M611 4.6 57.7 1.0 C5 B:L2M611 5.0 69.1 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