Iron in PDB 4i9d: X-Ray Structure of Nika in Complex with Fe-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl

All present enzymatic activity of X-Ray Structure of Nika in Complex with Fe-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl:
3.6.3.24;

The structure of X-Ray Structure of Nika in Complex with Fe-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl, PDB code: 4i9d was solved by M.V.Cherrier, P.Amara, M.Iannello, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.94 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.670, 94.730, 124.870, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 19.5

The binding sites of Iron atom in the X-Ray Structure of Nika in Complex with Fe-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl (pdb code 4i9d). 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-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl, PDB code: 4i9d:
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-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl


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-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe631 b:21.8 occ:1.00 FE A:L4D631 0.0 21.8 1.0 O A:HOH1362 1.8 16.9 0.4 NAT A:L4D631 1.9 27.9 0.6 NAT A:L4D631 1.9 22.5 0.4 N A:L4D631 2.0 15.7 0.4 OAE A:L4D631 2.1 12.0 0.4 NAS A:L4D631 2.2 19.6 0.6 OAE A:L4D631 2.2 13.5 0.6 NAZ A:L4D631 2.3 20.7 0.6 N A:L4D631 2.3 19.5 0.6 O A:HOH1363 2.4 22.5 0.6 NAS A:L4D631 2.4 19.9 0.4 NAZ A:L4D631 2.6 25.3 0.4 CAX A:L4D631 2.6 26.5 0.6 CAM A:L4D631 2.7 17.5 0.4 CAR A:L4D631 2.7 23.1 0.6 CAJ A:L4D631 2.8 23.1 0.4 CAN A:L4D631 2.8 21.7 0.4 CAX A:L4D631 2.9 21.6 0.4 C A:L4D631 2.9 11.2 0.4 CA A:L4D631 2.9 11.2 0.4 CAQ A:L4D631 2.9 14.0 0.4 CAI A:L4D631 2.9 22.1 0.6 CAN A:L4D631 2.9 16.9 0.6 CAJ A:L4D631 3.0 28.2 0.6 C A:L4D631 3.0 14.0 0.6 CAM A:L4D631 3.0 18.9 0.6 CAW A:L4D631 3.0 15.8 0.4 CA A:L4D631 3.1 16.4 0.6 CAR A:L4D631 3.1 26.0 0.4 CAW A:L4D631 3.2 22.0 0.6 CAQ A:L4D631 3.3 16.6 0.6 CAI A:L4D631 3.4 20.7 0.4 CAP A:L4D631 3.5 28.9 0.6 O A:HOH1365 3.7 21.4 0.6 CAP A:L4D631 3.9 27.1 0.4 CAL A:L4D631 4.0 31.5 0.6 O A:L4D631 4.1 10.5 0.4 CAF A:L4D631 4.1 24.7 0.4 CAL A:L4D631 4.1 22.0 0.4 CAF A:L4D631 4.2 32.6 0.6 O A:L4D631 4.2 13.2 0.6 CAE A:L4D631 4.2 25.4 0.6 CAK A:L4D631 4.4 7.1 0.4 NH2 A:ARG137 4.4 11.9 1.0 CAK A:L4D631 4.5 20.6 0.6 CAH A:L4D631 4.6 27.9 0.4 CAH A:L4D631 4.6 27.7 0.6 CAE A:L4D631 4.7 17.8 0.4 CAG A:L4D631 4.9 21.6 0.6 SD A:MET27 4.9 22.9 1.0 O A:HOH1364 5.0 34.6 0.6

Iron binding site 2 out of 2 in the X-Ray Structure of Nika in Complex with Fe-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl


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-N,N'-Bis(2-Pyridylmethyl)- N-Carboxymethyl-N'-Methyl within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe613 b:26.7 occ:1.00 FE B:L4D613 0.0 26.7 1.0 NAT B:L4D613 1.9 26.4 0.4 NAS B:L4D613 2.1 24.5 0.6 N B:L4D613 2.1 25.7 0.6 OAE B:L4D613 2.2 13.3 0.6 NAT B:L4D613 2.2 23.6 0.6 NAZ B:L4D613 2.2 27.4 0.4 O B:HOH1230 2.3 26.4 0.6 OAE B:L4D613 2.3 15.8 0.4 NAZ B:L4D613 2.4 30.1 0.6 O B:HOH1231 2.5 23.7 0.4 NAS B:L4D613 2.6 26.1 0.4 N B:L4D613 2.6 24.2 0.4 CAX B:L4D613 2.6 25.1 0.4 CAW B:L4D613 2.8 25.4 0.6 CAQ B:L4D613 2.8 22.6 0.6 CAJ B:L4D613 2.9 27.5 0.4 CAR B:L4D613 2.9 27.5 0.4 C B:L4D613 2.9 17.0 0.6 CAP B:L4D613 3.0 27.7 0.6 CA B:L4D613 3.0 21.3 0.6 CAN B:L4D613 3.0 24.3 0.4 CAI B:L4D613 3.0 25.2 0.6 CAM B:L4D613 3.0 28.0 0.6 CAX B:L4D613 3.1 28.7 0.6 CAJ B:L4D613 3.1 29.1 0.6 CAM B:L4D613 3.2 25.6 0.4 C B:L4D613 3.2 17.9 0.4 CAN B:L4D613 3.2 26.6 0.6 CAI B:L4D613 3.3 26.3 0.4 CAP B:L4D613 3.3 30.1 0.4 CAR B:L4D613 3.3 31.3 0.6 CA B:L4D613 3.4 17.7 0.4 CAW B:L4D613 3.6 25.7 0.4 CAQ B:L4D613 3.6 22.4 0.4 CAL B:L4D613 4.0 26.6 0.4 O B:L4D613 4.1 18.8 0.6 CAF B:L4D613 4.1 27.3 0.4 CAK B:L4D613 4.2 27.7 0.6 NH2 B:ARG137 4.3 17.8 1.0 CAE B:L4D613 4.3 26.3 0.6 O B:L4D613 4.3 18.6 0.4 CAL B:L4D613 4.4 31.6 0.6 CAF B:L4D613 4.5 31.0 0.6 CAH B:L4D613 4.6 27.9 0.4 O B:HOH1232 4.6 30.7 0.4 CAE B:L4D613 4.6 27.5 0.4 CAG B:L4D613 4.8 27.5 0.6 CAK B:L4D613 4.9 24.1 0.4 SD B:MET27 4.9 21.9 1.0

C.Esmieu, M.V.Cherrier, P.Amara, E.Girgenti, C.Marchi-Delapierre, F.Oddon, M.Iannello, A.Jorge-Robin, C.Cavazza, S.Menage. An Artificial Oxygenase Built From Scratch: Substrate Binding Site Identified Using A Docking Approach. Angew.Chem.Int.Ed.Engl. V. 52 3922 2013.
ISSN: ISSN 1433-7851
PubMed: 23440925
DOI: 10.1002/ANIE.201209021