Iron in PDB 3lpq: Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys

The structure of Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys, PDB code: 3lpq was solved by A.R.Conlan, C.Homer, H.L.Axelrod, A.E.Cohen, E.C.Abresch, J.Zuris, R.Nechushtai, M.L.Paddock, P.A.Jennings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.89 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.311, 49.587, 59.222, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.6

The binding sites of Iron atom in the Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys (pdb code 3lpq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys, PDB code: 3lpq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:19.9 occ:1.00 FE1 A:FES500 0.0 19.9 1.0 S1 A:FES500 2.2 22.5 1.0 SG A:CYS74 2.2 20.7 1.0 S2 A:FES500 2.2 19.9 1.0 SG A:CYS72 2.4 20.4 1.0 FE2 A:FES500 2.7 24.3 1.0 CB A:CYS74 3.3 19.6 1.0 CB A:CYS72 3.3 16.0 1.0 N A:CYS74 3.6 16.8 1.0 CA A:CYS72 3.7 18.0 1.0 CA A:CYS74 3.9 18.4 1.0 N A:ARG73 4.0 16.9 1.0 CB A:CYS87 4.0 22.3 0.5 CB A:CYS87 4.2 23.1 0.5 N A:CYS87 4.3 24.6 1.0 C A:CYS72 4.3 17.2 1.0 N A:TRP75 4.4 17.4 1.0 SG A:CYS87 4.4 21.2 0.5 C A:CYS74 4.5 17.6 1.0 CB A:SER77 4.5 24.0 1.0 N A:SER77 4.5 22.9 1.0 CA A:CYS87 4.6 24.7 0.5 CA A:CYS87 4.6 25.2 0.5 C A:ARG73 4.7 16.9 1.0 N A:ARG76 4.7 19.7 1.0 SG A:CYS83 4.7 28.9 1.0 SG A:CYS87 4.8 27.9 0.5 CA A:CYS83 4.9 24.6 1.0 CA A:ARG73 4.9 16.3 1.0 CB A:ALA86 4.9 26.0 1.0

Iron binding site 2 out of 4 in the Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:24.3 occ:1.00 FE2 A:FES500 0.0 24.3 1.0 S1 A:FES500 2.2 22.5 1.0 S2 A:FES500 2.2 19.9 1.0 SG A:CYS83 2.3 28.9 1.0 SG A:CYS87 2.4 21.2 0.5 FE1 A:FES500 2.7 19.9 1.0 SG A:CYS87 3.2 27.9 0.5 CB A:CYS87 3.3 23.1 0.5 CB A:CYS83 3.5 24.6 1.0 CB A:CYS87 3.6 22.3 0.5 CA A:CYS83 3.9 24.6 1.0 N A:CYS87 3.9 24.6 1.0 N A:GLY85 4.1 32.4 1.0 CA A:CYS87 4.3 24.7 0.5 SG A:CYS74 4.4 20.7 1.0 N A:ASP84 4.4 26.8 1.0 CA A:CYS87 4.4 25.2 0.5 CD A:PRO100 4.4 18.6 1.0 CB A:PRO100 4.5 22.7 1.0 CA A:GLY85 4.5 32.3 1.0 N A:ALA86 4.5 26.5 1.0 C A:CYS83 4.6 27.8 1.0 CG A:PRO100 4.7 21.7 1.0 SG A:CYS72 4.7 20.4 1.0 C A:GLY85 4.7 30.9 1.0 CA A:CYS72 4.7 18.0 1.0 CB A:CYS72 4.8 16.0 1.0 N A:PRO100 4.8 19.5 1.0 O B:HOH146 4.9 52.6 1.0

Iron binding site 3 out of 4 in the Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:18.3 occ:1.00 FE1 B:FES500 0.0 18.3 1.0 SG B:CYS74 2.2 18.5 1.0 S1 B:FES500 2.2 21.3 1.0 S2 B:FES500 2.3 20.1 1.0 SG B:CYS72 2.3 18.1 1.0 FE2 B:FES500 2.8 21.4 1.0 CB B:CYS72 3.3 16.1 1.0 CB B:CYS74 3.4 19.3 1.0 N B:CYS74 3.5 18.1 1.0 CA B:CYS72 3.8 19.0 1.0 N B:ARG73 3.9 17.2 1.0 CA B:CYS74 3.9 16.0 1.0 CB B:CYS87 4.1 18.4 0.5 CB B:CYS87 4.2 18.2 0.5 C B:CYS72 4.3 17.6 1.0 N B:CYS87 4.3 20.7 1.0 N B:TRP75 4.4 18.9 1.0 SG B:CYS87 4.4 16.5 0.5 N B:SER77 4.4 20.7 1.0 C B:CYS74 4.5 17.1 1.0 CB B:SER77 4.5 24.2 1.0 N B:ARG76 4.6 20.9 1.0 CA B:CYS87 4.6 20.3 0.5 CA B:CYS87 4.6 20.9 0.5 C B:ARG73 4.6 15.4 1.0 SG B:CYS83 4.7 26.2 1.0 SG B:CYS87 4.8 22.4 0.5 CA B:CYS83 4.8 24.0 1.0 CB B:CYS83 4.9 25.6 1.0 CA B:ARG73 4.9 16.1 1.0 CA B:SER77 4.9 21.7 1.0

Iron binding site 4 out of 4 in the Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Mitoneet with 2FE-2S Coordinating Ligand His 87 Replaced with Cys within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:21.4 occ:1.00 FE2 B:FES500 0.0 21.4 1.0 S1 B:FES500 2.3 21.3 1.0 S2 B:FES500 2.3 20.1 1.0 SG B:CYS83 2.3 26.2 1.0 SG B:CYS87 2.3 16.5 0.5 FE1 B:FES500 2.8 18.3 1.0 SG B:CYS87 3.2 22.4 0.5 CB B:CYS83 3.3 25.6 1.0 CB B:CYS87 3.4 18.2 0.5 CB B:CYS87 3.6 18.4 0.5 CA B:CYS83 3.9 24.0 1.0 N B:CYS87 4.0 20.7 1.0 N B:GLY85 4.1 26.7 1.0 CB B:PRO100 4.3 18.9 1.0 CA B:CYS87 4.3 20.3 0.5 SG B:CYS74 4.4 18.5 1.0 CA B:CYS87 4.4 20.9 0.5 N B:ASP84 4.4 25.5 1.0 CA B:GLY85 4.4 27.8 1.0 N B:ALA86 4.5 24.8 1.0 CD B:PRO100 4.5 20.5 1.0 CG B:PRO100 4.5 21.1 1.0 C B:CYS83 4.5 26.3 1.0 C B:GLY85 4.7 24.1 1.0 SG B:CYS72 4.7 18.1 1.0 CA B:CYS72 4.7 19.0 1.0 CB B:CYS72 4.8 16.1 1.0 N B:PRO100 4.8 20.5 1.0

A.R.Conlan, M.L.Paddock, C.Homer, H.L.Axelrod, A.E.Cohen, E.C.Abresch, J.A.Zuris, R.Nechushtai, P.A.Jennings. Mutation of the His Ligand in Mitoneet Stabilizes the 2FE-2S Cluster Despite Conformational Heterogeneity in the Ligand Environment. Acta Crystallogr.,Sect.D V. 67 516 2011.
ISSN: ISSN 0907-4449
PubMed: 21636891
DOI: 10.1107/S0907444911011577