Iron in PDB 1xdb: Crystal Structure of the Nitrogenase Fe Protein ASP129GLU

All present enzymatic activity of Crystal Structure of the Nitrogenase Fe Protein ASP129GLU:
1.18.6.1;

The structure of Crystal Structure of the Nitrogenase Fe Protein ASP129GLU, PDB code: 1xdb was solved by S.B.Jang, M.S.Jeong, L.C.Seefeldt, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.574, 92.138, 63.934, 90.00, 100.80, 90.00
R / Rfree (%)	22.7 / 29.9

The binding sites of Iron atom in the Crystal Structure of the Nitrogenase Fe Protein ASP129GLU (pdb code 1xdb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Nitrogenase Fe Protein ASP129GLU, PDB code: 1xdb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP129GLU


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Nitrogenase Fe Protein ASP129GLU within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe290 b:27.1 occ:1.00 FE1 A:SF4290 0.0 27.1 1.0 SG B:CYS97 1.9 70.1 1.0 S2 A:SF4290 2.2 19.5 1.0 S4 A:SF4290 2.2 23.0 1.0 S3 A:SF4290 2.4 29.9 1.0 FE2 A:SF4290 2.6 32.9 1.0 FE3 A:SF4290 2.6 32.0 1.0 FE4 A:SF4290 2.8 33.0 1.0 CB B:CYS97 2.9 63.6 1.0 CA B:CYS97 3.3 63.4 1.0 N B:ALA98 3.8 60.4 1.0 S1 A:SF4290 4.0 27.3 1.0 C B:CYS97 4.1 60.3 1.0 CA B:GLY134 4.1 52.2 1.0 N B:GLY134 4.4 52.7 1.0 SG B:CYS132 4.4 44.9 1.0 N B:CYS97 4.6 70.1 1.0 SG A:CYS97 4.6 60.4 1.0 SG A:CYS132 4.7 41.4 1.0 N B:GLY99 4.9 68.2 1.0 CB A:CYS132 5.0 44.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP129GLU


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Nitrogenase Fe Protein ASP129GLU within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe290 b:32.9 occ:1.00 FE2 A:SF4290 0.0 32.9 1.0 S4 A:SF4290 2.1 23.0 1.0 SG A:CYS97 2.2 60.4 1.0 S3 A:SF4290 2.2 29.9 1.0 S1 A:SF4290 2.3 27.3 1.0 FE4 A:SF4290 2.5 33.0 1.0 FE1 A:SF4290 2.6 27.1 1.0 FE3 A:SF4290 2.8 32.0 1.0 CB A:CYS97 2.9 58.0 1.0 CA A:CYS97 3.2 60.3 1.0 S2 A:SF4290 3.8 19.5 1.0 N A:ALA98 3.9 62.7 1.0 C A:CYS97 4.1 64.3 1.0 CA A:GLY134 4.3 44.4 1.0 SG B:CYS97 4.3 70.1 1.0 SG A:CYS132 4.5 41.4 1.0 N A:GLY134 4.5 46.1 1.0 N A:CYS97 4.5 71.6 1.0 SG B:CYS132 4.8 44.9 1.0 CB B:CYS97 4.9 63.6 1.0 CB B:CYS132 5.0 51.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP129GLU


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Nitrogenase Fe Protein ASP129GLU within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe290 b:32.0 occ:1.00 FE3 A:SF4290 0.0 32.0 1.0 SG A:CYS132 2.2 41.4 1.0 S4 A:SF4290 2.2 23.0 1.0 S2 A:SF4290 2.3 19.5 1.0 S1 A:SF4290 2.4 27.3 1.0 FE4 A:SF4290 2.6 33.0 1.0 FE1 A:SF4290 2.6 27.1 1.0 FE2 A:SF4290 2.8 32.9 1.0 CB A:CYS132 3.0 44.2 1.0 S3 A:SF4290 3.8 29.9 1.0 N A:GLY134 4.1 46.1 1.0 CA A:GLY134 4.3 44.4 1.0 CA A:CYS132 4.4 47.2 1.0 CA B:CYS97 4.4 63.4 1.0 SG B:CYS97 4.4 70.1 1.0 SG A:CYS97 4.5 60.4 1.0 SG B:CYS132 4.6 44.9 1.0 N B:ALA98 4.6 60.4 1.0 N A:GLY133 4.6 40.7 1.0 C A:CYS132 4.7 46.6 1.0 CB B:CYS97 4.8 63.6 1.0 O B:GLY96 4.9 76.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP129GLU


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Nitrogenase Fe Protein ASP129GLU within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe290 b:33.0 occ:1.00 FE4 A:SF4290 0.0 33.0 1.0 S3 A:SF4290 2.1 29.9 1.0 S1 A:SF4290 2.3 27.3 1.0 SG B:CYS132 2.4 44.9 1.0 FE2 A:SF4290 2.5 32.9 1.0 S2 A:SF4290 2.6 19.5 1.0 FE3 A:SF4290 2.6 32.0 1.0 FE1 A:SF4290 2.8 27.1 1.0 CB B:CYS132 3.0 51.5 1.0 S4 A:SF4290 3.7 23.0 1.0 N B:GLY134 4.2 52.7 1.0 CA A:CYS97 4.2 60.3 1.0 N A:ALA98 4.4 62.7 1.0 CA B:CYS132 4.4 49.4 1.0 SG A:CYS97 4.4 60.4 1.0 CA B:GLY134 4.5 52.2 1.0 SG A:CYS132 4.5 41.4 1.0 SG B:CYS97 4.5 70.1 1.0 N B:GLY133 4.7 47.9 1.0 CB A:CYS97 4.7 58.0 1.0 O A:GLY96 4.8 75.0 1.0 C B:CYS132 4.8 49.6 1.0 C A:CYS97 5.0 64.3 1.0

S.B.Jang, M.S.Jeong, L.C.Seefeldt, J.W.Peters. Structural and Biochemical Implications of Single Amino Acid Substitutions in the Nucleotide-Dependent Switch Regions of the Nitrogenase Fe Protein From Azotobacter Vinelandii J.Biol.Inorg.Chem. V. 9 1028 2004.
ISSN: ISSN 0949-8257
PubMed: 15549494
DOI: 10.1007/S00775-004-0605-5