Iron in PDB 1nit: Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound

All present enzymatic activity of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound:
4.2.1.3;

The structure of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound, PDB code: 1nit was solved by H.Lauble, M.C.Kennedy, H.Beinert, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.05
Space group	B 1 1 2
Cell size a, b, c (Å), α, β, γ (°)	185.500, 72.000, 73.000, 90.00, 90.00, 77.70
R / Rfree (%)	17.2 / n/a

The binding sites of Iron atom in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound (pdb code 1nit). 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 Aconitase with Trans-Aconitate and Nitrocitrate Bound, PDB code: 1nit:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound


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 Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:23.0 occ:1.00 FE1 A:SF4999 0.0 23.0 1.0 S3 A:SF4999 2.3 25.6 1.0 S2 A:SF4999 2.3 19.5 1.0 S4 A:SF4999 2.3 15.8 1.0 SG A:CYS358 2.3 22.4 1.0 FE4 A:SF4999 2.7 29.2 1.0 FE2 A:SF4999 2.7 22.1 1.0 FE3 A:SF4999 2.8 15.9 1.0 CB A:CYS358 3.6 20.2 1.0 S1 A:SF4999 3.9 17.2 1.0 CG2 A:ILE145 4.0 4.9 1.0 N A:CYS358 4.0 27.9 1.0 CD2 A:HIS147 4.3 7.3 1.0 CA A:CYS358 4.5 25.2 1.0 O A:HOH1000 4.5 19.3 0.2 SG A:CYS424 4.8 19.4 1.0 SG A:CYS421 4.8 7.3 1.0 ND2 A:ASN446 4.8 15.4 1.0 CB A:SER357 4.9 27.2 1.0 NE2 A:HIS147 4.9 7.5 1.0 CB A:HIS167 5.0 8.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound


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 Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:22.1 occ:1.00 FE2 A:SF4999 0.0 22.1 1.0 S1 A:SF4999 2.3 17.2 1.0 SG A:CYS424 2.3 19.4 1.0 S4 A:SF4999 2.3 15.8 1.0 S3 A:SF4999 2.3 25.6 1.0 FE1 A:SF4999 2.7 23.0 1.0 FE3 A:SF4999 2.7 15.9 1.0 FE4 A:SF4999 2.9 29.2 1.0 CB A:CYS424 3.1 16.6 1.0 O A:HOH1288 3.9 41.4 1.0 S2 A:SF4999 4.0 19.5 1.0 O A:HOH1000 4.1 19.3 0.2 CB A:SER357 4.4 27.2 1.0 CA A:CYS424 4.4 16.2 1.0 C A:CYS424 4.5 16.4 1.0 CB A:CYS421 4.6 6.5 1.0 SG A:CYS421 4.7 7.3 1.0 NH2 A:ARG452 4.7 22.1 1.0 SG A:CYS358 4.7 22.4 1.0 O A:CYS424 4.7 19.2 1.0 OG A:SER357 4.8 33.0 1.0 H1 A:HOH1000 4.8 0.0 0.2 ND2 A:ASN446 4.8 15.4 1.0 OD1 A:ASN446 4.9 22.8 1.0 CA A:CYS421 4.9 10.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound


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 Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:15.9 occ:1.00 FE3 A:SF4999 0.0 15.9 1.0 SG A:CYS421 2.2 7.3 1.0 S2 A:SF4999 2.4 19.5 1.0 S4 A:SF4999 2.4 15.8 1.0 S1 A:SF4999 2.4 17.2 1.0 FE2 A:SF4999 2.7 22.1 1.0 FE1 A:SF4999 2.8 23.0 1.0 FE4 A:SF4999 2.8 29.2 1.0 CB A:CYS421 3.1 6.5 1.0 CA A:CYS421 3.8 10.3 1.0 CE1 A:HIS101 3.8 6.7 1.0 S3 A:SF4999 3.9 25.6 1.0 O A:HOH1000 3.9 19.3 0.2 CG2 A:ILE145 4.1 4.9 1.0 NE2 A:HIS101 4.1 4.5 1.0 N A:CYS421 4.5 6.3 1.0 ND1 A:HIS101 4.6 10.0 1.0 SG A:CYS424 4.8 19.4 1.0 CB A:CYS424 4.8 16.6 1.0 H1 A:HOH1000 4.9 0.0 0.2 CG1 A:ILE425 4.9 18.9 1.0 SG A:CYS358 4.9 22.4 1.0 C A:CYS421 5.0 9.6 1.0 CD2 A:HIS101 5.0 8.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound


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 Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:29.2 occ:1.00 FE4 A:SF4999 0.0 29.2 1.0 O A:HOH1000 1.9 19.3 0.2 S3 A:SF4999 2.3 25.6 1.0 S2 A:SF4999 2.3 19.5 1.0 S1 A:SF4999 2.4 17.2 1.0 H1 A:HOH1000 2.6 0.0 0.2 FE1 A:SF4999 2.7 23.0 1.0 FE3 A:SF4999 2.8 15.9 1.0 FE2 A:SF4999 2.9 22.1 1.0 OD1 A:ASP165 3.9 10.7 1.0 S4 A:SF4999 4.0 15.8 1.0 ND1 A:HIS167 4.1 7.8 1.0 OD2 A:ASP165 4.1 10.1 1.0 NE2 A:HIS101 4.4 4.5 1.0 CG A:ASP165 4.5 10.1 1.0 CE1 A:HIS101 4.5 6.7 1.0 SG A:CYS358 4.7 22.4 1.0 SG A:CYS421 4.7 7.3 1.0 CG A:HIS167 4.8 8.2 1.0 NH2 A:ARG452 4.8 22.1 1.0 O A:HOH1288 4.8 41.4 1.0 CB A:HIS167 4.8 8.1 1.0 SG A:CYS424 4.9 19.4 1.0

H.Lauble, M.C.Kennedy, H.Beinert, C.D.Stout. Crystal Structures of Aconitase with Trans-Aconitate and Nitrocitrate Bound. J.Mol.Biol. V. 237 437 1994.
ISSN: ISSN 0022-2836
PubMed: 8151704
DOI: 10.1006/JMBI.1994.1246