Iron in PDB 1nis: 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: 1nis 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 1nis). 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: 1nis:
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:24.2 occ:1.00 FE1 A:SF4999 0.0 24.2 1.0 S3 A:SF4999 2.3 25.0 1.0 S4 A:SF4999 2.3 15.9 1.0 S2 A:SF4999 2.3 18.0 1.0 SG A:CYS358 2.3 22.0 1.0 FE3 A:SF4999 2.7 16.9 1.0 FE2 A:SF4999 2.7 20.4 1.0 FE4 A:SF4999 2.7 28.5 1.0 CB A:CYS358 3.6 20.8 1.0 S1 A:SF4999 3.9 16.9 1.0 CG2 A:ILE145 4.0 4.5 1.0 N A:CYS358 4.0 28.4 1.0 CD2 A:HIS147 4.4 6.3 1.0 O A:HOH1000 4.5 18.3 0.8 CA A:CYS358 4.5 25.5 1.0 SG A:CYS424 4.7 18.9 1.0 H2 A:HOH1000 4.8 0.0 0.8 SG A:CYS421 4.8 8.3 1.0 ND2 A:ASN446 4.9 15.5 1.0 CB A:SER357 4.9 26.6 1.0 ND1 A:HIS167 4.9 8.0 1.0 CB A:HIS167 4.9 7.6 1.0 NE2 A:HIS147 5.0 6.8 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:20.4 occ:1.00 FE2 A:SF4999 0.0 20.4 1.0 S1 A:SF4999 2.2 16.9 1.0 S4 A:SF4999 2.3 15.9 1.0 SG A:CYS424 2.3 18.9 1.0 S3 A:SF4999 2.4 25.0 1.0 FE3 A:SF4999 2.6 16.9 1.0 FE1 A:SF4999 2.7 24.2 1.0 FE4 A:SF4999 2.8 28.5 1.0 CB A:CYS424 3.2 16.7 1.0 S2 A:SF4999 3.9 18.0 1.0 O A:HOH1288 4.0 38.4 1.0 CA A:CYS424 4.4 16.2 1.0 CB A:SER357 4.5 26.6 1.0 C A:CYS424 4.5 16.3 1.0 CB A:CYS421 4.6 7.4 1.0 O A:CYS424 4.6 18.5 1.0 NH2 A:ARG452 4.6 23.9 1.0 HO7 A:NTC755 4.6 0.0 0.8 SG A:CYS421 4.7 8.3 1.0 SG A:CYS358 4.7 22.0 1.0 O5 A:NTC755 4.8 24.2 0.8 OD1 A:ASN446 4.8 22.7 1.0 OG A:SER357 4.8 32.7 1.0 ND2 A:ASN446 4.8 15.5 1.0 O A:HOH1000 4.9 18.3 0.8 CA A:CYS421 5.0 10.4 1.0 O7 A:NTC755 5.0 19.0 0.8

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:16.9 occ:1.00 FE3 A:SF4999 0.0 16.9 1.0 S2 A:SF4999 2.3 18.0 1.0 S4 A:SF4999 2.3 15.9 1.0 SG A:CYS421 2.3 8.3 1.0 S1 A:SF4999 2.3 16.9 1.0 FE2 A:SF4999 2.6 20.4 1.0 FE1 A:SF4999 2.7 24.2 1.0 FE4 A:SF4999 2.7 28.5 1.0 CB A:CYS421 3.2 7.4 1.0 HO7 A:NTC755 3.8 0.0 0.8 CE1 A:HIS101 3.8 6.4 1.0 S3 A:SF4999 3.8 25.0 1.0 CA A:CYS421 3.9 10.4 1.0 NE2 A:HIS101 4.1 5.5 1.0 CG2 A:ILE145 4.2 4.5 1.0 O7 A:NTC755 4.2 19.0 0.8 ND1 A:HIS101 4.6 10.3 1.0 N A:CYS421 4.6 6.8 1.0 SG A:CYS424 4.7 18.9 1.0 CB A:CYS424 4.8 16.7 1.0 SG A:CYS358 4.9 22.0 1.0 CG1 A:ILE425 4.9 18.7 1.0 O A:HOH1000 5.0 18.3 0.8 CD2 A:HIS101 5.0 8.8 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:28.5 occ:1.00 FE4 A:SF4999 0.0 28.5 1.0 S2 A:SF4999 2.3 18.0 1.0 S3 A:SF4999 2.3 25.0 1.0 O A:HOH1000 2.3 18.3 0.8 S1 A:SF4999 2.4 16.9 1.0 FE3 A:SF4999 2.7 16.9 1.0 FE1 A:SF4999 2.7 24.2 1.0 FE2 A:SF4999 2.8 20.4 1.0 O7 A:NTC755 2.8 19.0 0.8 HO7 A:NTC755 2.8 0.0 0.8 H2 A:HOH1000 3.0 0.0 0.8 H1 A:HOH1000 3.0 0.0 0.8 O5 A:NTC755 3.3 24.2 0.8 ND1 A:HIS167 3.9 8.0 1.0 OD2 A:ASP165 3.9 9.6 1.0 S4 A:SF4999 4.0 15.9 1.0 C3 A:NTC755 4.0 22.0 0.8 C6 A:NTC755 4.1 23.2 0.8 OD1 A:ASP165 4.1 9.7 1.0 H21 A:NTC755 4.3 0.0 0.8 NE2 A:HIS101 4.4 5.5 1.0 CE1 A:HIS101 4.5 6.4 1.0 CG A:ASP165 4.5 9.9 1.0 C2 A:NTC755 4.7 24.1 0.8 CG A:HIS167 4.7 8.2 1.0 SG A:CYS421 4.8 8.3 1.0 SG A:CYS358 4.8 22.0 1.0 CB A:HIS167 4.8 7.6 1.0 NH2 A:ARG452 4.8 23.9 1.0 CE1 A:HIS167 4.9 7.6 1.0 O A:HOH1288 4.9 38.4 1.0 SG A:CYS424 4.9 18.9 1.0 O2 A:NTC755 4.9 28.6 0.8

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