Iron in PDB 1ami: Steric and Conformational Features of the Aconitase Mechanism

All present enzymatic activity of Steric and Conformational Features of the Aconitase Mechanism:
4.2.1.3;

The structure of Steric and Conformational Features of the Aconitase Mechanism, PDB code: 1ami was solved by C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	B 1 1 2
Cell size a, b, c (Å), α, β, γ (°)	185.900, 71.800, 73.200, 90.00, 90.00, 77.70
R / Rfree (%)	18.2 / n/a

The binding sites of Iron atom in the Steric and Conformational Features of the Aconitase Mechanism (pdb code 1ami). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Steric and Conformational Features of the Aconitase Mechanism, PDB code: 1ami:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Steric and Conformational Features of the Aconitase Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Steric and Conformational Features of the Aconitase Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:23.5 occ:1.00 FE1 A:SF4999 0.0 23.5 1.0 S3 A:SF4999 2.3 25.3 1.0 S4 A:SF4999 2.3 18.1 1.0 S2 A:SF4999 2.3 19.7 1.0 SG A:CYS358 2.3 25.1 1.0 FE2 A:SF4999 2.6 23.0 1.0 FE3 A:SF4999 2.7 16.7 1.0 FE4 A:SF4999 2.7 26.5 1.0 CB A:CYS358 3.5 14.2 1.0 S1 A:SF4999 3.7 18.1 1.0 N A:CYS358 3.9 25.0 1.0 O A:HOH1000 4.0 21.0 1.0 CG2 A:ILE145 4.3 6.9 1.0 CA A:CYS358 4.4 22.9 1.0 CD2 A:HIS147 4.5 8.5 1.0 ND2 A:ASN446 4.6 18.6 1.0 ND1 A:HIS167 4.6 12.2 1.0 SG A:CYS424 4.6 20.7 1.0 CB A:SER357 4.9 23.7 1.0 CB A:HIS167 4.9 10.6 1.0 SG A:CYS421 4.9 12.2 1.0 CG A:HIS167 4.9 11.5 1.0 C A:SER357 5.0 25.5 1.0

Iron binding site 2 out of 4 in the Steric and Conformational Features of the Aconitase Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Steric and Conformational Features of the Aconitase Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:23.0 occ:1.00 FE2 A:SF4999 0.0 23.0 1.0 S1 A:SF4999 2.2 18.1 1.0 S4 A:SF4999 2.3 18.1 1.0 SG A:CYS424 2.3 20.7 1.0 S3 A:SF4999 2.3 25.3 1.0 FE1 A:SF4999 2.6 23.5 1.0 FE3 A:SF4999 2.7 16.7 1.0 FE4 A:SF4999 2.9 26.5 1.0 CB A:CYS424 3.2 19.6 1.0 S2 A:SF4999 3.9 19.7 1.0 NH2 A:ARG452 4.3 19.5 1.0 CB A:SER357 4.4 23.7 1.0 CA A:CYS424 4.4 18.9 1.0 O2 A:MIC755 4.4 23.4 1.0 C A:CYS424 4.5 18.8 1.0 SG A:CYS358 4.6 25.1 1.0 CB A:CYS421 4.6 10.9 1.0 SG A:CYS421 4.7 12.2 1.0 O A:CYS424 4.7 20.2 1.0 O A:HOH1000 4.7 21.0 1.0 ND2 A:ASN446 4.7 18.6 1.0 OG A:SER357 5.0 25.8 1.0

Iron binding site 3 out of 4 in the Steric and Conformational Features of the Aconitase Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Steric and Conformational Features of the Aconitase Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:16.7 occ:1.00 FE3 A:SF4999 0.0 16.7 1.0 S1 A:SF4999 2.3 18.1 1.0 S4 A:SF4999 2.3 18.1 1.0 S2 A:SF4999 2.3 19.7 1.0 SG A:CYS421 2.4 12.2 1.0 FE1 A:SF4999 2.7 23.5 1.0 FE2 A:SF4999 2.7 23.0 1.0 FE4 A:SF4999 2.8 26.5 1.0 CB A:CYS421 3.1 10.9 1.0 CE1 A:HIS101 3.8 9.6 1.0 CA A:CYS421 3.9 12.7 1.0 S3 A:SF4999 3.9 25.3 1.0 NE2 A:HIS101 4.0 9.1 1.0 CG2 A:ILE145 4.2 6.9 1.0 O7 A:MIC755 4.4 21.3 1.0 ND1 A:HIS101 4.6 11.8 1.0 N A:CYS421 4.7 11.4 1.0 SG A:CYS424 4.7 20.7 1.0 CD2 A:HIS101 4.7 11.1 1.0 SG A:CYS358 4.8 25.1 1.0 O A:HOH1000 4.8 21.0 1.0 CB A:CYS424 4.9 19.6 1.0 CG1 A:ILE425 4.9 22.5 1.0

Iron binding site 4 out of 4 in the Steric and Conformational Features of the Aconitase Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Steric and Conformational Features of the Aconitase Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe999 b:26.5 occ:1.00 FE4 A:SF4999 0.0 26.5 1.0 O A:HOH1000 2.1 21.0 1.0 S3 A:SF4999 2.3 25.3 1.0 S1 A:SF4999 2.3 18.1 1.0 S2 A:SF4999 2.3 19.7 1.0 O7 A:MIC755 2.5 21.3 1.0 FE1 A:SF4999 2.7 23.5 1.0 O2 A:MIC755 2.8 23.4 1.0 FE3 A:SF4999 2.8 16.7 1.0 FE2 A:SF4999 2.9 23.0 1.0 C2 A:MIC755 3.6 22.9 1.0 C1 A:MIC755 3.6 23.9 1.0 ND1 A:HIS167 4.0 12.2 1.0 OD2 A:ASP165 4.0 9.5 1.0 OD1 A:ASP165 4.1 10.8 1.0 S4 A:SF4999 4.1 18.1 1.0 NE2 A:HIS101 4.2 9.1 1.0 CM2 A:MIC755 4.3 23.0 1.0 NH2 A:ARG452 4.4 19.5 1.0 CE1 A:HIS101 4.5 9.6 1.0 O6 A:MIC755 4.5 22.0 1.0 CG A:ASP165 4.5 8.4 1.0 SG A:CYS358 4.7 25.1 1.0 C3 A:MIC755 4.7 21.2 1.0 O1 A:MIC755 4.8 28.5 1.0 CG A:HIS167 4.9 11.5 1.0 SG A:CYS421 4.9 12.2 1.0 CE1 A:HIS167 4.9 11.7 1.0 C6 A:MIC755 5.0 17.6 1.0 SG A:CYS424 5.0 20.7 1.0

H.Lauble, C.D.Stout. Steric and Conformational Features of the Aconitase Mechanism. Proteins V. 22 1 1995.
ISSN: ISSN 0887-3585
PubMed: 7675781
DOI: 10.1002/PROT.340220102