Iron in PDB 5j85: SER480ALA Mutant of L-Arabinonate Dehydratase

The structure of SER480ALA Mutant of L-Arabinonate Dehydratase, PDB code: 5j85 was solved by M.M.Rahman, J.Rouvinen, N.Hakulinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 2.60
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	318.440, 318.440, 318.440, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.3

The structure of SER480ALA Mutant of L-Arabinonate Dehydratase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the SER480ALA Mutant of L-Arabinonate Dehydratase (pdb code 5j85). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the SER480ALA Mutant of L-Arabinonate Dehydratase, PDB code: 5j85:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the SER480ALA Mutant of L-Arabinonate Dehydratase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of SER480ALA Mutant of L-Arabinonate Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:81.3 occ:0.60 FE1 A:FES601 0.0 81.3 0.6 SG A:CYS59 2.2 60.8 0.6 S1 A:FES601 2.2 95.3 0.6 S2 A:FES601 2.2 64.5 0.6 SG A:CYS127 2.4 84.7 0.6 SG A:CYS59 2.8 74.8 0.4 FE2 A:FES601 3.1 95.8 0.6 CB A:CYS59 3.2 66.9 0.4 CB A:CYS59 3.2 66.9 0.6 CB A:CYS127 3.3 67.3 0.6 CB A:CYS127 3.6 67.5 0.4 ND2 A:ASN92 3.6 87.4 1.0 CA A:CYS127 3.6 67.0 0.6 CA A:CYS127 3.7 66.5 0.4 SG A:CYS127 4.0 75.4 0.4 N A:ASP128 4.0 69.9 1.0 OD1 A:ASP128 4.1 93.4 1.0 C A:CYS127 4.4 68.0 0.6 C A:CYS127 4.4 67.9 0.4 CA A:CYS59 4.6 64.3 0.4 CA A:CYS59 4.6 64.3 0.6 OG A:SER90 4.7 87.9 1.0 CG A:ASP128 4.7 90.3 1.0 CG2 A:THR199 4.7 62.6 1.0 SG A:CYS200 4.8 85.1 0.6 CG A:ASN92 4.8 92.8 1.0 N A:CYS127 4.8 66.6 0.6 N A:CYS127 4.8 66.7 0.4 N A:GLU91 4.9 85.0 1.0

Iron binding site 2 out of 2 in the SER480ALA Mutant of L-Arabinonate Dehydratase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of SER480ALA Mutant of L-Arabinonate Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:95.8 occ:0.60 FE2 A:FES601 0.0 95.8 0.6 S1 A:FES601 2.2 95.3 0.6 S2 A:FES601 2.2 64.5 0.6 SG A:CYS200 2.3 85.1 0.6 FE1 A:FES601 3.1 81.3 0.6 OD1 A:ASP128 3.2 93.4 1.0 CB A:CYS200 3.7 73.3 0.6 CB A:CYS200 3.7 73.2 0.4 CG A:ASP128 3.9 90.3 1.0 OD2 A:ASP128 4.0 99.8 1.0 N A:CYS200 4.3 65.2 0.6 N A:CYS200 4.3 65.2 0.4 SG A:CYS59 4.4 60.8 0.6 CA A:CYS200 4.6 69.8 0.4 CA A:CYS200 4.6 70.4 0.6 SG A:CYS127 4.9 84.7 0.6 SG A:CYS200 4.9 69.6 0.4

M.M.Rahman, M.Andberg, S.K.Thangaraj, T.Parkkinen, M.Penttila, J.Janis, A.Koivula, J.Rouvinen, N.Hakulinen. The Crystal Structure of A Bacterial L-Arabinonate Dehydratase Contains A [2FE-2S] Cluster. Acs Chem. Biol. V. 12 1919 2017.
ISSN: ESSN 1554-8937
PubMed: 28574691
DOI: 10.1021/ACSCHEMBIO.7B00304