Magnesium 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:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the SER480ALA Mutant of L-Arabinonate Dehydratase (pdb code 5j85). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the SER480ALA Mutant of L-Arabinonate Dehydratase, PDB code: 5j85:

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SER480ALA Mutant of L-Arabinonate Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:78.6 occ:1.00 OE1 A:GLU453 2.1 87.2 1.0 OD2 A:ASP128 2.1 99.8 1.0 OE1 A:GLU91 2.3 90.3 1.0 OQ1 A:KCX129 2.4 82.9 1.0 CD A:GLU453 3.0 84.5 1.0 OG1 A:THR205 3.3 87.7 1.0 CG A:ASP128 3.3 90.3 1.0 OE2 A:GLU453 3.3 91.9 1.0 CD A:GLU91 3.4 0.3 1.0 CX A:KCX129 3.6 79.9 1.0 CB A:THR205 3.9 74.7 1.0 CG A:GLU91 3.9 97.5 1.0 ND2 A:ASN278 4.0 72.5 1.0 CB A:ASP128 4.1 75.0 1.0 NZ A:KCX129 4.1 78.2 1.0 OD1 A:ASP128 4.2 93.4 1.0 OE2 A:GLU91 4.4 96.0 1.0 CG A:GLU453 4.4 78.7 1.0 NH1 A:ARG478 4.4 63.8 1.0 OQ2 A:KCX129 4.6 74.2 1.0 CG2 A:THR205 4.6 72.9 1.0 CB A:GLU91 4.6 86.6 1.0 CA A:ALA480 4.8 88.3 1.0

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