Iron in PDB 9gyz: Crystal Structure of Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site)

The structure of Crystal Structure of Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site), PDB code: 9gyz was solved by M.Sharma, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.44 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.509, 82.509, 136.194, 90, 90, 120
R / Rfree (%)	20.8 / 25.5

The binding sites of Iron atom in the Crystal Structure of Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site) (pdb code 9gyz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site), PDB code: 9gyz:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site)


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 Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:53.3 occ:1.00 OE1 B:GLU97 2.1 43.6 1.0 NE2 B:HIS150 2.2 40.7 1.0 OE1 B:GLU103 2.2 37.0 1.0 NE2 B:HIS99 2.2 38.6 1.0 CD2 B:HIS150 3.1 44.9 1.0 CD B:GLU103 3.1 45.8 1.0 CE1 B:HIS99 3.1 36.2 1.0 CE1 B:HIS150 3.2 62.1 1.0 CD2 B:HIS99 3.2 36.7 1.0 CD B:GLU97 3.2 46.3 1.0 OE2 B:GLU103 3.3 47.1 1.0 CG B:GLU97 3.8 46.3 1.0 CG B:HIS150 4.2 46.6 1.0 OE2 B:GLU97 4.2 50.5 1.0 ND1 B:HIS99 4.2 36.1 1.0 ND1 B:HIS150 4.2 46.1 1.0 CG B:HIS99 4.3 33.2 1.0 CD1 B:LEU167 4.5 50.0 1.0 CG B:GLU103 4.5 39.4 1.0 ND2 B:ASN172 4.8 39.2 1.0 CB B:GLU103 5.0 39.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site)


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 Domain-of-Unknown-Function DUF4867 From Bacillus Megaterium (Unmodelled Additional Ligand Density at Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:48.6 occ:1.00 OE1 A:GLU103 2.1 42.5 1.0 OE1 A:GLU97 2.1 37.8 1.0 NE2 A:HIS150 2.1 41.1 1.0 NE2 A:HIS99 2.2 34.9 1.0 CD A:GLU103 3.1 40.9 1.0 CD2 A:HIS150 3.1 38.0 1.0 CE1 A:HIS99 3.2 44.0 1.0 CD2 A:HIS99 3.2 37.8 1.0 CE1 A:HIS150 3.2 40.9 1.0 CD A:GLU97 3.2 43.9 1.0 OE2 A:GLU103 3.4 49.7 1.0 CG A:GLU97 3.8 35.5 1.0 CG A:HIS150 4.2 41.7 1.0 ND1 A:HIS150 4.3 32.6 1.0 OE2 A:GLU97 4.3 40.3 1.0 ND1 A:HIS99 4.3 32.5 1.0 CG A:HIS99 4.3 38.9 1.0 CG A:GLU103 4.4 42.6 1.0 CD1 A:LEU167 4.5 38.3 1.0 ND2 A:ASN172 4.7 38.9 1.0 CB A:GLU103 4.8 36.6 1.0 CD2 A:LEU167 5.0 41.5 1.0

M.Sharma, N.Pudlo, M.A.Jarva, A.Kaur, A.John, L.Burchill, J.P.Lingford, R.Epa, P.Abayakoon, N.E.Scott, J.P.Turkenburg, G.J.Davies, E.C.Martens, E.D.Goddard-Borger, S.J.Williams. Sulfoglycolysis Sustains Eubacterium Rectale in Low-Fiber Diets. J.Biol.Chem. 08320 2025.
ISSN: ESSN 1083-351X
PubMed: 39956340
DOI: 10.1016/J.JBC.2025.108320