Iron in PDB 4ybn: Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis

The structure of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis, PDB code: 4ybn was solved by F.H.Ahmed, P.D.Carr, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.73 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.722, 59.876, 89.658, 90.00, 93.83, 90.00
R / Rfree (%)	17.4 / 22.3

The structure of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Iron atom in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis (pdb code 4ybn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis, PDB code: 4ybn:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe304 b:40.7 occ:0.51 FE A:HEM304 0.0 40.7 0.5 ND A:HEM304 1.9 40.1 0.5 NA A:HEM304 2.0 37.9 0.5 NC A:HEM304 2.1 36.3 0.5 NB A:HEM304 2.1 39.5 0.5 NE2 A:HIS63 2.5 37.3 1.0 O A:HOH490 2.7 52.0 1.0 C1D A:HEM304 2.9 39.8 0.5 C4D A:HEM304 2.9 41.5 0.5 C1A A:HEM304 3.0 41.2 0.5 C4A A:HEM304 3.0 36.9 0.5 C4C A:HEM304 3.1 34.3 0.5 C1B A:HEM304 3.1 39.0 0.5 C4B A:HEM304 3.1 35.6 0.5 C1C A:HEM304 3.1 37.7 0.5 CE1 A:HIS63 3.3 41.0 1.0 CHD A:HEM304 3.3 38.3 0.5 CHA A:HEM304 3.4 41.9 0.5 CD2 A:HIS63 3.4 33.5 1.0 CHB A:HEM304 3.4 39.0 0.5 CHC A:HEM304 3.5 37.4 0.5 O B:SER99 3.5 32.0 1.0 O B:PHE97 4.0 27.4 1.0 C3D A:HEM304 4.1 39.4 0.5 C2D A:HEM304 4.2 39.4 0.5 C3A A:HEM304 4.2 39.3 0.5 C2A A:HEM304 4.2 42.0 0.5 C3C A:HEM304 4.3 32.5 0.5 C2B A:HEM304 4.3 35.8 0.5 C2C A:HEM304 4.3 32.8 0.5 C3B A:HEM304 4.4 37.1 0.5 ND1 A:HIS63 4.4 32.3 1.0 CG A:HIS63 4.5 30.2 1.0 O B:SER96 4.6 28.9 1.0 C B:SER99 4.8 32.7 1.0 C B:PHE97 4.8 25.8 1.0

Iron binding site 2 out of 2 in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.9 occ:0.68 FE B:HEM301 0.0 30.9 0.7 ND B:HEM301 1.9 33.8 0.7 NA B:HEM301 2.0 30.2 0.7 NC B:HEM301 2.1 27.7 0.7 NB B:HEM301 2.1 30.4 0.7 NE2 B:HIS63 2.2 34.3 1.0 O A:HOH422 2.3 38.0 1.0 C4D B:HEM301 2.9 33.1 0.7 C1D B:HEM301 2.9 31.9 0.7 C4A B:HEM301 3.0 30.0 0.7 C1A B:HEM301 3.1 29.9 0.7 CE1 B:HIS63 3.1 32.7 1.0 C1C B:HEM301 3.1 29.5 0.7 C1B B:HEM301 3.1 29.8 0.7 C4C B:HEM301 3.1 30.6 0.7 C4B B:HEM301 3.1 30.1 0.7 CD2 B:HIS63 3.2 29.0 1.0 CHD B:HEM301 3.4 33.7 0.7 CHA B:HEM301 3.4 32.2 0.7 CHB B:HEM301 3.4 30.2 0.7 CHC B:HEM301 3.4 27.3 0.7 O A:SER99 4.0 29.5 1.0 C2D B:HEM301 4.2 33.4 0.7 C3D B:HEM301 4.2 33.8 0.7 ND1 B:HIS63 4.2 28.9 1.0 O A:HOH539 4.2 54.4 1.0 C3A B:HEM301 4.2 31.4 0.7 C2A B:HEM301 4.3 32.3 0.7 C2C B:HEM301 4.3 25.9 0.7 O A:PHE97 4.3 29.1 1.0 C3C B:HEM301 4.3 29.0 0.7 CG B:HIS63 4.3 24.9 1.0 C2B B:HEM301 4.3 30.1 0.7 C3B B:HEM301 4.4 31.0 0.7 O A:SER96 4.8 31.0 1.0 O A:HOH478 4.8 45.7 1.0

F.H.Ahmed, P.D.Carr, B.M.Lee, L.Afriat-Jurnou, A.E.Mohamed, N.S.Hong, J.Flanagan, M.C.Taylor, C.Greening, C.J.Jackson. Sequence-Structure-Function Classification of A Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. J.Mol.Biol. V. 427 3554 2015.
ISSN: ESSN 1089-8638
PubMed: 26434506
DOI: 10.1016/J.JMB.2015.09.021