Iron in PDB 7tcr: Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution

The structure of Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution, PDB code: 7tcr was solved by Y.Park, R.M.Reyes, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.50 / 2.62
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	49.78, 215.64, 214.15, 90, 90, 90
R / Rfree (%)	20.4 / 23.7

The binding sites of Iron atom in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution (pdb code 7tcr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution, PDB code: 7tcr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:62.6 occ:1.00 O A:HOH401 2.0 54.0 1.0 NE2 A:HIS90 2.1 45.7 1.0 O A:HOH418 2.2 46.7 1.0 OE1 A:GLU133 2.3 49.0 1.0 O1 A:SO4304 2.4 49.1 0.6 NE2 A:HIS54 2.4 47.9 1.0 CE1 A:HIS90 3.0 49.4 1.0 CD2 A:HIS90 3.2 43.7 1.0 CD A:GLU133 3.2 47.3 1.0 CD2 A:HIS54 3.4 49.2 1.0 CE1 A:HIS54 3.4 46.5 1.0 OE2 A:GLU133 3.5 49.8 1.0 S A:SO4304 3.6 58.5 0.6 FE A:FE302 3.8 54.4 1.0 O3 A:SO4304 3.9 55.7 0.6 O2 A:SO4304 4.1 62.2 0.6 ND1 A:HIS90 4.1 47.5 1.0 CG A:HIS90 4.3 44.7 1.0 OE1 A:GLU239 4.4 60.2 1.0 CE1 A:HIS192 4.4 50.3 1.0 CG A:GLU133 4.5 44.9 1.0 ND1 A:HIS54 4.5 47.8 1.0 CG A:HIS54 4.5 48.2 1.0 ND1 A:HIS192 4.5 46.8 1.0 SD A:MET56 4.7 62.3 1.0 O4 A:SO4304 4.8 59.6 0.6 CB A:GLU133 4.8 42.6 1.0 OE2 A:GLU239 4.9 54.9 1.0

Iron binding site 2 out of 6 in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:54.4 occ:1.00 OE2 A:GLU239 1.9 54.9 1.0 OE2 A:GLU133 2.1 49.8 1.0 O A:HOH401 2.2 54.0 1.0 O3 A:SO4304 2.3 55.7 0.6 OD2 A:ASP163 2.4 53.0 1.0 ND1 A:HIS192 2.4 46.8 1.0 CD A:GLU239 2.9 58.0 1.0 CD A:GLU133 3.1 47.3 1.0 CG A:HIS192 3.3 47.6 1.0 OE1 A:GLU239 3.3 60.2 1.0 CE1 A:HIS192 3.3 50.3 1.0 S A:SO4304 3.5 58.5 0.6 CB A:HIS192 3.5 48.6 1.0 CG A:ASP163 3.5 49.6 1.0 OE1 A:GLU133 3.5 49.0 1.0 O1 A:SO4304 3.6 49.1 0.6 FE A:FE301 3.8 62.6 1.0 CB A:ASP163 4.0 46.4 1.0 FE A:FE303 4.1 59.8 0.7 CE1 A:HIS210 4.2 68.0 1.0 CG A:GLU239 4.2 55.4 1.0 O4 A:SO4304 4.3 59.6 0.6 CG A:GLU133 4.4 44.9 1.0 O2 A:SO4304 4.4 62.2 0.6 CD2 A:HIS192 4.4 48.7 1.0 NE2 A:HIS192 4.4 51.2 1.0 ND2 A:ASN166 4.4 47.3 1.0 OD1 A:ASP163 4.5 51.6 1.0 NE2 A:HIS210 4.6 66.5 1.0 NE2 A:HIS54 4.9 47.9 1.0 OD1 A:ASN166 5.0 54.7 1.0 CA A:HIS192 5.0 46.7 1.0 CG A:ASN166 5.0 49.4 1.0

Iron binding site 3 out of 6 in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:59.8 occ:0.67 NE2 A:HIS210 2.2 66.5 1.0 OD1 A:ASN166 2.4 54.7 1.0 O3 A:SO4304 2.7 55.7 0.6 CE1 A:HIS210 3.1 68.0 1.0 CD2 A:HIS210 3.2 66.7 1.0 OD2 A:ASP163 3.3 53.0 1.0 CG A:ASN166 3.4 49.4 1.0 O4 A:SO4304 3.4 59.6 0.6 S A:SO4304 3.5 58.5 0.6 CB A:ASP208 3.5 76.5 1.0 OD1 A:ASP163 3.8 51.6 1.0 OG A:SER165 3.8 61.1 1.0 CG A:ASP163 3.8 49.6 1.0 ND2 A:ASN166 3.9 47.3 1.0 O2 A:SO4304 3.9 62.2 0.6 OD2 A:ASP208 3.9 74.6 1.0 FE A:FE302 4.1 54.4 1.0 CG A:ASP208 4.2 76.9 1.0 OE2 A:GLU239 4.2 54.9 1.0 ND1 A:HIS210 4.3 69.4 1.0 CG A:HIS210 4.3 68.5 1.0 CB A:SER165 4.4 54.0 1.0 CB A:ALA194 4.6 57.2 1.0 N A:ASN166 4.6 48.5 1.0 CA A:ASP208 4.7 78.1 1.0 CB A:ASN166 4.7 50.3 1.0 O A:HOH401 4.8 54.0 1.0 O1 A:SO4304 4.8 49.1 0.6 OE2 A:GLU133 4.9 49.8 1.0 CA A:ASN166 4.9 48.9 1.0

Iron binding site 4 out of 6 in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:75.0 occ:1.00 O2 B:SO4305 2.0 44.9 0.7 NE2 B:HIS90 2.1 41.0 1.0 O B:HOH402 2.1 44.8 1.0 OE1 B:GLU133 2.2 40.4 1.0 O B:HOH418 2.3 40.2 1.0 NE2 B:HIS54 2.4 41.5 1.0 CD2 B:HIS90 3.1 39.0 1.0 CE1 B:HIS90 3.1 42.1 1.0 CD B:GLU133 3.1 41.7 1.0 S B:SO4305 3.2 47.8 0.7 CE1 B:HIS54 3.3 42.7 1.0 OE2 B:GLU133 3.3 43.3 1.0 CD2 B:HIS54 3.4 41.1 1.0 O4 B:SO4305 3.6 46.8 0.7 O1 B:SO4305 3.7 51.4 0.7 FE B:FE302 3.8 51.3 1.0 ND1 B:HIS90 4.2 40.2 1.0 CG B:HIS90 4.2 41.2 1.0 O3 B:SO4305 4.4 50.9 0.7 ND1 B:HIS54 4.4 43.2 1.0 CE1 B:HIS192 4.4 41.7 1.0 CG B:GLU133 4.5 41.5 1.0 OE1 B:GLU239 4.5 52.1 1.0 CG B:HIS54 4.5 45.1 1.0 ND1 B:HIS192 4.6 39.9 1.0 CB B:GLU133 4.8 37.3 1.0 SD B:MET56 4.8 66.0 1.0 OE2 B:GLU239 4.9 49.3 1.0

Iron binding site 5 out of 6 in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:51.3 occ:1.00 OE2 B:GLU133 1.9 43.3 1.0 OE2 B:GLU239 2.0 49.3 1.0 OD2 B:ASP163 2.2 45.0 1.0 O B:HOH402 2.2 44.8 1.0 O4 B:SO4305 2.2 46.8 0.7 ND1 B:HIS192 2.5 39.9 1.0 CD B:GLU239 3.0 46.4 1.0 CD B:GLU133 3.0 41.7 1.0 CG B:ASP163 3.3 42.5 1.0 CG B:HIS192 3.4 39.9 1.0 CE1 B:HIS192 3.4 41.7 1.0 OE1 B:GLU239 3.5 52.1 1.0 S B:SO4305 3.5 47.8 0.7 OE1 B:GLU133 3.6 40.4 1.0 CB B:HIS192 3.7 38.3 1.0 O2 B:SO4305 3.7 44.9 0.7 FE B:FE303 3.7 52.7 0.5 FE B:FE301 3.8 75.0 1.0 CB B:ASP163 3.9 36.5 1.0 CE1 B:HIS210 4.2 53.0 1.0 CG B:GLU133 4.2 41.5 1.0 CG B:GLU239 4.3 43.6 1.0 O1 B:SO4305 4.4 51.4 0.7 ND2 B:ASN166 4.4 43.2 1.0 OD1 B:ASP163 4.4 44.0 1.0 O3 B:SO4305 4.4 50.9 0.7 NE2 B:HIS192 4.5 40.4 1.0 CD2 B:HIS192 4.6 40.0 1.0 NE2 B:HIS210 4.7 54.1 1.0 NE2 B:HIS54 4.8 41.5 1.0

Iron binding site 6 out of 6 in the Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Methanobactin Biosynthetic Protein Complex of Mbnb and Mbnc From Methylosinus Trichosporium OB3B at 2.62 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:52.7 occ:0.52 NE2 B:HIS210 2.2 54.1 1.0 OD2 B:ASP163 2.7 45.0 1.0 OD1 B:ASN166 2.8 45.9 1.0 CE1 B:HIS210 2.9 53.0 1.0 O4 B:SO4305 3.1 46.8 0.7 OD1 B:ASP163 3.3 44.0 1.0 CG B:ASP163 3.3 42.5 1.0 CD2 B:HIS210 3.3 54.5 1.0 OG B:SER165 3.5 47.5 1.0 CG B:ASN166 3.5 43.8 1.0 FE B:FE302 3.7 51.3 1.0 OE2 B:GLU239 3.8 49.3 1.0 ND2 B:ASN166 3.9 43.2 1.0 CB B:ASP208 4.1 53.0 1.0 ND1 B:HIS210 4.1 54.5 1.0 CB B:ALA194 4.2 45.9 1.0 S B:SO4305 4.2 47.8 0.7 O3 B:SO4305 4.3 50.9 0.7 CG B:HIS210 4.3 53.7 1.0 N B:ASN166 4.6 39.2 1.0 CB B:SER165 4.6 43.2 1.0 CB B:ASP163 4.7 36.5 1.0 CB B:ASN166 4.7 39.6 1.0 O1 B:SO4305 4.7 51.4 0.7 OE2 B:GLU133 4.8 43.3 1.0 CD B:GLU239 4.8 46.4 1.0 OD1 B:ASP208 4.9 54.0 1.0 CA B:ASN166 4.9 41.5 1.0 O B:HOH402 5.0 44.8 1.0 C B:SER165 5.0 38.9 1.0

Y.J.Park, R.J.Jodts, J.W.Slater, R.M.Reyes, V.J.Winton, R.A.Montaser, P.M.Thomas, W.B.Dowdle, A.Ruiz, N.L.Kelleher, J.M.Bollinger Jr., C.Krebs, B.M.Hoffman, A.C.Rosenzweig. A Mixed-Valent Fe(II)Fe(III) Species Converts Cysteine to An Oxazolone/Thioamide Pair in Methanobactin Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 119 66119 2022.
ISSN: ESSN 1091-6490
PubMed: 35320042
DOI: 10.1073/PNAS.2123566119