Iron in PDB 6y1x: X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme

The structure of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme, PDB code: 6y1x was solved by A.Sosa-Fajardo, P.Legrand, L.Paya-Tormo, L.Martin, M.T.Pellicer-Martinez, C.Echavarri-Erasun, X.Vernede, L.M.Rubio, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.75 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.180, 48.680, 80.380, 78.81, 87.73, 89.94
R / Rfree (%)	17.7 / 21.2

The structure of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme (pdb code 6y1x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme, PDB code: 6y1x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:47.7 occ:1.00 FE1 A:SF4301 0.0 47.7 1.0 OE2 A:GLU65 2.2 53.9 1.0 S2 A:SF4301 2.3 33.2 1.0 S3 A:SF4301 2.3 33.1 1.0 S4 A:SF4301 2.3 32.5 1.0 FE3 A:SF4301 2.7 56.9 1.0 FE2 A:SF4301 2.7 75.4 1.0 FE4 A:SF4301 2.7 58.9 1.0 CD A:GLU65 3.1 43.8 1.0 CG A:GLU65 3.2 30.2 1.0 OG1 A:THR152 3.9 19.2 1.0 S1 A:SF4301 3.9 36.4 1.0 NZ A:LYS205 3.9 28.7 0.6 OE1 A:GLU65 4.2 52.3 1.0 NZ A:LYS205 4.3 28.0 0.4 CB A:THR152 4.4 21.4 1.0 NE2 A:HIS42 4.6 40.1 1.0 CB A:SER130 4.6 13.9 1.0 CE A:LYS205 4.7 26.7 0.4 SG A:CYS29 4.7 50.6 1.0 SG A:CYS128 4.7 33.6 1.0 CB A:GLU65 4.7 23.5 1.0 CG2 A:THR152 4.8 22.4 1.0 CE1 A:HIS42 5.0 42.0 1.0

Iron binding site 2 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:75.4 occ:1.00 FE2 A:SF4301 0.0 75.4 1.0 SG A:CYS29 2.3 50.6 1.0 S4 A:SF4301 2.3 32.5 1.0 S3 A:SF4301 2.3 33.1 1.0 S1 A:SF4301 2.3 36.4 1.0 FE3 A:SF4301 2.7 56.9 1.0 FE1 A:SF4301 2.7 47.7 1.0 FE4 A:SF4301 2.7 58.9 1.0 CB A:CYS29 3.3 46.5 1.0 CE1 A:HIS27 3.6 41.8 1.0 S2 A:SF4301 3.9 33.2 1.0 CD A:ARG40 4.0 63.7 1.0 NE2 A:HIS27 4.4 39.8 1.0 OE2 A:GLU65 4.6 53.9 1.0 NE2 A:HIS42 4.6 40.1 1.0 NH1 A:ARG40 4.6 66.0 1.0 ND1 A:HIS27 4.6 43.0 1.0 CA A:CYS29 4.7 44.6 1.0 SG A:CYS128 4.7 33.6 1.0 NE A:ARG40 4.7 67.7 1.0 CG A:ARG40 5.0 58.9 1.0

Iron binding site 3 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:56.9 occ:1.00 FE3 A:SF4301 0.0 56.9 1.0 NE2 A:HIS42 2.3 40.1 1.0 S1 A:SF4301 2.3 36.4 1.0 S4 A:SF4301 2.3 32.5 1.0 S2 A:SF4301 2.3 33.2 1.0 FE1 A:SF4301 2.7 47.7 1.0 FE2 A:SF4301 2.7 75.4 1.0 FE4 A:SF4301 2.8 58.9 1.0 CD2 A:HIS42 3.2 39.1 1.0 CE1 A:HIS42 3.2 42.0 1.0 CB A:ALA98 3.8 26.2 1.0 S3 A:SF4301 3.9 33.1 1.0 ND1 A:HIS42 4.3 41.6 1.0 CG A:HIS42 4.3 39.4 1.0 CG A:GLU65 4.4 30.2 1.0 NE A:ARG40 4.4 67.7 1.0 CZ A:ARG40 4.4 67.2 1.0 NH1 A:ARG40 4.5 66.0 1.0 CD A:ARG40 4.5 63.7 1.0 CB A:ALA100 4.6 23.6 1.0 OE2 A:GLU65 4.6 53.9 1.0 SG A:CYS29 4.8 50.6 1.0 NH2 A:ARG40 4.9 67.5 1.0 SG A:CYS128 5.0 33.6 1.0

Iron binding site 4 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:58.9 occ:1.00 FE4 A:SF4301 0.0 58.9 1.0 S3 A:SF4301 2.3 33.1 1.0 S2 A:SF4301 2.3 33.2 1.0 S1 A:SF4301 2.3 36.4 1.0 SG A:CYS128 2.3 33.6 1.0 FE2 A:SF4301 2.7 75.4 1.0 FE1 A:SF4301 2.7 47.7 1.0 FE3 A:SF4301 2.8 56.9 1.0 CB A:CYS128 3.4 25.4 1.0 NE2 A:HIS27 3.9 39.8 1.0 CB A:ALA98 3.9 26.2 1.0 S4 A:SF4301 3.9 32.5 1.0 CE1 A:HIS27 4.0 41.8 1.0 CA A:CYS128 4.6 22.1 1.0 C A:CYS128 4.7 25.6 1.0 OG1 A:THR152 4.7 19.2 1.0 N A:ILE129 4.7 24.8 1.0 OE2 A:GLU65 4.8 53.9 1.0 SG A:CYS29 4.8 50.6 1.0 O A:ILE129 4.9 25.9 1.0 NE2 A:HIS42 4.9 40.1 1.0 C A:ILE129 5.0 20.1 1.0 CG1 A:VAL96 5.0 25.6 1.0 CE1 A:PHE30 5.0 38.4 1.0

Iron binding site 5 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:30.5 occ:1.00 FE1 A:SF4302 0.0 30.5 1.0 S2 A:SF4302 2.3 16.7 1.0 S4 A:SF4302 2.3 17.6 1.0 SG A:CYS56 2.3 19.8 1.0 S3 A:SF4302 2.3 20.4 1.0 FE2 A:SF4302 2.7 31.7 1.0 FE3 A:SF4302 2.7 29.3 1.0 FE4 A:SF4302 2.7 32.2 1.0 CB A:CYS56 3.1 21.1 1.0 S1 A:SF4302 3.9 17.4 1.0 CD A:ARG58 3.9 32.0 1.0 O A:HOH509 4.0 19.0 1.0 CA A:CYS56 4.5 19.6 1.0 NE A:ARG58 4.6 33.0 1.0 SG A:CYS53 4.7 21.1 1.0 CA A:CYS62 4.7 22.4 1.0 SG A:CYS62 4.8 19.2 1.0 CB A:CYS53 4.9 15.2 1.0 SG A:CYS49 4.9 17.7 1.0 NE2 A:GLN52 4.9 17.6 1.0 CB A:CYS62 5.0 20.4 1.0 N A:CYS53 5.0 15.3 1.0

Iron binding site 6 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:31.7 occ:1.00 FE2 A:SF4302 0.0 31.7 1.0 S1 A:SF4302 2.3 17.4 1.0 S3 A:SF4302 2.3 20.4 1.0 SG A:CYS53 2.3 21.1 1.0 S4 A:SF4302 2.3 17.6 1.0 FE1 A:SF4302 2.7 30.5 1.0 FE4 A:SF4302 2.7 32.2 1.0 FE3 A:SF4302 2.7 29.3 1.0 CB A:CYS53 3.3 15.2 1.0 S2 A:SF4302 3.9 16.7 1.0 N A:CYS53 3.9 15.3 1.0 CG1 A:ILE51 4.1 18.0 1.0 CD1 A:ILE51 4.2 20.6 1.0 ND2 A:ASN64 4.2 27.9 1.0 CA A:CYS53 4.2 16.2 1.0 CB A:CYS56 4.3 21.1 1.0 O A:HOH521 4.4 38.6 1.0 SG A:CYS56 4.6 19.8 1.0 SG A:CYS49 4.7 17.7 1.0 SG A:CYS62 4.8 19.2 1.0 C A:GLN52 5.0 19.6 1.0 CG A:ASN64 5.0 25.0 1.0 OH A:TYR55 5.0 22.0 1.0

Iron binding site 7 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:29.3 occ:1.00 FE3 A:SF4302 0.0 29.3 1.0 S4 A:SF4302 2.3 17.6 1.0 SG A:CYS62 2.3 19.2 1.0 S2 A:SF4302 2.3 16.7 1.0 S1 A:SF4302 2.3 17.4 1.0 FE1 A:SF4302 2.7 30.5 1.0 FE2 A:SF4302 2.7 31.7 1.0 FE4 A:SF4302 2.7 32.2 1.0 CB A:CYS62 3.2 20.4 1.0 CA A:CYS62 3.7 22.4 1.0 ND2 A:ASN64 3.9 27.9 1.0 S3 A:SF4302 3.9 20.4 1.0 O A:HOH497 4.0 26.2 1.0 C A:CYS62 4.3 18.1 1.0 N A:VAL63 4.4 16.2 1.0 CG A:ASN64 4.5 25.0 1.0 O A:HOH476 4.5 30.5 1.0 SG A:CYS49 4.7 17.7 1.0 SG A:CYS56 4.8 19.8 1.0 N A:ASN64 4.8 23.4 1.0 SG A:CYS53 4.8 21.1 1.0 CB A:ASN64 4.9 21.6 1.0 O A:HOH509 4.9 19.0 1.0 N A:CYS62 4.9 20.6 1.0

Iron binding site 8 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:32.2 occ:1.00 FE4 A:SF4302 0.0 32.2 1.0 S2 A:SF4302 2.3 16.7 1.0 S3 A:SF4302 2.3 20.4 1.0 SG A:CYS49 2.3 17.7 1.0 S1 A:SF4302 2.3 17.4 1.0 FE2 A:SF4302 2.7 31.7 1.0 FE1 A:SF4302 2.7 30.5 1.0 FE3 A:SF4302 2.7 29.3 1.0 CB A:CYS49 3.4 18.4 1.0 S4 A:SF4302 3.9 17.6 1.0 O A:ILE51 4.1 18.4 1.0 CG1 A:ILE51 4.2 18.0 1.0 CD A:ARG58 4.5 32.0 1.0 ND2 A:ASN132 4.7 20.0 1.0 NE A:ARG58 4.7 33.0 1.0 C A:ILE51 4.8 15.2 1.0 SG A:CYS62 4.8 19.2 1.0 CA A:CYS49 4.8 22.0 1.0 SG A:CYS53 4.8 21.1 1.0 CD1 A:ILE51 4.9 20.6 1.0 SG A:CYS56 4.9 19.8 1.0

Iron binding site 9 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:43.1 occ:1.00 FE1 B:SF4304 0.0 43.1 1.0 OE2 B:GLU65 2.2 51.4 1.0 S2 B:SF4304 2.3 31.1 1.0 S3 B:SF4304 2.3 35.5 1.0 S4 B:SF4304 2.3 28.9 1.0 FE3 B:SF4304 2.7 46.0 1.0 FE2 B:SF4304 2.7 52.2 1.0 FE4 B:SF4304 2.7 44.1 1.0 CD B:GLU65 3.1 43.5 1.0 CG B:GLU65 3.4 36.7 1.0 S1 B:SF4304 3.9 31.7 1.0 OG1 B:THR152 3.9 20.5 1.0 NZ B:LYS205 4.0 34.5 1.0 OE1 B:GLU65 4.3 45.7 1.0 CB B:THR152 4.4 22.2 1.0 CE B:LYS205 4.5 33.1 1.0 NE2 B:HIS42 4.6 32.0 1.0 CB B:SER130 4.6 18.6 1.0 SG B:CYS29 4.7 42.2 1.0 SG B:CYS128 4.7 32.8 1.0 CG2 B:THR152 4.8 21.3 1.0 CB B:GLU65 4.9 25.3 1.0 CE1 B:HIS42 4.9 33.2 1.0

Iron binding site 10 out of 16 in the X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of X-Ray Structure of the Radical Sam Protein Nifb, A Key Nitrogenase Maturating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:52.2 occ:1.00 FE2 B:SF4304 0.0 52.2 1.0 S4 B:SF4304 2.3 28.9 1.0 SG B:CYS29 2.3 42.2 1.0 S3 B:SF4304 2.3 35.5 1.0 S1 B:SF4304 2.3 31.7 1.0 FE3 B:SF4304 2.7 46.0 1.0 FE1 B:SF4304 2.7 43.1 1.0 FE4 B:SF4304 2.7 44.1 1.0 CB B:CYS29 3.2 37.8 1.0 CE1 B:HIS27 3.7 40.2 1.0 S2 B:SF4304 3.9 31.1 1.0 NE2 B:HIS27 4.4 37.6 1.0 NE2 B:HIS42 4.5 32.0 1.0 NE B:ARG40 4.6 59.0 1.0 OE2 B:GLU65 4.6 51.4 1.0 CG B:ARG40 4.7 46.5 1.0 CA B:CYS29 4.7 40.0 1.0 ND1 B:HIS27 4.7 39.5 1.0 SG B:CYS128 4.7 32.8 1.0 CD B:ARG40 4.8 53.8 1.0 N B:CYS29 5.0 38.7 1.0

A.Sosa Fajardo, P.Legrand, L.Paya-Tormo, L.Martin, M.T.Pellicer Martinez, C.Echavarri-Erasun, X.Vernede, L.M.Rubio, Y.Nicolet. Structural Insights Into the Mechanism of the Radical Sam Carbide Synthase Nifb, A Key Nitrogenase Cofactor Maturating Enzyme. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 32476412
DOI: 10.1021/JACS.0C02243