Iron in PDB 5koj: Nitrogenase Mofep Protein in the Ids Oxidized State

All present enzymatic activity of Nitrogenase Mofep Protein in the Ids Oxidized State:
1.18.6.1;

The structure of Nitrogenase Mofep Protein in the Ids Oxidized State, PDB code: 5koj was solved by C.P.Owens, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.59 / 2.59
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	201.569, 201.569, 132.208, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.8

The structure of Nitrogenase Mofep Protein in the Ids Oxidized State also contains other interesting chemical elements:

Molybdenum

(Mo)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the Nitrogenase Mofep Protein in the Ids Oxidized State (pdb code 5koj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Nitrogenase Mofep Protein in the Ids Oxidized State, PDB code: 5koj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.4 occ:1.00 FE1 A:ICS502 0.0 31.4 1.0 S2A A:ICS502 2.2 31.8 1.0 S4A A:ICS502 2.3 34.0 1.0 S1A A:ICS502 2.3 37.6 1.0 SG A:CYS291 2.3 35.1 1.0 FE4 A:ICS502 2.6 34.5 1.0 FE2 A:ICS502 2.7 31.6 1.0 FE3 A:ICS502 2.7 33.4 1.0 CB A:CYS291 3.1 34.7 1.0 CX A:ICS502 3.5 32.1 1.0 OG A:SER294 3.9 32.5 1.0 CB A:LEU374 4.1 33.6 1.0 CB A:SER294 4.2 34.2 1.0 CE2 A:TYR245 4.4 29.9 1.0 CA A:CYS291 4.4 33.6 1.0 CD2 A:LEU374 4.7 37.1 1.0 N A:SER294 4.7 34.5 1.0 S2B A:ICS502 4.8 28.1 1.0 S3A A:ICS502 4.8 33.9 1.0 S5A A:ICS502 4.8 32.3 1.0 CD2 A:TYR245 4.9 29.2 1.0 N A:LEU374 4.9 35.4 1.0

Iron binding site 2 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.6 occ:1.00 FE2 A:ICS502 0.0 31.6 1.0 CX A:ICS502 2.0 32.1 1.0 S2A A:ICS502 2.2 31.8 1.0 S2B A:ICS502 2.2 28.1 1.0 S1A A:ICS502 2.2 37.6 1.0 FE6 A:ICS502 2.6 31.5 1.0 FE4 A:ICS502 2.6 34.5 1.0 FE3 A:ICS502 2.6 33.4 1.0 FE1 A:ICS502 2.7 31.4 1.0 FE7 A:ICS502 3.7 30.8 1.0 FE5 A:ICS502 3.7 31.5 1.0 S4A A:ICS502 3.8 34.0 1.0 S3B A:ICS502 4.1 32.4 1.0 S1B A:ICS502 4.2 27.9 1.0 NE2 A:HIS211 4.2 41.5 1.0 CZ A:PHE397 4.2 31.9 1.0 CE1 A:HIS211 4.3 41.9 1.0 CG1 A:VAL86 4.4 37.6 1.0 S3A A:ICS502 4.5 33.9 1.0 S5A A:ICS502 4.5 32.3 1.0 CE2 A:PHE397 4.5 31.6 1.0 SG A:CYS291 4.7 35.1 1.0 CG2 A:VAL86 4.9 40.7 1.0 CB A:SER294 4.9 34.2 1.0 MO1 A:ICS502 5.0 32.0 1.0

Iron binding site 3 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:33.4 occ:1.00 FE3 A:ICS502 0.0 33.4 1.0 CX A:ICS502 2.0 32.1 1.0 S5A A:ICS502 2.2 32.3 1.0 S2A A:ICS502 2.2 31.8 1.0 S4A A:ICS502 2.3 34.0 1.0 FE7 A:ICS502 2.6 30.8 1.0 FE4 A:ICS502 2.6 34.5 1.0 FE2 A:ICS502 2.6 31.6 1.0 FE1 A:ICS502 2.7 31.4 1.0 FE5 A:ICS502 3.7 31.5 1.0 FE6 A:ICS502 3.7 31.5 1.0 S1A A:ICS502 3.8 37.6 1.0 NH2 A:ARG112 4.0 38.0 1.0 CD2 A:TYR245 4.1 29.2 1.0 S3B A:ICS502 4.2 32.4 1.0 S4B A:ICS502 4.2 32.0 1.0 CE2 A:TYR245 4.4 29.9 1.0 S2B A:ICS502 4.5 28.1 1.0 S3A A:ICS502 4.5 33.9 1.0 SG A:CYS291 4.9 35.1 1.0

Iron binding site 4 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:34.5 occ:1.00 FE4 A:ICS502 0.0 34.5 1.0 CX A:ICS502 2.0 32.1 1.0 S3A A:ICS502 2.3 33.9 1.0 S1A A:ICS502 2.3 37.6 1.0 S4A A:ICS502 2.3 34.0 1.0 FE5 A:ICS502 2.6 31.5 1.0 FE2 A:ICS502 2.6 31.6 1.0 FE3 A:ICS502 2.6 33.4 1.0 FE1 A:ICS502 2.6 31.4 1.0 FE7 A:ICS502 3.7 30.8 1.0 FE6 A:ICS502 3.7 31.5 1.0 S2A A:ICS502 3.7 31.8 1.0 N A:LEU374 3.9 35.4 1.0 CB A:LEU374 4.0 33.6 1.0 N A:GLY373 4.2 34.6 1.0 S1B A:ICS502 4.2 27.9 1.0 S4B A:ICS502 4.3 32.0 1.0 S5A A:ICS502 4.4 32.3 1.0 S2B A:ICS502 4.5 28.1 1.0 CA A:LEU374 4.5 36.0 1.0 N A:ARG375 4.6 33.2 1.0 SG A:CYS291 4.6 35.1 1.0 C A:GLY373 4.7 35.3 1.0 CA A:GLY373 4.8 34.1 1.0 CD A:ARG375 4.8 35.6 1.0 CG A:ARG375 5.0 35.7 1.0 NE A:ARG375 5.0 36.6 1.0 CA A:GLY372 5.0 29.2 1.0

Iron binding site 5 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.5 occ:1.00 FE5 A:ICS502 0.0 31.5 1.0 CX A:ICS502 2.0 32.1 1.0 S3A A:ICS502 2.2 33.9 1.0 S1B A:ICS502 2.2 27.9 1.0 S4B A:ICS502 2.3 32.0 1.0 FE4 A:ICS502 2.6 34.5 1.0 FE7 A:ICS502 2.6 30.8 1.0 FE6 A:ICS502 2.6 31.5 1.0 MO1 A:ICS502 2.7 32.0 1.0 FE2 A:ICS502 3.7 31.6 1.0 FE3 A:ICS502 3.7 33.4 1.0 S3B A:ICS502 3.8 32.4 1.0 ND1 A:HIS458 3.9 35.3 1.0 N A:GLY372 4.0 27.4 1.0 CG1 A:VAL371 4.2 29.6 1.0 CA A:GLY372 4.3 29.2 1.0 S1A A:ICS502 4.3 37.6 1.0 S4A A:ICS502 4.3 34.0 1.0 S5A A:ICS502 4.4 32.3 1.0 S2B A:ICS502 4.5 28.1 1.0 CE1 A:HIS458 4.5 36.8 1.0 CD A:ARG375 4.6 35.6 1.0 O7 A:HCA501 4.6 28.7 1.0 O5 A:HCA501 4.8 28.5 1.0 N A:GLY373 4.8 34.6 1.0 CG A:HIS458 4.8 35.2 1.0 CB A:VAL371 4.9 29.1 1.0 NE A:ARG375 4.9 36.6 1.0

Iron binding site 6 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.5 occ:1.00 FE6 A:ICS502 0.0 31.5 1.0 CX A:ICS502 2.0 32.1 1.0 S2B A:ICS502 2.2 28.1 1.0 S1B A:ICS502 2.2 27.9 1.0 S3B A:ICS502 2.2 32.4 1.0 FE2 A:ICS502 2.6 31.6 1.0 FE7 A:ICS502 2.6 30.8 1.0 FE5 A:ICS502 2.6 31.5 1.0 MO1 A:ICS502 2.6 32.0 1.0 O7 A:HCA501 3.5 28.7 1.0 FE4 A:ICS502 3.7 34.5 1.0 FE3 A:ICS502 3.7 33.4 1.0 S4B A:ICS502 3.8 32.0 1.0 CZ A:PHE397 4.1 31.9 1.0 S2A A:ICS502 4.3 31.8 1.0 S1A A:ICS502 4.3 37.6 1.0 CG2 A:VAL86 4.4 40.7 1.0 S5A A:ICS502 4.5 32.3 1.0 O5 A:HCA501 4.5 28.5 1.0 S3A A:ICS502 4.5 33.9 1.0 O1 A:HCA501 4.6 36.2 1.0 C3 A:HCA501 4.7 34.0 1.0 CE1 A:PHE397 4.8 30.4 1.0 ND1 A:HIS458 4.9 35.3 1.0 C7 A:HCA501 5.0 31.6 1.0

Iron binding site 7 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:30.8 occ:1.00 FE7 A:ICS502 0.0 30.8 1.0 CX A:ICS502 2.0 32.1 1.0 S3B A:ICS502 2.2 32.4 1.0 S5A A:ICS502 2.2 32.3 1.0 S4B A:ICS502 2.2 32.0 1.0 FE3 A:ICS502 2.6 33.4 1.0 FE6 A:ICS502 2.6 31.5 1.0 FE5 A:ICS502 2.6 31.5 1.0 MO1 A:ICS502 2.6 32.0 1.0 FE2 A:ICS502 3.7 31.6 1.0 FE4 A:ICS502 3.7 34.5 1.0 O5 A:HCA501 3.7 28.5 1.0 O A:HOH650 3.8 29.2 1.0 S1B A:ICS502 3.8 27.9 1.0 NE A:ARG112 4.1 40.0 1.0 S2A A:ICS502 4.3 31.8 1.0 NH2 A:ARG112 4.3 38.0 1.0 S4A A:ICS502 4.3 34.0 1.0 S2B A:ICS502 4.4 28.1 1.0 O7 A:HCA501 4.5 28.7 1.0 S3A A:ICS502 4.5 33.9 1.0 CZ A:ARG112 4.7 40.1 1.0 C7 A:HCA501 4.7 31.6 1.0 NH1 A:ARG375 4.7 36.4 1.0 CZ A:ARG375 4.7 34.9 1.0 ND1 A:HIS458 4.9 35.3 1.0 CD A:ARG112 5.0 39.2 1.0

Iron binding site 8 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:38.9 occ:1.00 FE1 A:CLF503 0.0 38.9 1.0 S3A A:CLF503 2.3 33.7 1.0 S2A A:CLF503 2.3 39.0 1.0 SG B:CYS94 2.4 38.0 1.0 S1 A:CLF503 2.4 33.4 1.0 FE2 A:CLF503 2.5 36.5 1.0 FE4 A:CLF503 2.6 37.4 1.0 FE3 A:CLF503 2.7 33.9 1.0 FE8 A:CLF503 3.2 44.9 1.0 N B:CYS94 3.3 30.9 1.0 CA B:CYS94 3.5 33.3 1.0 CB B:CYS94 3.5 35.5 1.0 S4A A:CLF503 3.7 36.6 1.0 C B:GLY93 4.1 32.2 1.0 S4B A:CLF503 4.1 36.3 1.0 O B:HOH757 4.2 46.3 1.0 FE5 A:CLF503 4.3 34.0 0.7 SG A:CYS170 4.6 34.3 1.0 FE6 A:CLF503 4.6 28.6 0.8 CA B:GLY93 4.6 34.0 1.0 SG A:CYS78 4.7 30.6 1.0 SG A:CYS104 4.7 29.9 1.0 O B:GLY93 4.8 30.3 1.0 N B:GLY93 4.9 32.8 1.0 CB B:SER91 4.9 55.0 1.0 OH B:TYR98 5.0 20.0 1.0

Iron binding site 9 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:36.5 occ:1.00 FE2 A:CLF503 0.0 36.5 1.0 S4A A:CLF503 2.3 36.6 1.0 S2A A:CLF503 2.3 39.0 1.0 SG A:CYS170 2.4 34.3 1.0 FE1 A:CLF503 2.5 38.9 1.0 S1 A:CLF503 2.5 33.4 1.0 FE4 A:CLF503 2.6 37.4 1.0 FE3 A:CLF503 2.8 33.9 1.0 CB A:CYS170 3.3 36.3 1.0 O B:HOH757 3.4 46.3 1.0 N A:CYS170 3.7 35.6 1.0 S3A A:CLF503 3.8 33.7 1.0 CA A:CYS170 4.0 38.4 1.0 CA A:GLY201 4.1 36.7 1.0 N A:GLY201 4.2 35.3 1.0 SG B:CYS94 4.3 38.0 1.0 FE6 A:CLF503 4.5 28.6 0.8 SG A:CYS104 4.6 29.9 1.0 CB B:SER91 4.7 55.0 1.0 FE8 A:CLF503 4.8 44.9 1.0 C A:GLU169 4.8 35.5 1.0 SG A:CYS78 4.9 30.6 1.0 SG B:CYS152 4.9 39.9 1.0

Iron binding site 10 out of 32 in the Nitrogenase Mofep Protein in the Ids Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Nitrogenase Mofep Protein in the Ids Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:33.9 occ:1.00 FE3 A:CLF503 0.0 33.9 1.0 S2A A:CLF503 2.2 39.0 1.0 S3A A:CLF503 2.2 33.7 1.0 SG A:CYS78 2.2 30.6 1.0 S4A A:CLF503 2.3 36.6 1.0 FE1 A:CLF503 2.7 38.9 1.0 FE4 A:CLF503 2.7 37.4 1.0 FE2 A:CLF503 2.8 36.5 1.0 CB A:CYS78 3.3 30.2 1.0 CA A:GLY201 4.0 36.7 1.0 CB A:TYR80 4.1 30.4 1.0 S1 A:CLF503 4.3 33.4 1.0 CA B:GLY93 4.4 34.0 1.0 N B:CYS94 4.5 30.9 1.0 N A:GLY201 4.5 35.3 1.0 C B:GLY93 4.5 32.2 1.0 SG A:CYS170 4.6 34.3 1.0 CA A:CYS78 4.7 30.8 1.0 CG A:TYR80 4.8 29.2 1.0 CD1 A:TYR80 4.9 30.2 1.0 SG A:CYS104 4.9 29.9 1.0 N A:TYR80 5.0 28.8 1.0 N B:GLY93 5.0 32.8 1.0 O B:HOH767 5.0 23.9 1.0

C.P.Owens, F.E.Katz, C.H.Carter, V.F.Oswald, F.A.Tezcan. Tyrosine-Coordinated P-Cluster in G. Diazotrophicus Nitrogenase: Evidence For the Importance of O-Based Ligands in Conformationally Gated Electron Transfer. J.Am.Chem.Soc. V. 138 10124 2016.
ISSN: ESSN 1520-5126
PubMed: 27487256
DOI: 10.1021/JACS.6B06783