Iron in PDB 8q5x: Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis, PDB code: 8q5x was solved by N.Maslac, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.89 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.546, 111.094, 78.82, 90, 90.01, 90
R / Rfree (%)	16 / 18.6

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Iron atom in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis (pdb code 8q5x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis, PDB code: 8q5x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:13.2 occ:1.00 FE1 A:SF4303 0.0 13.2 1.0 S2 A:SF4303 2.3 13.6 1.0 SG C:CYS132 2.3 16.2 1.0 S4 A:SF4303 2.3 12.7 1.0 S3 A:SF4303 2.4 14.2 1.0 FE2 A:SF4303 2.7 13.9 1.0 FE3 A:SF4303 2.7 13.4 1.0 FE4 A:SF4303 2.7 13.2 1.0 CB C:CYS132 3.5 15.9 1.0 S1 A:SF4303 4.0 12.1 1.0 N A:ALA98 4.2 13.6 1.0 C C:CYS132 4.2 16.2 1.0 O C:CYS132 4.4 11.4 1.0 CA C:CYS132 4.4 16.4 1.0 N C:GLY133 4.4 16.3 1.0 CG2 C:VAL130 4.5 22.8 1.0 SG A:CYS97 4.5 13.2 1.0 CA A:CYS97 4.6 13.2 1.0 CB A:ALA98 4.7 13.4 1.0 SG C:CYS97 4.7 13.1 1.0 SG A:CYS132 4.8 16.0 1.0 C A:CYS97 4.9 16.0 1.0 CB C:VAL130 4.9 17.3 1.0 N C:CYS132 4.9 15.2 1.0 CA C:GLY133 5.0 16.5 1.0

Iron binding site 2 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:13.9 occ:1.00 FE2 A:SF4303 0.0 13.9 1.0 SG A:CYS97 2.3 13.2 1.0 S1 A:SF4303 2.3 12.1 1.0 S3 A:SF4303 2.3 14.2 1.0 S4 A:SF4303 2.3 12.7 1.0 FE4 A:SF4303 2.7 13.2 1.0 FE3 A:SF4303 2.7 13.4 1.0 FE1 A:SF4303 2.7 13.2 1.0 CB A:CYS97 3.3 13.3 1.0 CA A:CYS97 3.8 13.2 1.0 S2 A:SF4303 3.9 13.6 1.0 N A:ALA98 4.1 13.6 1.0 NE2 D:GLN174 4.2 61.0 1.0 C A:CYS97 4.3 16.0 1.0 SG C:CYS132 4.4 16.2 1.0 N A:GLY99 4.6 11.4 1.0 CA A:GLY133 4.7 20.3 1.0 SG C:CYS97 4.7 13.1 1.0 O A:HOH606 4.8 24.2 1.0 SG A:CYS132 4.8 16.0 1.0 O A:HOH674 4.9 31.2 1.0 N A:GLY133 4.9 16.7 1.0

Iron binding site 3 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:13.4 occ:1.00 FE3 A:SF4303 0.0 13.4 1.0 SG C:CYS97 2.2 13.1 1.0 S4 A:SF4303 2.3 12.7 1.0 S2 A:SF4303 2.3 13.6 1.0 S1 A:SF4303 2.4 12.1 1.0 FE4 A:SF4303 2.6 13.2 1.0 FE2 A:SF4303 2.7 13.9 1.0 FE1 A:SF4303 2.7 13.2 1.0 CB C:CYS97 3.4 13.6 1.0 CA C:CYS97 3.7 19.4 1.0 S3 A:SF4303 3.9 14.2 1.0 N C:ALA98 4.1 15.0 1.0 C C:CYS97 4.2 13.9 1.0 SG A:CYS132 4.5 16.0 1.0 O C:HOH609 4.5 23.5 1.0 N C:GLY99 4.5 12.1 1.0 CA C:GLY133 4.7 16.5 1.0 SG C:CYS132 4.8 16.2 1.0 SG A:CYS97 4.8 13.2 1.0 N C:GLY133 4.9 16.3 1.0 O A:HOH674 4.9 31.2 1.0 CB A:CYS132 4.9 21.6 1.0

Iron binding site 4 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:13.2 occ:1.00 FE4 A:SF4303 0.0 13.2 1.0 S3 A:SF4303 2.3 14.2 1.0 SG A:CYS132 2.3 16.0 1.0 S1 A:SF4303 2.4 12.1 1.0 S2 A:SF4303 2.4 13.6 1.0 FE3 A:SF4303 2.6 13.4 1.0 FE2 A:SF4303 2.7 13.9 1.0 FE1 A:SF4303 2.7 13.2 1.0 CB A:CYS132 3.3 21.6 1.0 S4 A:SF4303 3.9 12.7 1.0 C A:CYS132 4.2 15.7 1.0 N C:ALA98 4.2 15.0 1.0 CA A:CYS132 4.3 15.0 1.0 N A:GLY133 4.4 16.7 1.0 O A:CYS132 4.4 20.7 1.0 CG2 A:VAL130 4.5 14.9 1.0 SG C:CYS97 4.5 13.1 1.0 CA C:CYS97 4.6 19.4 1.0 SG A:CYS97 4.7 13.2 1.0 CB C:ALA98 4.8 12.1 1.0 N A:CYS132 4.8 21.8 1.0 SG C:CYS132 4.8 16.2 1.0 CA A:GLY133 4.9 20.3 1.0 CB A:VAL130 4.9 14.5 1.0 C C:CYS97 5.0 13.9 1.0

Iron binding site 5 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe305 b:13.9 occ:1.00 FE1 B:SF4305 0.0 13.9 1.0 S2 B:SF4305 2.3 12.4 1.0 SG D:CYS132 2.3 10.8 1.0 S4 B:SF4305 2.3 11.5 1.0 S3 B:SF4305 2.4 9.8 1.0 FE3 B:SF4305 2.7 11.4 1.0 FE2 B:SF4305 2.7 12.6 1.0 FE4 B:SF4305 2.7 10.1 1.0 CB D:CYS132 3.4 13.1 1.0 S1 B:SF4305 3.9 11.1 1.0 C D:CYS132 4.0 10.2 1.0 N D:GLY133 4.2 14.0 1.0 N B:ALA98 4.2 8.0 1.0 CA D:CYS132 4.3 11.3 1.0 CG2 D:VAL130 4.3 13.3 1.0 O D:CYS132 4.3 13.2 1.0 SG B:CYS97 4.5 10.1 1.0 CA B:CYS97 4.6 9.2 1.0 CA D:GLY133 4.7 15.5 1.0 SG D:CYS97 4.8 11.7 1.0 CB D:VAL130 4.9 16.3 1.0 N D:CYS132 4.9 11.4 1.0 CB B:ALA98 4.9 11.8 1.0 SG B:CYS132 4.9 13.3 1.0 CB B:CYS97 4.9 11.0 1.0 C B:CYS97 4.9 11.0 1.0

Iron binding site 6 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe305 b:12.6 occ:1.00 FE2 B:SF4305 0.0 12.6 1.0 SG B:CYS97 2.3 10.1 1.0 S1 B:SF4305 2.3 11.1 1.0 S3 B:SF4305 2.3 9.8 1.0 S4 B:SF4305 2.4 11.5 1.0 FE1 B:SF4305 2.7 13.9 1.0 FE3 B:SF4305 2.7 11.4 1.0 FE4 B:SF4305 2.7 10.1 1.0 CB B:CYS97 3.3 11.0 1.0 CA B:CYS97 3.8 9.2 1.0 S2 B:SF4305 3.9 12.4 1.0 CB A:ASP68 4.0 14.2 1.0 N B:ALA98 4.2 8.0 1.0 C B:CYS97 4.3 11.0 1.0 CA A:ASP68 4.4 13.9 1.0 SG D:CYS132 4.5 10.8 1.0 N B:GLY99 4.5 8.0 1.0 O B:HOH606 4.6 21.5 1.0 CA B:GLY133 4.7 15.6 1.0 SG B:CYS132 4.8 13.3 1.0 SG D:CYS97 4.9 11.7 1.0 N A:ASP68 5.0 15.1 1.0

Iron binding site 7 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe305 b:11.4 occ:1.00 FE3 B:SF4305 0.0 11.4 1.0 S4 B:SF4305 2.3 11.5 1.0 S2 B:SF4305 2.3 12.4 1.0 SG D:CYS97 2.4 11.7 1.0 S1 B:SF4305 2.4 11.1 1.0 FE4 B:SF4305 2.7 10.1 1.0 FE1 B:SF4305 2.7 13.9 1.0 FE2 B:SF4305 2.7 12.6 1.0 CB D:CYS97 3.3 11.8 1.0 CA D:CYS97 3.7 12.7 1.0 S3 B:SF4305 3.9 9.8 1.0 N D:ALA98 4.2 10.5 1.0 CB A:ASP68 4.2 14.2 1.0 C D:CYS97 4.3 11.7 1.0 CA D:GLY133 4.4 15.5 1.0 SG B:CYS132 4.5 13.3 1.0 N D:GLY133 4.6 14.0 1.0 N D:GLY99 4.7 11.6 1.0 SG B:CYS97 4.8 10.1 1.0 SG D:CYS132 4.9 10.8 1.0 O D:HOH538 4.9 28.4 1.0

Iron binding site 8 out of 8 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe305 b:10.1 occ:1.00 FE4 B:SF4305 0.0 10.1 1.0 S3 B:SF4305 2.2 9.8 1.0 SG B:CYS132 2.3 13.3 1.0 S1 B:SF4305 2.3 11.1 1.0 S2 B:SF4305 2.4 12.4 1.0 FE3 B:SF4305 2.7 11.4 1.0 FE2 B:SF4305 2.7 12.6 1.0 FE1 B:SF4305 2.7 13.9 1.0 CB B:CYS132 3.5 11.2 1.0 S4 B:SF4305 3.9 11.5 1.0 C B:CYS132 4.2 12.2 1.0 N D:ALA98 4.2 10.5 1.0 O B:CYS132 4.3 13.8 1.0 CG2 B:VAL130 4.3 13.0 1.0 CA B:CYS132 4.4 12.7 1.0 N B:GLY133 4.5 13.1 1.0 SG D:CYS97 4.5 11.7 1.0 CA D:CYS97 4.6 12.7 1.0 SG B:CYS97 4.8 10.1 1.0 SG D:CYS132 4.9 10.8 1.0 CB D:ALA98 4.9 10.7 1.0 CB B:VAL130 4.9 13.2 1.0 C D:CYS97 4.9 11.7 1.0 CB D:CYS97 5.0 11.8 1.0 CA B:GLY133 5.0 15.6 1.0

N.Maslac, C.Cadoux, P.Bolte, F.Murken, W.Gu, R.D.Milton, T.Wagner. Structural Comparison of (Hyper-)Thermophilic Nitrogenase Reductases From Three Marine Methanococcales. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38696373
DOI: 10.1111/FEBS.17148