Iron in PDB 8q5t: Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution

The structure of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution, PDB code: 8q5t 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)	48.47 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.821, 83.984, 116.598, 90, 91.14, 90
R / Rfree (%)	19.4 / 23.5

The binding sites of Iron atom in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution (pdb code 8q5t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution, PDB code: 8q5t:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.1 occ:1.00 FE1 B:SF4301 0.0 26.1 1.0 S2 B:SF4301 2.3 18.2 1.0 S4 B:SF4301 2.3 24.6 1.0 S3 B:SF4301 2.3 22.3 1.0 SG A:CYS105 2.3 26.1 1.0 FE4 B:SF4301 2.7 35.3 1.0 FE3 B:SF4301 2.7 27.5 1.0 FE2 B:SF4301 2.7 37.1 1.0 CB A:CYS105 3.3 27.0 1.0 CA A:CYS105 3.7 25.2 1.0 S1 B:SF4301 3.9 22.8 1.0 CA A:GLY142 4.1 30.8 1.0 N A:ALA106 4.1 28.4 1.0 C A:CYS105 4.2 26.0 1.0 NH1 A:ARG108 4.5 37.6 1.0 N A:GLY142 4.5 33.0 1.0 N A:GLY107 4.6 25.0 1.0 SG A:CYS140 4.6 30.8 1.0 SG B:CYS140 4.9 25.3 1.0 SG B:CYS105 5.0 28.3 1.0 CB B:CYS140 5.0 25.4 1.0

Iron binding site 2 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:37.1 occ:1.00 FE2 B:SF4301 0.0 37.1 1.0 S4 B:SF4301 2.3 24.6 1.0 S3 B:SF4301 2.3 22.3 1.0 S1 B:SF4301 2.3 22.8 1.0 SG A:CYS140 2.4 30.8 1.0 FE4 B:SF4301 2.6 35.3 1.0 FE3 B:SF4301 2.7 27.5 1.0 FE1 B:SF4301 2.7 26.1 1.0 CB A:CYS140 3.2 32.4 1.0 S2 B:SF4301 3.9 18.2 1.0 N A:GLY142 4.1 33.0 1.0 CA A:GLY142 4.3 30.8 1.0 CA A:CYS140 4.6 37.1 1.0 CA B:CYS105 4.7 32.4 1.0 SG A:CYS105 4.7 26.1 1.0 N B:ALA106 4.8 34.9 1.0 C A:CYS140 4.8 36.3 1.0 SG B:CYS105 4.8 28.3 1.0 SG B:CYS140 4.9 25.3 1.0 CB B:CYS105 4.9 25.5 1.0 CD2 A:PHE143 5.0 33.3 1.0 N A:GLY141 5.0 34.4 1.0 N A:PHE143 5.0 33.5 1.0

Iron binding site 3 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.5 occ:1.00 FE3 B:SF4301 0.0 27.5 1.0 S4 B:SF4301 2.3 24.6 1.0 S2 B:SF4301 2.3 18.2 1.0 S1 B:SF4301 2.3 22.8 1.0 SG B:CYS105 2.5 28.3 1.0 FE4 B:SF4301 2.6 35.3 1.0 FE2 B:SF4301 2.7 37.1 1.0 FE1 B:SF4301 2.7 26.1 1.0 CB B:CYS105 3.0 25.5 1.0 CA B:CYS105 3.5 32.4 1.0 S3 B:SF4301 3.9 22.3 1.0 N B:ALA106 4.0 34.9 1.0 CA B:GLY142 4.0 26.7 1.0 N B:GLY142 4.1 25.6 1.0 C B:CYS105 4.2 34.7 1.0 SG B:CYS140 4.6 25.3 1.0 N B:CYS105 4.8 37.8 1.0 SG A:CYS140 4.9 30.8 1.0 SG A:CYS105 4.9 26.1 1.0 N B:GLY107 4.9 29.6 1.0

Iron binding site 4 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:35.3 occ:1.00 FE4 B:SF4301 0.0 35.3 1.0 S3 B:SF4301 2.3 22.3 1.0 S2 B:SF4301 2.3 18.2 1.0 S1 B:SF4301 2.3 22.8 1.0 SG B:CYS140 2.4 25.3 1.0 FE3 B:SF4301 2.6 27.5 1.0 FE2 B:SF4301 2.6 37.1 1.0 FE1 B:SF4301 2.7 26.1 1.0 CB B:CYS140 3.3 25.4 1.0 S4 B:SF4301 3.9 24.6 1.0 N B:GLY142 4.0 25.6 1.0 CA B:GLY142 4.3 26.7 1.0 N A:ALA106 4.6 28.4 1.0 CA B:CYS140 4.6 24.7 1.0 SG B:CYS105 4.7 28.3 1.0 N B:GLY141 4.7 24.3 1.0 CD2 B:PHE143 4.7 27.9 1.0 SG A:CYS105 4.7 26.1 1.0 C B:CYS140 4.8 24.4 1.0 SG A:CYS140 4.8 30.8 1.0 CA A:CYS105 4.8 25.2 1.0 N B:PHE143 4.8 28.3 1.0

Iron binding site 5 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:39.3 occ:1.00 FE1 D:SF4301 0.0 39.3 1.0 S2 D:SF4301 2.3 31.0 1.0 S3 D:SF4301 2.3 26.9 1.0 S4 D:SF4301 2.3 26.0 1.0 SG D:CYS140 2.5 34.1 1.0 FE4 D:SF4301 2.6 37.9 1.0 FE3 D:SF4301 2.6 31.8 1.0 FE2 D:SF4301 2.7 31.3 1.0 CB D:CYS140 3.1 36.3 1.0 S1 D:SF4301 3.9 28.7 1.0 N D:GLY142 4.2 44.0 1.0 CA D:GLY142 4.4 43.4 1.0 N C:ALA106 4.5 28.3 1.0 CA D:CYS140 4.5 39.7 1.0 CD2 D:PHE143 4.7 43.7 1.0 SG D:CYS105 4.7 35.0 1.0 SG C:CYS105 4.7 27.9 1.0 CA C:CYS105 4.8 32.1 1.0 SG C:CYS140 4.8 27.6 1.0 C D:CYS140 4.9 37.4 1.0 CE2 D:PHE143 4.9 46.5 1.0 N D:PHE143 5.0 33.9 1.0 N D:GLY141 5.0 40.8 1.0

Iron binding site 6 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:31.3 occ:1.00 FE2 D:SF4301 0.0 31.3 1.0 S3 D:SF4301 2.3 26.9 1.0 SG C:CYS105 2.3 27.9 1.0 S1 D:SF4301 2.3 28.7 1.0 S4 D:SF4301 2.3 26.0 1.0 FE4 D:SF4301 2.6 37.9 1.0 FE1 D:SF4301 2.7 39.3 1.0 FE3 D:SF4301 2.7 31.8 1.0 CB C:CYS105 3.2 32.7 1.0 CA C:CYS105 3.7 32.1 1.0 S2 D:SF4301 3.9 31.0 1.0 N C:ALA106 4.0 28.3 1.0 CA C:GLY142 4.1 35.1 1.0 C C:CYS105 4.2 27.6 1.0 N C:GLY107 4.4 28.8 1.0 N C:GLY142 4.5 34.2 1.0 SG C:CYS140 4.7 27.6 1.0 CB D:CYS140 4.9 36.3 1.0 SG D:CYS105 4.9 35.0 1.0 SG D:CYS140 4.9 34.1 1.0

Iron binding site 7 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:31.8 occ:1.00 FE3 D:SF4301 0.0 31.8 1.0 SG D:CYS105 2.3 35.0 1.0 S4 D:SF4301 2.3 26.0 1.0 S1 D:SF4301 2.3 28.7 1.0 S2 D:SF4301 2.3 31.0 1.0 FE1 D:SF4301 2.6 39.3 1.0 FE4 D:SF4301 2.7 37.9 1.0 FE2 D:SF4301 2.7 31.3 1.0 CB D:CYS105 3.3 39.8 1.0 CA D:CYS105 3.7 40.7 1.0 S3 D:SF4301 3.9 26.9 1.0 NH1 D:ARG108 3.9 47.3 1.0 N D:ALA106 4.1 36.7 1.0 CA D:GLY142 4.1 43.4 1.0 C D:CYS105 4.3 38.9 1.0 N D:GLY142 4.4 44.0 1.0 SG D:CYS140 4.6 34.1 1.0 N D:GLY107 4.7 35.9 1.0 SG C:CYS105 4.9 27.9 1.0 SG C:CYS140 4.9 27.6 1.0

Iron binding site 8 out of 8 in the Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Nitrogenase Fe Protein From Methanothermococcus Thermolithotrophicus, Monoclinic Crystalline Form at 2.31-A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:37.9 occ:1.00 FE4 D:SF4301 0.0 37.9 1.0 S1 D:SF4301 2.3 28.7 1.0 S2 D:SF4301 2.3 31.0 1.0 S3 D:SF4301 2.3 26.9 1.0 SG C:CYS140 2.4 27.6 1.0 FE1 D:SF4301 2.6 39.3 1.0 FE2 D:SF4301 2.6 31.3 1.0 FE3 D:SF4301 2.7 31.8 1.0 CB C:CYS140 3.2 32.0 1.0 S4 D:SF4301 3.9 26.0 1.0 N C:GLY142 4.1 34.2 1.0 CA C:GLY142 4.2 35.1 1.0 N D:ALA106 4.5 36.7 1.0 CA C:CYS140 4.6 34.0 1.0 SG C:CYS105 4.7 27.9 1.0 SG D:CYS105 4.7 35.0 1.0 CA D:CYS105 4.7 40.7 1.0 CD2 C:PHE143 4.9 32.5 1.0 C C:CYS140 4.9 35.5 1.0 SG D:CYS140 5.0 34.1 1.0 N C:GLY141 5.0 34.2 1.0 N C:PHE143 5.0 34.9 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