Iron in PDB 8q5v: Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus, PDB code: 8q5v 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)	39.93 / 2.74
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.478, 87.594, 182.048, 93.98, 98.58, 109.65
R / Rfree (%)	21.7 / 25.4

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

Magnesium	(Mg)	18 atoms
Chlorine	(Cl)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus (pdb code 8q5v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus, PDB code: 8q5v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:44.9 occ:1.00 FE1 B:SF4401 0.0 44.9 1.0 SG B:CYS140 2.2 40.7 1.0 S2 B:SF4401 2.3 34.4 1.0 S3 B:SF4401 2.3 39.9 1.0 S4 B:SF4401 2.3 33.2 1.0 FE3 B:SF4401 2.7 37.8 1.0 FE4 B:SF4401 2.7 35.4 1.0 FE2 B:SF4401 2.7 39.8 1.0 CB B:CYS140 3.5 34.7 1.0 S1 B:SF4401 3.9 33.4 1.0 O B:CYS140 4.0 29.7 1.0 C B:CYS140 4.1 32.5 1.0 N A:ALA106 4.1 27.7 1.0 CA B:CYS140 4.4 34.5 1.0 CG2 B:VAL138 4.5 24.6 1.0 CA A:CYS105 4.6 29.9 1.0 N B:GLY141 4.6 40.4 1.0 SG A:CYS105 4.6 29.5 1.0 SG B:CYS105 4.6 39.6 1.0 CB A:ALA106 4.7 33.0 1.0 SG A:CYS140 4.8 35.8 1.0 C A:CYS105 4.9 32.8 1.0 N B:CYS140 4.9 32.5 1.0 CB B:VAL138 4.9 25.6 1.0 CD2 B:PHE143 5.0 23.5 1.0

Iron binding site 2 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:39.8 occ:1.00 FE2 B:SF4401 0.0 39.8 1.0 SG A:CYS105 2.2 29.5 1.0 S1 B:SF4401 2.3 33.4 1.0 S4 B:SF4401 2.3 33.2 1.0 S3 B:SF4401 2.4 39.9 1.0 FE1 B:SF4401 2.7 44.9 1.0 FE3 B:SF4401 2.7 37.8 1.0 FE4 B:SF4401 2.7 35.4 1.0 CB A:CYS105 3.2 30.4 1.0 CA A:CYS105 3.5 29.9 1.0 S2 B:SF4401 3.9 34.4 1.0 N A:ALA106 4.0 27.7 1.0 C A:CYS105 4.1 32.8 1.0 SG B:CYS140 4.3 40.7 1.0 N A:GLY107 4.5 31.6 1.0 SG A:CYS140 4.8 35.8 1.0 SG B:CYS105 4.8 39.6 1.0 CA A:GLY141 4.9 37.1 1.0 N A:CYS105 4.9 29.7 1.0

Iron binding site 3 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:37.8 occ:1.00 FE3 B:SF4401 0.0 37.8 1.0 SG B:CYS105 2.3 39.6 1.0 S4 B:SF4401 2.3 33.2 1.0 S2 B:SF4401 2.3 34.4 1.0 S1 B:SF4401 2.3 33.4 1.0 FE1 B:SF4401 2.7 44.9 1.0 FE4 B:SF4401 2.7 35.4 1.0 FE2 B:SF4401 2.7 39.8 1.0 CB B:CYS105 3.2 30.5 1.0 CA B:CYS105 3.6 40.0 1.0 S3 B:SF4401 3.9 39.9 1.0 N B:ALA106 4.0 28.1 1.0 C B:CYS105 4.1 37.2 1.0 SG A:CYS140 4.4 35.8 1.0 N B:GLY107 4.5 36.9 1.0 SG B:CYS140 4.7 40.7 1.0 CA B:GLY141 4.8 41.2 1.0 SG A:CYS105 4.8 29.5 1.0 N B:CYS105 4.9 44.9 1.0

Iron binding site 4 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:35.4 occ:1.00 FE4 B:SF4401 0.0 35.4 1.0 SG A:CYS140 2.2 35.8 1.0 S1 B:SF4401 2.3 33.4 1.0 S2 B:SF4401 2.3 34.4 1.0 S3 B:SF4401 2.3 39.9 1.0 FE1 B:SF4401 2.7 44.9 1.0 FE3 B:SF4401 2.7 37.8 1.0 FE2 B:SF4401 2.7 39.8 1.0 CB A:CYS140 3.5 34.6 1.0 S4 B:SF4401 3.9 33.2 1.0 O A:CYS140 4.1 37.0 1.0 C A:CYS140 4.1 38.7 1.0 N B:ALA106 4.2 28.1 1.0 CA A:CYS140 4.4 35.8 1.0 CG2 A:VAL138 4.5 33.2 1.0 CA B:CYS105 4.5 40.0 1.0 SG B:CYS105 4.6 39.6 1.0 N A:GLY141 4.6 43.0 1.0 SG A:CYS105 4.6 29.5 1.0 CB B:ALA106 4.7 26.2 1.0 SG B:CYS140 4.7 40.7 1.0 C B:CYS105 4.9 37.2 1.0 N A:CYS140 4.9 35.6 1.0 CB A:VAL138 4.9 31.2 1.0

Iron binding site 5 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe303 b:39.4 occ:1.00 FE1 C:SF4303 0.0 39.4 1.0 S2 C:SF4303 2.3 38.4 1.0 S3 C:SF4303 2.3 53.6 1.0 S4 C:SF4303 2.3 43.5 1.0 SG D:CYS140 2.5 52.6 1.0 FE2 C:SF4303 2.7 47.2 1.0 FE4 C:SF4303 2.7 41.1 1.0 FE3 C:SF4303 2.7 50.1 1.0 CB D:CYS140 3.7 58.7 1.0 S1 C:SF4303 3.9 36.2 1.0 O D:CYS140 4.1 48.0 1.0 N C:ALA106 4.2 55.6 1.0 C D:CYS140 4.2 48.1 1.0 CA D:CYS140 4.5 49.0 1.0 CA C:CYS105 4.6 54.3 1.0 SG C:CYS105 4.6 42.1 1.0 CG2 D:VAL138 4.6 47.1 1.0 SG D:CYS105 4.6 56.1 1.0 N D:GLY141 4.6 48.3 1.0 CB C:ALA106 4.7 50.0 1.0 SG C:CYS140 4.7 52.1 1.0 CD2 D:PHE143 4.9 48.6 1.0 C C:CYS105 4.9 55.3 1.0 CE2 D:PHE143 5.0 51.4 1.0

Iron binding site 6 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe303 b:47.2 occ:1.00 FE2 C:SF4303 0.0 47.2 1.0 SG C:CYS105 2.2 42.1 1.0 S1 C:SF4303 2.3 36.2 1.0 S3 C:SF4303 2.3 53.6 1.0 S4 C:SF4303 2.3 43.5 1.0 FE1 C:SF4303 2.7 39.4 1.0 FE3 C:SF4303 2.7 50.1 1.0 FE4 C:SF4303 2.7 41.1 1.0 CB C:CYS105 3.1 53.9 1.0 CA C:CYS105 3.5 54.3 1.0 S2 C:SF4303 3.9 38.4 1.0 N C:ALA106 3.9 55.6 1.0 C C:CYS105 4.1 55.3 1.0 SG D:CYS140 4.4 52.6 1.0 N C:GLY107 4.4 56.4 1.0 SG C:CYS140 4.7 52.1 1.0 SG D:CYS105 4.8 56.1 1.0 N C:CYS105 4.8 54.4 1.0 CA C:GLY141 4.9 37.5 1.0

Iron binding site 7 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe303 b:50.1 occ:1.00 FE3 C:SF4303 0.0 50.1 1.0 S4 C:SF4303 2.3 43.5 1.0 S1 C:SF4303 2.3 36.2 1.0 SG D:CYS105 2.3 56.1 1.0 S2 C:SF4303 2.3 38.4 1.0 FE4 C:SF4303 2.7 41.1 1.0 FE2 C:SF4303 2.7 47.2 1.0 FE1 C:SF4303 2.7 39.4 1.0 CB D:CYS105 3.4 46.9 1.0 CA D:CYS105 3.5 46.5 1.0 N D:ALA106 3.9 47.0 1.0 S3 C:SF4303 3.9 53.6 1.0 C D:CYS105 4.1 53.3 1.0 SG C:CYS140 4.2 52.1 1.0 N D:GLY107 4.3 78.4 1.0 SG C:CYS105 4.7 42.1 1.0 N D:CYS105 4.9 46.8 1.0 SG D:CYS140 5.0 52.6 1.0 CA D:ALA106 5.0 48.0 1.0 CA D:GLY141 5.0 48.5 1.0

Iron binding site 8 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


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 Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe303 b:41.1 occ:1.00 FE4 C:SF4303 0.0 41.1 1.0 SG C:CYS140 2.2 52.1 1.0 S2 C:SF4303 2.3 38.4 1.0 S1 C:SF4303 2.3 36.2 1.0 S3 C:SF4303 2.3 53.6 1.0 FE1 C:SF4303 2.7 39.4 1.0 FE3 C:SF4303 2.7 50.1 1.0 FE2 C:SF4303 2.7 47.2 1.0 CB C:CYS140 3.5 40.4 1.0 S4 C:SF4303 3.9 43.5 1.0 O C:CYS140 4.0 48.1 1.0 C C:CYS140 4.1 43.1 1.0 N D:ALA106 4.2 47.0 1.0 CA C:CYS140 4.4 39.7 1.0 CG2 C:VAL138 4.5 65.7 1.0 N C:GLY141 4.6 38.2 1.0 SG C:CYS105 4.6 42.1 1.0 CB D:ALA106 4.7 48.6 1.0 SG D:CYS105 4.8 56.1 1.0 CA D:CYS105 4.8 46.5 1.0 N C:CYS140 4.9 40.5 1.0 SG D:CYS140 4.9 52.6 1.0 CB C:VAL138 4.9 59.9 1.0

Iron binding site 9 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe303 b:48.7 occ:1.00 FE1 E:SF4303 0.0 48.7 1.0 S3 E:SF4303 2.3 43.9 1.0 SG F:CYS140 2.3 32.7 1.0 S2 E:SF4303 2.3 42.9 1.0 S4 E:SF4303 2.3 49.2 1.0 FE4 E:SF4303 2.6 76.4 1.0 FE2 E:SF4303 2.6 44.4 1.0 FE3 E:SF4303 2.7 42.7 1.0 CB F:CYS140 3.4 32.7 1.0 S1 E:SF4303 3.9 26.1 1.0 O F:CYS140 4.1 39.9 1.0 C F:CYS140 4.1 35.3 1.0 N E:ALA106 4.1 23.0 1.0 CA F:CYS140 4.3 28.5 1.0 SG E:CYS105 4.4 47.7 1.0 CA E:CYS105 4.5 36.6 1.0 CG2 F:VAL138 4.5 24.1 1.0 N F:GLY141 4.6 27.2 1.0 CB E:ALA106 4.7 26.9 1.0 SG E:CYS140 4.7 42.0 1.0 SG F:CYS105 4.8 44.4 1.0 CB E:CYS105 4.9 29.9 1.0 CB F:VAL138 4.9 23.7 1.0 C E:CYS105 4.9 28.3 1.0 N F:CYS140 4.9 32.4 1.0

Iron binding site 10 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe303 b:44.4 occ:1.00 FE2 E:SF4303 0.0 44.4 1.0 SG E:CYS105 2.2 47.7 1.0 S4 E:SF4303 2.3 49.2 1.0 S3 E:SF4303 2.3 43.9 1.0 S1 E:SF4303 2.3 26.1 1.0 FE1 E:SF4303 2.6 48.7 1.0 FE4 E:SF4303 2.6 76.4 1.0 FE3 E:SF4303 2.7 42.7 1.0 CB E:CYS105 3.0 29.9 1.0 CA E:CYS105 3.6 36.6 1.0 S2 E:SF4303 3.9 42.9 1.0 N E:ALA106 4.0 23.0 1.0 C E:CYS105 4.2 28.3 1.0 C1 F:GOL301 4.2 45.3 1.0 C3 F:GOL301 4.3 57.8 1.0 SG F:CYS140 4.4 32.7 1.0 N E:GLY107 4.5 28.8 1.0 C2 F:GOL301 4.7 51.8 1.0 SG E:CYS140 4.8 42.0 1.0 CA E:GLY141 4.8 23.2 1.0 N E:CYS105 4.8 40.9 1.0 SG F:CYS105 5.0 44.4 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