Chlorine 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
Iron	(Fe)	24 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus, PDB code: 8q5v:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 C:Cl304 b:105.5 occ:1.00 O C:LEU58 2.4 107.5 1.0 NZ C:LYS61 2.8 112.6 1.0 C C:LEU58 3.4 101.4 1.0 ND1 C:HIS59 3.6 87.3 1.0 CB C:HIS59 3.7 87.9 1.0 CE C:LYS61 3.8 118.2 1.0 CG C:HIS59 4.1 92.0 1.0 N C:HIS59 4.2 101.4 1.0 CB C:LYS61 4.3 112.6 1.0 CD C:LYS61 4.3 128.6 1.0 CA C:LEU58 4.3 92.7 1.0 CA C:HIS59 4.4 96.9 1.0 O C:HIS59 4.4 99.1 1.0 CB C:LEU58 4.7 87.7 1.0 C C:HIS59 4.7 97.4 1.0 CE1 C:HIS59 4.8 90.6 1.0 CG C:LYS61 4.9 117.1 1.0

Chlorine binding site 2 out of 4 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 E:Cl308 b:52.3 occ:1.00 NE E:ARG84 3.1 26.9 1.0 NH2 E:ARG84 3.2 23.6 1.0 O E:ARG84 3.5 33.6 1.0 CZ E:ARG84 3.6 25.3 1.0 CA E:GLU81 4.2 43.0 1.0 CB E:ARG84 4.3 33.2 1.0 CD E:ARG84 4.3 24.1 1.0 O E:LEU80 4.4 44.4 1.0 CG E:ARG84 4.4 21.5 1.0 CG E:GLU81 4.4 71.0 1.0 C E:ARG84 4.4 31.0 1.0 N E:GLU81 4.6 39.2 1.0 C E:LEU80 4.7 37.1 1.0 CB E:GLU81 4.8 55.4 1.0 CG E:LEU80 4.8 40.3 1.0 CD2 E:LEU92 4.8 24.2 1.0 CD2 E:LEU80 4.9 41.8 1.0 NH1 E:ARG84 4.9 21.8 1.0 CA E:ARG84 5.0 39.0 1.0

Chlorine binding site 3 out of 4 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 F:Cl304 b:65.8 occ:1.00 NE F:ARG108 3.2 46.3 1.0 CE F:MET67 3.4 43.9 1.0 CD F:ARG108 3.5 50.1 1.0 OG1 F:THR112 3.7 37.7 1.0 CG F:ARG108 3.7 49.2 1.0 CZ F:ARG108 4.4 50.3 1.0 CB F:THR112 4.7 41.8 1.0 NH2 F:ARG108 4.7 60.5 1.0 SD F:MET67 4.7 56.8 1.0 CG2 F:THR112 4.8 49.9 1.0 CB F:ARG108 4.9 33.8 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 M:Cl406 b:66.7 occ:1.00 O M:GLY20 3.5 36.4 1.0 O M:GLY19 3.6 41.6 1.0 NZ L:LYS18 3.7 53.3 1.0 C M:GLY20 3.9 40.1 1.0 CG L:MET164 4.0 39.4 1.0 OE1 L:GLU162 4.1 52.3 1.0 CA M:GLY20 4.1 33.4 1.0 CB L:MET164 4.1 37.4 1.0 CD L:GLU162 4.2 58.2 1.0 OE2 L:GLU162 4.5 68.9 1.0 CG L:GLU162 4.6 42.4 1.0 C M:GLY19 4.6 37.4 1.0 NZ M:LYS18 4.7 74.2 1.0 N M:ILE21 4.8 41.2 1.0 N M:GLY20 4.8 31.6 1.0 CE M:LYS18 4.9 62.9 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