Magnesium 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:

Chlorine	(Cl)	4 atoms
Iron	(Fe)	24 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus, PDB code: 8q5v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg302 b:34.4 occ:1.00 OG A:SER24 2.0 61.4 1.0 O3B A:ADP301 2.5 64.8 1.0 OD1 A:ASP52 3.0 62.0 1.0 CB A:SER24 3.1 66.8 1.0 O1B A:ADP301 3.5 54.5 1.0 PB A:ADP301 3.6 55.0 1.0 OD2 A:ASP48 3.7 61.3 1.0 O1A A:ADP301 3.8 47.9 1.0 CG A:ASP52 4.0 57.2 1.0 OG A:SER53 4.2 58.0 1.0 OD2 A:ASP133 4.2 57.8 1.0 CA A:SER24 4.2 58.7 1.0 N A:SER24 4.3 62.5 1.0 OD2 A:ASP52 4.3 53.1 1.0 CG A:ASP48 4.4 62.7 1.0 CD A:LYS50 4.4 47.7 1.0 O3A A:ADP301 4.6 42.5 1.0 N A:SER53 4.6 49.2 1.0 PA A:ADP301 4.7 45.5 1.0 CB A:LYS50 4.7 45.1 1.0 CA A:SER53 4.7 51.9 1.0 O2B A:ADP301 4.7 45.8 1.0 C A:ASP52 4.7 47.7 1.0 O A:ASP52 4.8 48.6 1.0 CB A:ASP48 4.8 60.2 1.0 CB A:SER53 4.9 57.6 1.0 O2A A:ADP301 4.9 57.7 1.0 CG A:ASP133 5.0 50.2 1.0

Magnesium binding site 2 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg403 b:25.7 occ:1.00 OG B:SER24 2.1 32.5 1.0 O B:HOH501 2.2 32.2 1.0 O1B B:ADP402 2.4 19.6 1.0 OD2 B:ASP48 2.8 39.4 1.0 OD2 B:ASP133 3.2 26.1 1.0 CB B:SER24 3.4 25.3 1.0 OD1 B:ASP133 3.5 35.7 1.0 PB B:ADP402 3.5 34.6 1.0 CG B:ASP133 3.7 30.9 1.0 CG B:ASP48 3.7 38.0 1.0 O3B B:ADP402 3.7 32.3 1.0 N B:SER24 3.8 22.9 1.0 OG B:SER53 3.8 30.9 1.0 CB B:ASP48 4.0 34.5 1.0 CA B:SER24 4.1 21.5 1.0 CE B:LYS23 4.1 23.8 1.0 O2B B:ADP402 4.1 30.5 1.0 OD1 B:ASP52 4.4 41.2 1.0 CB B:LYS23 4.5 19.6 1.0 NZ B:LYS23 4.7 21.7 1.0 CB B:SER53 4.7 35.3 1.0 C B:LYS23 4.7 24.0 1.0 OD1 B:ASP48 4.8 29.7 1.0 O2A B:ADP402 4.8 22.6 1.0 O3A B:ADP402 4.9 31.0 1.0 CA B:SER53 5.0 30.8 1.0

Magnesium binding site 3 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 C:Mg302 b:39.3 occ:1.00 OG C:SER24 2.6 65.0 1.0 O1B C:ADP301 3.0 71.5 1.0 OD1 C:ASP52 3.1 86.5 1.0 OD2 C:ASP48 3.1 59.2 1.0 O3B C:ADP301 3.2 67.6 1.0 PB C:ADP301 3.7 79.4 1.0 CB C:SER24 3.8 70.6 1.0 CG C:ASP48 3.8 58.6 1.0 CD C:LYS50 4.1 77.0 1.0 CG C:ASP52 4.1 82.6 1.0 CB C:LYS50 4.1 64.3 1.0 O2A C:ADP301 4.2 63.9 1.0 OG C:SER53 4.2 87.1 1.0 CB C:ASP48 4.3 52.2 1.0 OD2 C:ASP133 4.5 69.8 1.0 OD2 C:ASP52 4.5 86.4 1.0 OD1 C:ASP48 4.5 57.0 1.0 CG C:LYS50 4.6 67.8 1.0 O2B C:ADP301 4.7 58.3 1.0 N C:SER24 4.8 65.5 1.0 O3A C:ADP301 4.8 68.0 1.0 CA C:SER24 4.9 67.8 1.0 N C:SER53 4.9 88.4 1.0 PA C:ADP301 5.0 57.2 1.0 CE D:MET164 5.0 72.3 1.0

Magnesium binding site 4 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 D:Mg302 b:51.2 occ:1.00 OG D:SER24 2.2 65.6 1.0 O3B D:ADP301 2.4 69.6 1.0 OD1 D:ASP52 3.2 69.8 1.0 OD2 D:ASP48 3.3 81.1 1.0 CB D:SER24 3.4 66.5 1.0 O1B D:ADP301 3.4 76.8 1.0 PB D:ADP301 3.5 76.4 1.0 OD2 D:ASP133 3.9 74.8 1.0 O1A D:ADP301 4.1 55.8 1.0 CG D:ASP48 4.1 69.8 1.0 OG D:SER53 4.1 88.7 1.0 CG D:ASP52 4.3 66.9 1.0 CA D:SER24 4.4 67.0 1.0 O2B D:ADP301 4.5 60.6 1.0 N D:SER24 4.5 65.9 1.0 CB D:ASP48 4.6 68.5 1.0 O3A D:ADP301 4.6 77.8 1.0 CB D:LYS50 4.6 72.4 1.0 OD2 D:ASP52 4.6 72.7 1.0 CD D:LYS50 4.7 69.8 1.0 CG D:ASP133 4.8 73.9 1.0 PA D:ADP301 4.8 71.1 1.0 N D:SER53 4.9 66.8 1.0 CG D:LYS50 4.9 67.3 1.0 OD1 D:ASP48 4.9 66.0 1.0 CA D:SER53 4.9 70.6 1.0 OD1 D:ASP133 4.9 76.8 1.0

Magnesium binding site 5 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 E:Mg302 b:19.1 occ:1.00 O E:HOH401 2.1 23.5 1.0 OG E:SER24 2.4 18.2 1.0 OD2 E:ASP48 2.5 32.5 1.0 O3B E:ADP301 2.6 16.1 1.0 CG E:ASP48 3.4 26.4 1.0 OD2 E:ASP133 3.5 20.2 1.0 PB E:ADP301 3.6 22.5 1.0 O1B E:ADP301 3.6 31.2 1.0 OD1 E:ASP133 3.7 31.1 1.0 CB E:ASP48 3.7 27.9 1.0 CB E:SER24 3.7 19.8 1.0 OG E:SER53 3.9 22.4 1.0 CG E:ASP133 3.9 27.0 1.0 N E:SER24 4.2 17.4 1.0 O2B E:ADP301 4.2 29.1 1.0 CE E:LYS23 4.2 19.1 1.0 OD1 E:ASP52 4.3 42.0 1.0 NZ E:LYS23 4.4 21.4 1.0 OD1 E:ASP48 4.4 16.5 1.0 CA E:SER24 4.4 15.7 1.0 CB E:LYS23 4.8 17.7 1.0 CB E:SER53 4.8 25.9 1.0 O1A E:ADP301 4.9 26.3 1.0 O3A E:ADP301 5.0 23.3 1.0

Magnesium binding site 6 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 F:Mg303 b:35.1 occ:1.00 O3B F:ADP302 2.3 52.6 1.0 OG F:SER24 2.4 55.5 1.0 O2B F:ADP302 3.1 39.1 1.0 OD2 F:ASP48 3.1 55.4 1.0 PB F:ADP302 3.3 40.1 1.0 OD1 F:ASP52 3.5 57.9 1.0 CB F:SER24 3.6 52.8 1.0 CG F:ASP48 3.9 59.5 1.0 O2A F:ADP302 4.1 48.0 1.0 OD2 F:ASP133 4.2 66.0 1.0 O1B F:ADP302 4.2 37.7 1.0 OG F:SER53 4.4 59.0 1.0 N F:SER24 4.4 56.9 1.0 CD F:LYS50 4.4 41.0 1.0 O3A F:ADP302 4.4 38.5 1.0 CB F:ASP48 4.5 48.7 1.0 CG F:ASP52 4.5 47.9 1.0 CA F:SER24 4.6 49.6 1.0 CB F:LYS50 4.6 42.4 1.0 OD1 F:ASP48 4.7 41.6 1.0 PA F:ADP302 4.8 39.1 1.0 OD1 F:ASP133 4.8 74.3 1.0 OD2 F:ASP52 4.9 52.1 1.0 CG F:ASP133 4.9 67.1 1.0 CE F:LYS23 5.0 37.1 1.0

Magnesium binding site 7 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 G:Mg302 b:23.8 occ:1.00 OG G:SER24 2.2 36.3 1.0 O3B G:ADP301 2.4 48.1 1.0 OD2 G:ASP48 3.2 46.7 1.0 CB G:SER24 3.3 51.6 1.0 OD1 G:ASP52 3.4 48.5 1.0 O1B G:ADP301 3.4 52.3 1.0 PB G:ADP301 3.5 42.7 1.0 CG G:ASP48 4.0 46.7 1.0 OD2 G:ASP133 4.1 48.3 1.0 O1A G:ADP301 4.1 39.4 1.0 OG G:SER53 4.1 50.9 1.0 N G:SER24 4.3 31.9 1.0 CA G:SER24 4.4 39.2 1.0 CG G:ASP52 4.4 43.1 1.0 O2B G:ADP301 4.4 43.2 1.0 CB G:ASP48 4.5 42.1 1.0 CD G:LYS50 4.6 38.4 1.0 O3A G:ADP301 4.6 42.2 1.0 CB G:LYS50 4.6 36.1 1.0 OD1 G:ASP133 4.7 53.0 1.0 CG G:ASP133 4.7 38.4 1.0 OD2 G:ASP52 4.8 52.8 1.0 PA G:ADP301 4.8 45.9 1.0 OD1 G:ASP48 4.8 36.5 1.0 CA G:SER53 4.9 46.1 1.0 N G:SER53 4.9 37.3 1.0 CB G:SER53 5.0 50.5 1.0 NZ G:LYS23 5.0 42.4 1.0

Magnesium binding site 8 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 G:Mg304 b:37.7 occ:1.00 CA G:PRO124 3.4 37.5 1.0 N G:ASP125 3.4 54.9 1.0 C G:PRO124 3.9 42.1 1.0 OD1 G:ASP125 4.0 82.0 1.0 CG G:ASP125 4.0 73.8 1.0 O G:TYR123 4.0 43.4 1.0 OD2 G:ASP125 4.2 83.5 1.0 CB G:PRO124 4.2 35.8 1.0 N G:PRO124 4.3 37.7 1.0 CB G:ASP125 4.5 58.1 1.0 C G:TYR123 4.5 35.1 1.0 CA G:ASP125 4.6 56.1 1.0 O G:GLU121 4.6 41.7 1.0

Magnesium binding site 9 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 H:Mg302 b:30.0 occ:1.00 OG H:SER24 2.1 56.8 1.0 O1B H:ADP301 2.6 48.6 1.0 OD2 H:ASP48 3.0 59.8 1.0 CB H:SER24 3.4 49.4 1.0 OD1 H:ASP52 3.5 55.8 1.0 OD2 H:ASP133 3.7 52.5 1.0 OG H:SER53 3.7 62.0 1.0 O3B H:ADP301 3.7 60.1 1.0 CG H:ASP48 3.8 52.6 1.0 PB H:ADP301 3.8 47.4 1.0 CB H:ASP48 4.1 45.9 1.0 N H:SER24 4.3 48.7 1.0 CA H:SER24 4.3 49.7 1.0 OD1 H:ASP133 4.3 63.2 1.0 CG H:ASP133 4.3 50.0 1.0 O2A H:ADP301 4.5 55.4 1.0 CG H:ASP52 4.6 60.7 1.0 CB H:SER53 4.6 52.5 1.0 O2B H:ADP301 4.7 39.4 1.0 CA H:SER53 4.7 55.8 1.0 OD1 H:ASP48 4.7 44.5 1.0 N H:SER53 4.7 54.0 1.0 CB H:LYS50 4.7 48.9 1.0 CD H:LYS50 4.9 48.6 1.0 O3A H:ADP301 5.0 46.0 1.0 C H:ASP52 5.0 57.0 1.0

Magnesium binding site 10 out of 18 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanothermococcus Thermolithotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 J:Mg302 b:39.9 occ:1.00 OG J:SER24 1.9 28.7 1.0 O1B J:ADP301 2.3 21.4 1.0 CB J:SER24 3.0 28.5 1.0 OD1 J:ASP52 3.3 44.7 1.0 PB J:ADP301 3.4 26.2 1.0 O3B J:ADP301 3.5 27.5 1.0 OD2 J:ASP48 3.5 32.0 1.0 O2A J:ADP301 3.9 30.6 1.0 OD2 J:ASP133 3.9 30.1 1.0 CA J:SER24 4.1 19.9 1.0 N J:SER24 4.1 30.6 1.0 CG J:ASP48 4.3 25.7 1.0 OG J:SER53 4.3 37.8 1.0 CG J:ASP52 4.3 40.2 1.0 O2B J:ADP301 4.5 22.9 1.0 O3A J:ADP301 4.5 22.6 1.0 PA J:ADP301 4.6 84.3 1.0 OD2 J:ASP52 4.7 48.3 1.0 CB J:ASP48 4.7 37.0 1.0 CD J:LYS50 4.7 29.1 1.0 CG J:ASP133 4.7 23.6 1.0 OD1 J:ASP133 4.7 41.6 1.0 CA J:SER53 4.8 28.4 1.0 O1A J:ADP301 4.8 24.4 1.0 N J:SER53 4.8 39.0 1.0 CB J:LYS50 4.9 27.0 1.0 CB J:SER53 4.9 37.4 1.0 C J:ASP52 4.9 35.2 1.0 O J:ASP52 5.0 38.4 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