Magnesium in PDB 8q5w: Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus, PDB code: 8q5w 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)	49.26 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	147.948, 156.729, 206.454, 90, 90, 90
R / Rfree (%)	22.1 / 24.2

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

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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus (pdb code 8q5w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus, PDB code: 8q5w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.4 occ:1.00 O A:HOH602 1.9 50.0 1.0 OG A:SER24 2.3 51.1 1.0 O3B A:ADP501 2.4 53.3 1.0 O2B A:ADP501 3.4 53.5 1.0 PB A:ADP501 3.4 49.7 1.0 OD1 A:ASP52 3.4 58.4 1.0 CB A:SER24 3.5 50.0 1.0 OD2 A:ASP48 3.7 51.3 1.0 OG A:SER53 3.9 52.1 1.0 O2A A:ADP501 4.0 51.3 1.0 CG A:ASP48 4.1 50.4 1.0 OD2 A:ASP133 4.3 55.8 1.0 N A:SER24 4.3 59.4 1.0 O1B A:ADP501 4.4 51.9 1.0 CG A:ASP52 4.4 58.9 1.0 CD A:LYS50 4.4 57.3 1.0 CA A:SER24 4.5 50.5 1.0 OD1 A:ASP133 4.5 54.9 1.0 CB A:ASP48 4.6 54.4 1.0 O3A A:ADP501 4.6 53.5 1.0 OD2 A:ASP52 4.7 68.5 1.0 CB A:LYS50 4.7 54.2 1.0 CG A:ASP133 4.7 50.3 1.0 OD1 A:ASP48 4.7 51.0 1.0 PA A:ADP501 4.8 42.5 1.0 NZ A:LYS23 5.0 51.5 1.0 CB A:SER53 5.0 51.6 1.0

Magnesium binding site 2 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:61.5 occ:1.00 OG B:SER24 2.3 65.6 1.0 O3B B:ADP302 2.8 62.8 1.0 OD1 B:ASP52 3.2 75.0 1.0 O1B B:ADP302 3.4 61.0 1.0 CB B:SER24 3.6 65.0 1.0 OD2 B:ASP48 3.7 57.0 1.0 PB B:ADP302 3.7 61.0 1.0 OG B:SER53 3.7 67.3 1.0 CG B:ASP48 4.0 54.8 1.0 CG B:ASP52 4.2 72.0 1.0 O1A B:ADP302 4.3 59.4 1.0 OD2 B:ASP133 4.3 63.0 1.0 CD B:LYS50 4.4 62.7 1.0 CB B:ASP48 4.4 54.6 1.0 OD1 B:ASP133 4.5 64.4 1.0 N B:SER24 4.5 64.2 1.0 OD2 B:ASP52 4.5 74.1 1.0 CB B:LYS50 4.5 59.6 1.0 CA B:SER24 4.6 62.9 1.0 OD1 B:ASP48 4.6 53.1 1.0 O2B B:ADP302 4.7 61.1 1.0 CG B:ASP133 4.7 61.6 1.0 CB B:SER53 4.8 71.1 1.0 N B:SER53 4.8 68.5 1.0 O3A B:ADP302 4.8 65.9 1.0 CA B:SER53 4.9 73.7 1.0 PA B:ADP302 5.0 60.1 1.0

Magnesium binding site 3 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:63.4 occ:1.00 OG C:SER24 2.3 63.5 1.0 O3B C:ADP302 2.4 68.2 1.0 OD1 C:ASP52 3.4 75.8 1.0 O2B C:ADP302 3.4 70.6 1.0 PB C:ADP302 3.5 70.3 1.0 CB C:SER24 3.5 68.5 1.0 OD2 C:ASP48 3.7 64.0 1.0 OG C:SER53 3.9 60.6 1.0 O2A C:ADP302 4.1 66.0 1.0 CG C:ASP48 4.1 61.5 1.0 OD2 C:ASP133 4.3 65.2 1.0 N C:SER24 4.3 70.8 1.0 CG C:ASP52 4.4 63.5 1.0 CD C:LYS50 4.4 68.0 1.0 O1B C:ADP302 4.4 69.2 1.0 OD1 C:ASP133 4.4 61.6 1.0 CA C:SER24 4.5 65.2 1.0 CB C:ASP48 4.5 64.0 1.0 O3A C:ADP302 4.6 69.7 1.0 OD2 C:ASP52 4.7 64.9 1.0 CB C:LYS50 4.7 62.6 1.0 CG C:ASP133 4.7 59.6 1.0 OD1 C:ASP48 4.7 60.0 1.0 PA C:ADP302 4.8 69.2 1.0 CB C:SER53 4.9 58.4 1.0 NZ C:LYS23 5.0 67.8 1.0 N C:SER53 5.0 58.2 1.0

Magnesium binding site 4 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:105.3 occ:1.00 OG D:SER24 2.3 125.6 1.0 O3B D:ADP401 2.8 112.3 1.0 OD1 D:ASP52 3.2 115.3 1.0 O1B D:ADP401 3.4 101.7 1.0 CB D:SER24 3.5 138.1 1.0 OD2 D:ASP48 3.7 90.2 1.0 PB D:ADP401 3.7 109.4 1.0 CG D:ASP48 4.0 89.6 1.0 OD2 D:ASP133 4.2 115.9 1.0 CG D:ASP52 4.3 115.0 1.0 O1A D:ADP401 4.3 107.5 1.0 CD D:LYS50 4.3 105.4 1.0 CB D:ASP48 4.4 91.4 1.0 OD1 D:ASP133 4.4 105.5 1.0 NZ D:LYS23 4.5 99.8 1.0 N D:SER24 4.5 125.7 1.0 CB D:LYS50 4.5 105.0 1.0 CA D:SER24 4.5 131.7 1.0 OD2 D:ASP52 4.6 112.8 1.0 OD1 D:ASP48 4.6 88.4 1.0 CG D:ASP133 4.6 110.3 1.0 O2B D:ADP401 4.7 106.3 1.0 CB D:SER53 4.8 129.3 1.0 N D:SER53 4.8 123.9 1.0 CA D:SER53 4.8 128.6 1.0 O3A D:ADP401 4.8 110.5 1.0

Magnesium binding site 5 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg304 b:88.2 occ:1.00 OG E:SER24 2.2 94.6 1.0 OD1 E:ASP52 3.0 99.9 1.0 O3B E:ADP303 3.1 88.7 1.0 CB E:SER24 3.5 95.8 1.0 OD2 E:ASP133 3.7 96.6 1.0 OD2 E:ASP48 3.8 85.5 1.0 CG E:ASP48 4.0 78.3 1.0 CG E:ASP52 4.0 98.4 1.0 CB E:ASP48 4.1 78.7 1.0 CB E:SER53 4.2 98.1 1.0 N E:SER53 4.2 99.0 1.0 O1B E:ADP303 4.2 84.7 1.0 PB E:ADP303 4.3 88.0 1.0 CA E:SER53 4.3 98.8 1.0 CA E:SER24 4.5 91.3 1.0 OD2 E:ASP52 4.5 95.1 1.0 CB E:LYS50 4.5 79.3 1.0 N E:SER24 4.6 92.7 1.0 C E:ASP52 4.6 100.4 1.0 OD1 E:ASP48 4.6 77.2 1.0 CD E:LYS50 4.6 80.0 1.0 O1A E:ADP303 4.7 86.8 1.0 NZ E:LYS23 4.8 84.6 1.0 CG E:ASP133 4.8 105.4 1.0 N E:ASP52 4.9 100.8 1.0 O E:ASP52 5.0 101.2 1.0

Magnesium binding site 6 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:58.7 occ:1.00 OG F:SER24 2.4 60.1 1.0 O3B F:ADP401 2.8 59.8 1.0 OD1 F:ASP52 3.2 79.9 1.0 O2B F:ADP401 3.3 60.4 1.0 CB F:SER24 3.6 65.6 1.0 PB F:ADP401 3.7 60.0 1.0 OD2 F:ASP48 3.7 60.1 1.0 OG F:SER53 3.7 58.6 1.0 CG F:ASP48 4.0 56.9 1.0 CG F:ASP52 4.2 64.5 1.0 O2A F:ADP401 4.3 61.8 1.0 CD F:LYS50 4.3 63.2 1.0 OD2 F:ASP133 4.3 57.8 1.0 CB F:ASP48 4.4 56.9 1.0 CB F:LYS50 4.5 61.5 1.0 OD1 F:ASP133 4.5 60.2 1.0 N F:SER24 4.5 60.6 1.0 OD2 F:ASP52 4.5 64.9 1.0 CA F:SER24 4.6 65.1 1.0 OD1 F:ASP48 4.6 57.1 1.0 O1B F:ADP401 4.7 58.4 1.0 CG F:ASP133 4.7 56.6 1.0 N F:SER53 4.8 59.1 1.0 O3A F:ADP401 4.8 70.7 1.0 CB F:SER53 4.8 57.8 1.0 CA F:SER53 4.9 58.2 1.0 PA F:ADP401 5.0 60.1 1.0

Magnesium binding site 7 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg502 b:49.8 occ:1.00 O3B G:ADP501 2.3 51.0 1.0 OG G:SER24 2.3 52.9 1.0 O2B G:ADP501 3.4 51.2 1.0 PB G:ADP501 3.4 48.9 1.0 OD1 G:ASP52 3.4 57.5 1.0 CB G:SER24 3.5 52.0 1.0 OD2 G:ASP48 3.7 52.5 1.0 OG G:SER53 4.0 58.1 1.0 O2A G:ADP501 4.0 50.8 1.0 CG G:ASP48 4.1 56.7 1.0 OD2 G:ASP133 4.3 48.8 1.0 N G:SER24 4.3 51.2 1.0 O1B G:ADP501 4.4 53.7 1.0 CG G:ASP52 4.4 59.0 1.0 CD G:LYS50 4.4 51.6 1.0 CA G:SER24 4.5 48.8 1.0 OD1 G:ASP133 4.5 49.6 1.0 O3A G:ADP501 4.6 52.0 1.0 CB G:ASP48 4.6 67.5 1.0 OD2 G:ASP52 4.6 61.7 1.0 CB G:LYS50 4.7 51.8 1.0 OD1 G:ASP48 4.7 51.4 1.0 PA G:ADP501 4.7 38.4 1.0 CG G:ASP133 4.7 48.3 1.0 NZ G:LYS23 5.0 49.3 1.0 O1A G:ADP501 5.0 51.6 1.0

Magnesium binding site 8 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg303 b:56.1 occ:1.00 OG H:SER24 2.3 57.8 1.0 O3B H:ADP302 2.8 55.7 1.0 OD1 H:ASP52 3.2 63.6 1.0 O1B H:ADP302 3.4 54.9 1.0 CB H:SER24 3.6 58.8 1.0 OD2 H:ASP48 3.6 50.1 1.0 PB H:ADP302 3.7 54.7 1.0 OG H:SER53 3.7 64.3 1.0 CG H:ASP48 4.0 50.2 1.0 CG H:ASP52 4.2 62.8 1.0 O1A H:ADP302 4.3 54.6 1.0 OD2 H:ASP133 4.3 60.4 1.0 CD H:LYS50 4.4 59.0 1.0 CB H:ASP48 4.4 55.9 1.0 OD1 H:ASP133 4.4 56.4 1.0 OD2 H:ASP52 4.5 65.6 1.0 N H:SER24 4.5 54.9 1.0 CB H:LYS50 4.5 54.8 1.0 CA H:SER24 4.6 56.2 1.0 OD1 H:ASP48 4.6 48.9 1.0 O2B H:ADP302 4.7 55.2 1.0 CG H:ASP133 4.7 56.3 1.0 N H:SER53 4.8 61.0 1.0 CB H:SER53 4.8 66.2 1.0 O3A H:ADP302 4.8 56.5 1.0 CA H:SER53 4.9 61.3 1.0 PA H:ADP302 5.0 54.1 1.0

Magnesium binding site 9 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg303 b:50.5 occ:1.00 OG I:SER24 2.3 50.6 1.0 O3B I:ADP302 2.4 50.3 1.0 OD1 I:ASP52 3.4 60.0 1.0 O2B I:ADP302 3.4 50.0 1.0 PB I:ADP302 3.5 43.2 1.0 CB I:SER24 3.5 55.9 1.0 OD2 I:ASP48 3.7 52.3 1.0 OG I:SER53 3.9 51.0 1.0 O2A I:ADP302 4.0 49.9 1.0 CG I:ASP48 4.1 50.8 1.0 OD2 I:ASP133 4.3 57.9 1.0 N I:SER24 4.3 54.3 1.0 CG I:ASP52 4.4 54.7 1.0 CD I:LYS50 4.4 55.0 1.0 O1B I:ADP302 4.4 50.3 1.0 OD1 I:ASP133 4.5 52.6 1.0 CA I:SER24 4.5 47.0 1.0 CB I:ASP48 4.5 56.1 1.0 O I:HOH402 4.6 51.7 1.0 O3A I:ADP302 4.6 50.1 1.0 OD2 I:ASP52 4.6 56.0 1.0 CB I:LYS50 4.7 52.6 1.0 OD1 I:ASP48 4.7 49.7 1.0 CG I:ASP133 4.7 52.5 1.0 PA I:ADP302 4.8 43.4 1.0 CB I:SER53 5.0 50.2 1.0 N I:SER53 5.0 52.0 1.0 NZ I:LYS23 5.0 49.7 1.0

Magnesium binding site 10 out of 12 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


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 Methanocaldococcus Infernus within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg402 b:66.6 occ:1.00 OG J:SER24 2.3 72.1 1.0 O3B J:ADP401 2.8 67.9 1.0 OD1 J:ASP52 3.2 73.2 1.0 O1B J:ADP401 3.4 65.1 1.0 CB J:SER24 3.5 73.7 1.0 OD2 J:ASP48 3.7 62.7 1.0 PB J:ADP401 3.7 65.6 1.0 CG J:ASP48 4.0 62.8 1.0 CG J:ASP52 4.2 72.4 1.0 O1A J:ADP401 4.3 66.2 1.0 OD2 J:ASP133 4.3 71.4 1.0 CD J:LYS50 4.4 62.8 1.0 CB J:ASP48 4.4 65.5 1.0 OD1 J:ASP133 4.4 80.2 1.0 N J:SER24 4.5 67.4 1.0 OD2 J:ASP52 4.5 69.6 1.0 CA J:SER24 4.5 68.2 1.0 CB J:LYS50 4.6 62.7 1.0 OD1 J:ASP48 4.6 61.7 1.0 O2B J:ADP401 4.6 65.5 1.0 CG J:ASP133 4.7 73.2 1.0 CB J:SER53 4.8 81.0 1.0 N J:SER53 4.8 74.8 1.0 O3A J:ADP401 4.8 66.2 1.0 CA J:SER53 4.9 76.2 1.0 PA J:ADP401 5.0 67.5 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