Magnesium in PDB 4wza: Asymmetric Nucleotide Binding in the Nitrogenase Complex

All present enzymatic activity of Asymmetric Nucleotide Binding in the Nitrogenase Complex:
1.18.6.1;

The structure of Asymmetric Nucleotide Binding in the Nitrogenase Complex, PDB code: 4wza was solved by F.A.Tezcan, J.T.Kaiser, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	110.201, 120.412, 264.318, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.7

The structure of Asymmetric Nucleotide Binding in the Nitrogenase Complex also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Iron	(Fe)	40 atoms

The binding sites of Magnesium atom in the Asymmetric Nucleotide Binding in the Nitrogenase Complex (pdb code 4wza). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Asymmetric Nucleotide Binding in the Nitrogenase Complex, PDB code: 4wza:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Asymmetric Nucleotide Binding in the Nitrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Asymmetric Nucleotide Binding in the Nitrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1291 b:39.2 occ:1.00 O E:HOH1320 2.1 30.4 1.0 O E:HOH1319 2.2 27.9 1.0 O E:HOH1317 2.2 43.5 1.0 O E:HOH1318 2.2 39.9 1.0 O1B E:ADP1292 2.5 27.5 1.0 OG E:SER16 2.6 43.1 1.0 CB E:SER16 3.2 43.0 1.0 O2B E:ADP1292 3.4 41.0 1.0 PB E:ADP1292 3.4 34.7 1.0 OD2 E:ASP125 3.8 44.7 1.0 OD1 E:ASP43 3.9 63.3 1.0 OD1 E:ASP39 3.9 59.7 1.0 N E:SER16 3.9 32.2 1.0 CA E:SER16 4.1 32.8 1.0 OD2 E:ASP43 4.2 64.5 1.0 O2A E:ADP1292 4.2 31.1 1.0 OD1 E:ASP125 4.3 37.4 1.0 CG E:ASP43 4.4 61.4 1.0 CG E:ASP125 4.4 36.9 1.0 O3A E:ADP1292 4.5 31.9 1.0 O3B E:ADP1292 4.6 36.0 1.0 OG E:SER44 4.6 39.6 1.0 PA E:ADP1292 4.6 33.3 1.0 CG E:ASP39 4.6 56.4 1.0 O E:HOH1370 4.7 47.0 1.0 O1A E:ADP1292 4.7 29.2 1.0 CB E:LYS15 4.9 32.8 1.0 NZ E:LYS15 4.9 32.1 1.0 CE E:LYS15 5.0 40.4 1.0 C E:LYS15 5.0 32.1 1.0

Magnesium binding site 2 out of 4 in the Asymmetric Nucleotide Binding in the Nitrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Asymmetric Nucleotide Binding in the Nitrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1291 b:27.2 occ:1.00 O F:HOH1310 2.2 26.4 1.0 O F:HOH1312 2.2 24.2 1.0 O F:HOH1311 2.2 26.3 1.0 O3G F:ACP1292 2.4 31.9 1.0 OG F:SER16 2.5 29.6 1.0 O1B F:ACP1292 2.5 20.5 1.0 CB F:SER16 3.3 26.1 1.0 PB F:ACP1292 3.5 28.2 1.0 PG F:ACP1292 3.5 33.7 1.0 C3B F:ACP1292 3.6 24.4 1.0 OD2 F:ASP125 4.0 26.6 1.0 N F:SER16 4.0 25.0 1.0 OD1 F:ASP43 4.0 30.5 1.0 OD2 F:ASP43 4.2 31.9 1.0 OD2 F:ASP39 4.2 37.3 1.0 CA F:SER16 4.2 26.5 1.0 OD1 F:ASP125 4.3 28.8 1.0 O1G F:ACP1292 4.4 49.5 1.0 O2B F:ACP1292 4.4 26.0 1.0 O1A F:ACP1292 4.5 32.8 1.0 CE F:LYS15 4.5 34.4 1.0 CG F:ASP43 4.5 30.9 1.0 O2G F:ACP1292 4.5 36.6 1.0 CG F:ASP125 4.5 26.8 1.0 O F:VAL126 4.5 32.2 1.0 CB F:LYS15 4.6 25.5 1.0 NZ F:LYS41 4.6 34.9 1.0 O3A F:ACP1292 4.6 39.5 1.0 CE F:LYS41 4.7 38.4 1.0 PA F:ACP1292 4.9 26.6 1.0 C F:LYS15 5.0 26.2 1.0

Magnesium binding site 3 out of 4 in the Asymmetric Nucleotide Binding in the Nitrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Asymmetric Nucleotide Binding in the Nitrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1291 b:32.0 occ:1.00 O G:HOH1321 2.2 25.2 1.0 O G:HOH1318 2.2 25.4 1.0 O G:HOH1320 2.2 25.1 1.0 O G:HOH1319 2.2 25.1 1.0 O2B G:ADP1292 2.4 19.7 1.0 OG G:SER16 2.5 24.6 1.0 CB G:SER16 3.3 20.5 1.0 PB G:ADP1292 3.4 26.0 1.0 O3B G:ADP1292 3.5 25.6 1.0 OD1 G:ASP39 3.6 37.6 1.0 OD1 G:ASP43 4.0 34.9 1.0 N G:SER16 4.1 24.8 1.0 OD2 G:ASP125 4.2 28.9 1.0 O2A G:ADP1292 4.2 22.5 1.0 CA G:SER16 4.3 27.4 1.0 NZ G:LYS41 4.3 58.4 1.0 CE G:LYS41 4.3 49.3 1.0 OD1 G:ASP125 4.3 30.1 1.0 O1B G:ADP1292 4.4 27.5 1.0 CG G:ASP39 4.4 36.5 1.0 OD2 G:ASP43 4.4 40.8 1.0 O3A G:ADP1292 4.5 23.7 1.0 CG G:ASP43 4.6 36.6 1.0 OG G:SER44 4.6 31.4 1.0 PA G:ADP1292 4.6 24.6 1.0 CG G:ASP125 4.6 30.8 1.0 O G:HOH1370 4.8 33.5 1.0 CE G:LYS15 4.8 25.5 1.0 O1A G:ADP1292 4.8 26.1 1.0 CB G:ASP39 4.9 30.9 1.0 O G:HOH1371 4.9 30.2 1.0 CB G:LYS15 4.9 17.9 1.0 NZ G:LYS15 4.9 20.2 1.0

Magnesium binding site 4 out of 4 in the Asymmetric Nucleotide Binding in the Nitrogenase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Asymmetric Nucleotide Binding in the Nitrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1291 b:23.7 occ:1.00 O H:HOH1315 2.2 21.3 1.0 O H:HOH1317 2.2 19.1 1.0 O H:HOH1316 2.2 16.5 1.0 O3G H:ACP1292 2.4 22.3 1.0 OG H:SER16 2.4 20.5 1.0 O1B H:ACP1292 2.4 17.6 1.0 CB H:SER16 3.3 22.1 1.0 PB H:ACP1292 3.4 23.5 1.0 PG H:ACP1292 3.4 29.5 1.0 C3B H:ACP1292 3.5 25.2 1.0 N H:SER16 3.9 18.5 1.0 OD2 H:ASP125 4.0 22.5 1.0 OD1 H:ASP43 4.1 26.9 1.0 OD2 H:ASP43 4.1 32.4 1.0 OD2 H:ASP39 4.1 35.2 1.0 CA H:SER16 4.1 21.1 1.0 O1G H:ACP1292 4.3 42.0 1.0 OD1 H:ASP125 4.3 22.8 1.0 O1A H:ACP1292 4.4 23.0 1.0 O2B H:ACP1292 4.4 16.9 1.0 CE H:LYS15 4.5 21.6 1.0 NZ H:LYS41 4.5 33.0 1.0 O2G H:ACP1292 4.5 29.5 1.0 CG H:ASP43 4.5 27.1 1.0 O3A H:ACP1292 4.6 23.1 1.0 CG H:ASP125 4.6 25.2 1.0 CB H:LYS15 4.6 18.5 1.0 O H:VAL126 4.7 21.5 1.0 PA H:ACP1292 4.8 21.1 1.0 NZ H:LYS15 4.9 24.5 1.0 C H:LYS15 5.0 18.8 1.0

F.A.Tezcan, J.T.Kaiser, J.B.Howard, D.C.Rees. Structural Evidence For Asymmetrical Nucleotide Interactions in Nitrogenase. J.Am.Chem.Soc. V. 137 146 2015.
ISSN: ESSN 1520-5126
PubMed: 25522159
DOI: 10.1021/JA511945E