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Magnesium in PDB 1g21: Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein

Enzymatic activity of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein

All present enzymatic activity of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein:
1.18.6.1;

Protein crystallography data

The structure of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein, PDB code: 1g21 was solved by H.-J.Chiu, J.W.Peters, W.N.Lanzilotta, M.J.Ryle, L.C.Seefeldt, 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) 20.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.500, 121.500, 264.900, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 28.5

Other elements in 1g21:

The structure of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Iron (Fe) 38 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein (pdb code 1g21). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein, PDB code: 1g21:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1g21

Go back to Magnesium Binding Sites List in 1g21
Magnesium binding site 1 out of 4 in the Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg293

b:24.0
occ:1.00
 OG E:SER16 2.0 50.8 1.0
O3G E:ATP5292 2.4 93.2 1.0
O3B E:ATP5292 3.0 79.8 1.0
CB E:SER16 3.3 47.8 1.0
PG E:ATP5292 3.3 95.6 1.0
OD2 E:ASP43 3.4 55.6 1.0
OD1 E:ASP43 3.5 59.7 1.0
OD2 E:ASP39 3.6 47.4 1.0
OD1 E:ASP125 3.6 9.6 1.0
CG E:ASP43 3.7 56.1 1.0
O2G E:ATP5292 3.9 95.3 1.0
O1B E:ATP5292 4.0 75.6 1.0
N E:SER16 4.0 40.4 1.0
PB E:ATP5292 4.1 69.7 1.0
CA E:SER16 4.2 45.3 1.0
OD2 E:ASP125 4.4 16.2 1.0
O3A E:ATP5292 4.4 72.2 1.0
CG E:ASP125 4.4 15.5 1.0
O1G E:ATP5292 4.5 96.2 1.0
O2A E:ATP5292 4.5 78.4 1.0
OG E:SER44 4.6 47.7 1.0
CG E:ASP39 4.6 40.9 1.0
PA E:ATP5292 4.8 80.5 1.0
CB E:LYS15 4.9 41.8 1.0
N E:SER44 4.9 35.2 1.0
O1A E:ATP5292 4.9 80.0 1.0

Magnesium binding site 2 out of 4 in 1g21

Go back to Magnesium Binding Sites List in 1g21
Magnesium binding site 2 out of 4 in the Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg293

b:23.3
occ:1.00
 O3G F:ATP6292 2.3 81.9 1.0
OG F:SER16 2.3 54.2 1.0
CB F:SER16 2.6 36.6 1.0
O3B F:ATP6292 2.6 61.9 1.0
PG F:ATP6292 3.0 92.3 1.0
O1B F:ATP6292 3.2 40.4 1.0
N F:SER16 3.2 33.2 1.0
OD1 F:ASP125 3.3 13.1 1.0
CA F:SER16 3.4 27.8 1.0
PB F:ATP6292 3.6 48.8 1.0
O2G F:ATP6292 3.8 0.9 1.0
OD2 F:ASP125 3.9 16.0 1.0
O3A F:ATP6292 4.0 42.1 1.0
CG F:ASP125 4.1 6.0 1.0
O1G F:ATP6292 4.1 0.2 1.0
O2A F:ATP6292 4.2 56.5 1.0
OD2 F:ASP43 4.2 79.6 1.0
CB F:LYS15 4.3 37.5 1.0
C F:LYS15 4.4 32.9 1.0
PA F:ATP6292 4.5 46.8 1.0
CG F:ASP43 4.6 71.8 1.0
O1A F:ATP6292 4.7 54.6 1.0
OD1 F:ASP43 4.7 77.2 1.0
OG F:SER44 4.7 41.0 1.0
OD2 F:ASP39 4.8 63.0 1.0
C F:SER16 4.8 24.8 1.0
O2B F:ATP6292 4.8 39.7 1.0
CA F:LYS15 4.8 35.2 1.0
CA F:SER44 4.9 31.6 1.0

Magnesium binding site 3 out of 4 in 1g21

Go back to Magnesium Binding Sites List in 1g21
Magnesium binding site 3 out of 4 in the Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg293

b:34.0
occ:1.00
 O3G H:ATP8292 2.2 95.7 1.0
CB H:SER16 2.5 36.7 0.0
OG H:SER16 2.5 40.5 0.0
O3B H:ATP8292 2.9 83.5 1.0
PG H:ATP8292 3.0 99.8 1.0
OD1 H:ASP125 3.4 5.7 1.0
O1B H:ATP8292 3.6 67.5 1.0
N H:SER16 3.6 34.9 1.0
CA H:SER16 3.6 32.2 1.0
O2G H:ATP8292 3.7 98.7 1.0
PB H:ATP8292 3.8 66.6 1.0
OD2 H:ASP43 3.8 73.7 1.0
OD1 H:ASP43 3.9 54.3 1.0
CG H:ASP43 4.1 65.7 1.0
OD2 H:ASP125 4.1 13.3 1.0
CG H:ASP125 4.1 6.2 1.0
O3A H:ATP8292 4.1 64.0 1.0
O2A H:ATP8292 4.1 69.4 1.0
O1G H:ATP8292 4.3 0.4 1.0
PA H:ATP8292 4.5 58.0 1.0
OD2 H:ASP39 4.5 49.9 1.0
O1A H:ATP8292 4.6 63.0 1.0
CB H:LYS15 4.8 21.9 1.0
N H:SER44 4.8 49.9 1.0
C H:LYS15 4.8 27.8 1.0
OG H:SER44 4.8 36.0 1.0
CA H:SER44 4.8 41.0 1.0
C H:ASP43 5.0 61.1 1.0

Magnesium binding site 4 out of 4 in 1g21

Go back to Magnesium Binding Sites List in 1g21
Magnesium binding site 4 out of 4 in the Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between LEU127DEL-Fe Protein and the Mofe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg293

b:57.0
occ:1.00
 OG G:SER16 2.6 64.7 1.0
O3G G:ATP7292 2.7 87.2 1.0
CB G:SER16 2.8 71.0 1.0
O2G G:ATP7292 3.2 85.0 1.0
PG G:ATP7292 3.2 86.4 1.0
OD1 G:ASP125 3.3 11.8 1.0
N G:SER16 3.4 60.6 1.0
O3B G:ATP7292 3.4 78.6 1.0
CA G:SER16 3.6 64.8 1.0
OD2 G:ASP125 3.6 18.9 1.0
CG G:ASP125 3.8 24.7 1.0
OD2 G:ASP43 4.1 72.3 1.0
OD2 G:ASP39 4.2 69.9 1.0
OD1 G:ASP43 4.3 73.9 1.0
CB G:LYS15 4.3 46.6 1.0
CG G:ASP43 4.4 65.4 1.0
OG G:SER44 4.5 56.5 1.0
C G:LYS15 4.5 55.6 1.0
O1G G:ATP7292 4.7 77.8 1.0
PB G:ATP7292 4.9 69.8 1.0
CA G:LYS15 5.0 52.2 1.0

Reference:

H.Chiu, J.W.Peters, W.N.Lanzilotta, M.J.Ryle, L.C.Seefeldt, J.B.Howard, D.C.Rees. Mgatp-Bound and Nucleotide-Free Structures of A Nitrogenase Protein Complex Between the Leu 127 Delta-Fe-Protein and the Mofe-Protein. Biochemistry V. 40 641 2001.
ISSN: ISSN 0006-2960
PubMed: 11170380
DOI: 10.1021/BI001645E
Page generated: Mon Dec 14 05:57:01 2020

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