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Magnesium in PDB 1fp6: The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp

Enzymatic activity of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp

All present enzymatic activity of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp:
1.18.6.1;

Protein crystallography data

The structure of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp, PDB code: 1fp6 was solved by S.B.Jang, L.C.Seefeldt, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.250, 119.530, 120.940, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.8

Other elements in 1fp6:

The structure of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp (pdb code 1fp6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp, PDB code: 1fp6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1fp6

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Magnesium binding site 1 out of 4 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5292

b:31.2
occ:1.00
 O A:HOH5447 2.2 33.0 1.0
OG A:SER16 2.2 25.7 1.0
O A:HOH5457 2.2 28.7 1.0
O3B A:ADP5291 2.3 20.9 1.0
O A:HOH5436 2.3 33.9 1.0
O A:HOH5504 2.3 34.5 1.0
CB A:SER16 3.2 29.1 1.0
O2B A:ADP5291 3.6 26.2 1.0
PB A:ADP5291 3.7 24.1 1.0
OD1 A:ASP43 3.7 34.4 1.0
OG A:SER44 3.8 32.2 1.0
OD2 A:ASP39 4.0 26.2 1.0
N A:SER16 4.1 31.3 1.0
OD2 A:ASP125 4.1 26.7 1.0
O1A A:ADP5291 4.2 30.8 1.0
CA A:SER16 4.2 27.9 1.0
OD1 A:ASP125 4.5 28.2 1.0
O3A A:ADP5291 4.5 31.7 1.0
O A:HOH5301 4.5 23.5 1.0
O1B A:ADP5291 4.5 27.5 1.0
CG A:ASP39 4.6 23.0 1.0
PA A:ADP5291 4.6 33.5 1.0
CG A:ASP125 4.7 23.5 1.0
CG A:ASP43 4.7 35.0 1.0
O2A A:ADP5291 4.8 33.0 1.0
CD A:LYS41 4.8 39.7 1.0
CB A:ASP39 4.9 23.6 1.0
CA A:SER44 4.9 33.7 1.0
CG A:LYS15 4.9 30.5 1.0
CB A:SER44 4.9 29.6 1.0
N A:SER44 5.0 34.5 1.0

Magnesium binding site 2 out of 4 in 1fp6

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Magnesium binding site 2 out of 4 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6292

b:29.9
occ:1.00
 O3B B:ADP6291 2.2 25.5 1.0
O B:HOH6450 2.3 30.5 1.0
OG B:SER16 2.3 28.5 1.0
O B:HOH6483 2.3 34.2 1.0
O B:HOH6439 2.3 29.2 1.0
O B:HOH6433 2.4 29.4 1.0
CB B:SER16 3.2 27.8 1.0
O2B B:ADP6291 3.3 23.6 1.0
PB B:ADP6291 3.5 28.1 1.0
OD1 B:ASP43 3.8 29.6 1.0
O1A B:ADP6291 3.8 33.9 1.0
OD2 B:ASP39 4.0 31.7 1.0
N B:SER16 4.1 27.6 1.0
CA B:SER16 4.2 29.1 1.0
OG B:SER44 4.2 32.0 1.0
O3A B:ADP6291 4.2 33.0 1.0
PA B:ADP6291 4.3 32.1 1.0
OD2 B:ASP125 4.3 32.3 1.0
O B:HOH6470 4.3 38.0 1.0
O1B B:ADP6291 4.4 31.3 1.0
CG B:ASP39 4.5 30.8 1.0
O2A B:ADP6291 4.6 28.6 1.0
OD1 B:ASP125 4.7 28.2 1.0
CG B:ASP43 4.9 32.2 1.0
CG B:ASP125 4.9 29.1 1.0
CD B:LYS41 4.9 34.0 1.0
CG B:LYS15 4.9 30.9 1.0
CB B:ASP39 5.0 29.6 1.0

Magnesium binding site 3 out of 4 in 1fp6

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Magnesium binding site 3 out of 4 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg7292

b:25.4
occ:1.00
 O1B C:ADP7291 2.2 32.9 1.0
O C:HOH7490 2.2 29.9 1.0
O C:HOH7453 2.3 20.3 1.0
OG C:SER16 2.3 27.5 1.0
O C:HOH7450 2.3 34.4 1.0
O C:HOH7504 2.4 33.5 1.0
CB C:SER16 3.4 29.7 1.0
PB C:ADP7291 3.6 32.3 1.0
OD1 C:ASP39 3.7 30.9 1.0
O3B C:ADP7291 3.8 26.4 1.0
OD2 C:ASP43 3.9 37.6 1.0
OG C:SER44 4.0 24.9 1.0
OD2 C:ASP125 4.1 26.9 1.0
N C:SER16 4.2 26.3 1.0
CG C:ASP39 4.3 29.5 1.0
OD1 C:ASP125 4.3 24.6 1.0
CA C:SER16 4.4 27.3 1.0
O1A C:ADP7291 4.4 28.7 1.0
O2B C:ADP7291 4.5 32.2 1.0
O3A C:ADP7291 4.6 30.5 1.0
CG C:ASP125 4.6 25.3 1.0
CB C:ASP39 4.6 29.8 1.0
O C:LYS41 4.7 47.2 1.0
PA C:ADP7291 4.7 30.2 1.0
NZ C:LYS15 4.7 22.7 1.0
CG C:ASP43 4.9 36.9 1.0
CB C:LYS15 4.9 22.6 1.0
OD2 C:ASP39 4.9 32.8 1.0
O2A C:ADP7291 5.0 24.3 1.0

Magnesium binding site 4 out of 4 in 1fp6

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Magnesium binding site 4 out of 4 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg8292

b:31.2
occ:1.00
 O1B D:ADP8291 2.2 31.9 1.0
O D:HOH8402 2.2 36.0 1.0
O D:HOH8415 2.3 25.5 1.0
OG D:SER16 2.3 27.8 1.0
O D:HOH8433 2.4 38.8 1.0
O D:HOH8401 2.4 58.6 1.0
CB D:SER16 3.3 31.2 1.0
PB D:ADP8291 3.4 30.8 1.0
O3B D:ADP8291 3.4 30.1 1.0
OD2 D:ASP43 3.5 41.2 1.0
O1A D:ADP8291 4.0 33.3 1.0
OD1 D:ASP39 4.0 34.2 1.0
OG D:SER44 4.2 32.3 1.0
N D:SER16 4.2 30.6 1.0
O3A D:ADP8291 4.3 36.8 1.0
CA D:SER16 4.4 32.4 1.0
PA D:ADP8291 4.5 35.5 1.0
O2B D:ADP8291 4.5 33.3 1.0
CE D:LYS41 4.5 37.5 1.0
OD2 D:ASP125 4.5 34.5 1.0
CG D:ASP43 4.6 37.9 1.0
O D:LYS41 4.6 48.5 1.0
O D:HOH8448 4.6 45.2 1.0
CG D:ASP39 4.6 34.4 1.0
OD1 D:ASP125 4.9 34.7 1.0
O2A D:ADP8291 4.9 34.2 1.0
CD D:LYS41 4.9 38.3 1.0
N D:SER44 5.0 35.9 1.0

Reference:

S.B.Jang, L.C.Seefeldt, J.W.Peters. Insights Into Nucleotide Signal Transduction in Nitrogenase: Structure of An Iron Protein with Mgadp Bound. Biochemistry V. 39 14745 2000.
ISSN: ISSN 0006-2960
PubMed: 11101289
DOI: 10.1021/BI001705G
Page generated: Mon Dec 14 05:56:18 2020

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