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Magnesium in PDB 1m34: Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate

Enzymatic activity of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate

All present enzymatic activity of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate, PDB code: 1m34 was solved by B.Schmid, O.Einsle, H.-J.Chiu, A.Willing, M.Yoshida, 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 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 326.100, 75.800, 312.200, 90.00, 102.60, 90.00
R / Rfree (%) 20 / 23.6

Other elements in 1m34:

The structure of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate also contains other interesting chemical elements:

Fluorine (F) 32 atoms
Molybdenum (Mo) 4 atoms
Aluminium (Al) 8 atoms
Iron (Fe) 76 atoms
Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate (pdb code 1m34). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate, PDB code: 1m34:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1m34

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Magnesium binding site 1 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3092

b:35.6
occ:1.00
 O E:HOH3131 2.0 46.2 1.0
O E:HOH3133 2.1 38.6 1.0
O E:HOH3132 2.2 31.4 1.0
OG E:SER16 2.3 36.3 1.0
F4 E:ALF3093 2.6 38.2 1.0
O2B E:ADP3091 2.6 31.9 1.0
F2 E:ALF3093 3.1 33.4 1.0
O1B E:ADP3091 3.3 38.9 1.0
CB E:SER16 3.4 33.7 1.0
PB E:ADP3091 3.5 33.1 1.0
AL E:ALF3093 3.7 38.5 1.0
OD2 E:ASP39 4.1 40.0 1.0
OD2 E:ASP125 4.1 42.9 1.0
N E:SER16 4.3 32.7 1.0
O E:HOH3130 4.3 34.1 1.0
CA E:SER16 4.4 32.6 1.0
O2A E:ADP3091 4.4 32.7 1.0
OD2 E:ASP43 4.5 54.7 1.0
OD1 E:ASP43 4.5 55.4 1.0
O3B E:ADP3091 4.5 30.9 1.0
CG E:LYS15 4.5 36.4 1.0
O3A E:ADP3091 4.5 35.5 1.0
OD1 E:ASP125 4.6 40.0 1.0
NZ E:LYS41 4.7 50.6 1.0
CG E:ASP125 4.7 41.1 1.0
OG E:SER44 4.8 51.6 1.0
O E:VAL126 4.8 36.2 1.0
CG E:ASP43 4.8 53.8 1.0
F1 E:ALF3093 4.8 38.9 1.0
NZ E:LYS15 4.9 32.1 1.0
PA E:ADP3091 4.9 37.1 1.0
CG E:ASP39 5.0 40.7 1.0
CA E:LEU127 5.0 38.2 1.0
O1A E:ADP3091 5.0 30.7 1.0

Magnesium binding site 2 out of 8 in 1m34

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Magnesium binding site 2 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg3192

b:31.0
occ:1.00
 O F:HOH3196 2.1 25.9 1.0
OG F:SER16 2.2 28.8 1.0
O F:HOH3197 2.2 27.0 1.0
O F:HOH3198 2.2 41.2 1.0
O2B F:ADP3191 2.3 28.9 1.0
F4 F:ALF3193 2.7 40.1 1.0
F2 F:ALF3193 2.8 40.5 1.0
CB F:SER16 3.3 29.8 1.0
PB F:ADP3191 3.3 28.1 1.0
O1B F:ADP3191 3.5 32.0 1.0
AL F:ALF3193 3.7 41.3 1.0
OD2 F:ASP125 4.1 42.4 1.0
N F:SER16 4.1 30.0 1.0
OD2 F:ASP39 4.2 38.1 1.0
O2A F:ADP3191 4.2 31.6 1.0
CA F:SER16 4.2 30.2 1.0
O3A F:ADP3191 4.3 32.0 1.0
OD2 F:ASP43 4.3 46.6 1.0
O3B F:ADP3191 4.4 31.3 1.0
CG F:LYS15 4.4 33.9 1.0
O E:HOH3134 4.5 39.0 1.0
NZ F:LYS41 4.6 46.6 1.0
OD1 F:ASP43 4.6 48.1 1.0
PA F:ADP3191 4.7 34.5 1.0
OD1 F:ASP125 4.8 43.0 1.0
CG F:ASP43 4.8 46.7 1.0
CG F:ASP125 4.8 41.4 1.0
NZ E:LYS10 4.9 33.5 1.0
OG F:SER44 4.9 44.5 1.0
F1 F:ALF3193 4.9 42.5 1.0

Magnesium binding site 3 out of 8 in 1m34

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Magnesium binding site 3 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3292

b:48.6
occ:1.00
 O G:HOH3347 2.2 26.4 1.0
O G:HOH3346 2.2 27.1 1.0
O G:HOH3348 2.2 42.7 1.0
OG G:SER16 2.4 37.6 1.0
F4 G:ALF3293 2.6 44.3 1.0
O2B G:ADP3291 2.6 37.2 1.0
O1B G:ADP3291 2.9 39.4 1.0
F2 G:ALF3293 3.1 44.9 1.0
PB G:ADP3291 3.2 31.6 1.0
CB G:SER16 3.4 33.2 1.0
AL G:ALF3293 3.7 45.0 1.0
OD2 G:ASP39 4.0 35.4 1.0
O G:HOH3345 4.1 43.7 1.0
OD2 G:ASP125 4.2 40.4 1.0
O3B G:ADP3291 4.2 33.6 1.0
N G:SER16 4.3 32.3 1.0
O2A G:ADP3291 4.3 35.2 1.0
O3A G:ADP3291 4.4 38.7 1.0
CG G:LYS15 4.4 34.7 1.0
OD2 G:ASP43 4.4 56.7 1.0
CA G:SER16 4.4 33.9 1.0
NZ G:LYS41 4.6 44.8 1.0
NZ G:LYS15 4.8 29.4 1.0
OD1 G:ASP125 4.8 38.0 1.0
F1 G:ALF3293 4.8 47.3 1.0
OD1 G:ASP43 4.8 54.2 1.0
OG G:SER44 4.8 45.6 1.0
PA G:ADP3291 4.8 38.3 1.0
CG G:ASP125 4.9 39.3 1.0
NZ H:LYS10 4.9 33.1 1.0
CG G:ASP43 5.0 54.0 1.0
CG G:ASP39 5.0 39.9 1.0
O G:VAL126 5.0 39.5 1.0

Magnesium binding site 4 out of 8 in 1m34

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Magnesium binding site 4 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg3392

b:41.6
occ:1.00
 O H:HOH3418 2.1 41.3 1.0
O H:HOH3417 2.1 31.6 1.0
O H:HOH3419 2.2 41.8 1.0
OG H:SER16 2.3 33.4 1.0
F4 H:ALF3393 2.5 35.3 1.0
O1B H:ADP3391 2.5 43.9 1.0
F2 H:ALF3393 3.2 35.5 1.0
CB H:SER16 3.4 32.6 1.0
PB H:ADP3391 3.5 37.9 1.0
O2B H:ADP3391 3.5 43.4 1.0
AL H:ALF3393 3.8 36.0 1.0
OD2 H:ASP39 3.8 39.9 1.0
OD2 H:ASP43 4.0 52.3 1.0
OD2 H:ASP125 4.2 44.3 1.0
O G:HOH3349 4.3 34.9 1.0
OD1 H:ASP43 4.3 53.4 1.0
N H:SER16 4.4 32.7 1.0
O2A H:ADP3391 4.4 33.1 1.0
CA H:SER16 4.5 32.0 1.0
O3B H:ADP3391 4.5 39.8 1.0
CG H:ASP43 4.5 53.0 1.0
CG H:LYS15 4.5 37.8 1.0
OD1 H:ASP125 4.6 42.5 1.0
NZ H:LYS41 4.6 54.4 1.0
O3A H:ADP3391 4.6 37.2 1.0
OG H:SER44 4.7 49.9 1.0
CG H:ASP39 4.7 41.5 1.0
CG H:ASP125 4.8 43.9 1.0
F1 H:ALF3393 4.8 36.7 1.0
O H:VAL126 4.8 38.8 1.0
PA H:ADP3391 4.9 35.0 1.0
O1A H:ADP3391 4.9 36.4 1.0
NZ G:LYS10 5.0 32.8 1.0

Magnesium binding site 5 out of 8 in 1m34

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Magnesium binding site 5 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg5092

b:30.8
occ:1.00
 O M:HOH5152 2.0 26.1 1.0
O2B M:ADP5091 2.2 30.8 1.0
O M:HOH5153 2.2 26.1 1.0
O M:HOH5154 2.2 48.4 1.0
OG M:SER16 2.2 33.0 1.0
F4 M:ALF5093 2.6 42.2 1.0
F2 M:ALF5093 3.0 44.3 1.0
CB M:SER16 3.2 31.5 1.0
PB M:ADP5091 3.5 29.3 1.0
AL M:ALF5093 3.7 42.4 1.0
O1B M:ADP5091 3.8 34.9 1.0
OD2 M:ASP125 4.1 38.4 1.0
N M:SER16 4.1 32.3 1.0
CA M:SER16 4.2 31.8 1.0
OD2 M:ASP39 4.2 42.4 1.0
O2A M:ADP5091 4.2 31.9 1.0
O3A M:ADP5091 4.3 35.0 1.0
CG M:LYS15 4.4 35.4 1.0
O M:HOH5151 4.4 42.6 1.0
OD2 M:ASP43 4.4 53.2 1.0
O3B M:ADP5091 4.5 34.0 1.0
OD1 M:ASP125 4.6 38.1 1.0
OD1 M:ASP43 4.6 51.1 1.0
PA M:ADP5091 4.7 31.8 1.0
OG M:SER44 4.7 48.0 1.0
CG M:ASP125 4.7 39.1 1.0
F1 M:ALF5093 4.8 42.9 1.0
O1A M:ADP5091 4.8 34.2 1.0
NZ M:LYS41 4.8 56.1 1.0
CG M:ASP43 4.9 51.4 1.0

Magnesium binding site 6 out of 8 in 1m34

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Magnesium binding site 6 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg5192

b:35.0
occ:1.00
 O N:HOH5232 2.1 28.4 1.0
O N:HOH5234 2.1 41.0 1.0
O N:HOH5233 2.1 30.3 1.0
OG N:SER16 2.3 34.0 1.0
O2B N:ADP5191 2.5 27.1 1.0
F4 N:ALF5193 2.6 39.3 1.0
F2 N:ALF5193 3.1 36.1 1.0
CB N:SER16 3.3 30.4 1.0
O1B N:ADP5191 3.4 33.1 1.0
PB N:ADP5191 3.4 25.7 1.0
AL N:ALF5193 3.7 36.6 1.0
OD2 N:ASP39 4.0 37.0 1.0
N N:SER16 4.2 30.0 1.0
OD2 N:ASP125 4.3 40.5 1.0
O M:HOH5155 4.3 36.3 1.0
CA N:SER16 4.3 29.6 1.0
CG N:LYS15 4.4 34.0 1.0
O2A N:ADP5191 4.4 28.7 1.0
OD2 N:ASP43 4.4 53.8 1.0
O3B N:ADP5191 4.4 27.1 1.0
O3A N:ADP5191 4.4 29.5 1.0
NZ N:LYS41 4.5 51.0 1.0
OD1 N:ASP125 4.6 40.2 1.0
OD1 N:ASP43 4.6 53.6 1.0
PA N:ADP5191 4.8 30.8 1.0
O1A N:ADP5191 4.8 31.4 1.0
OG N:SER44 4.8 42.6 1.0
O N:VAL126 4.8 36.0 1.0
F1 N:ALF5193 4.8 40.1 1.0
CG N:ASP125 4.8 38.8 1.0
CG N:ASP43 4.9 52.2 1.0
NZ N:LYS15 4.9 29.1 1.0
NZ M:LYS10 4.9 24.6 1.0
CG N:ASP39 5.0 39.6 1.0

Magnesium binding site 7 out of 8 in 1m34

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Magnesium binding site 7 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg5292

b:41.8
occ:1.00
 O O:HOH5296 2.1 41.5 1.0
O O:HOH5297 2.2 39.4 1.0
OG O:SER16 2.3 44.3 1.0
O O:HOH5298 2.3 42.9 1.0
O2B O:ADP5291 2.5 37.1 1.0
F4 O:ALF5293 2.6 49.4 1.0
F2 O:ALF5293 3.0 49.2 1.0
O1B O:ADP5291 3.3 42.7 1.0
PB O:ADP5291 3.4 37.8 1.0
CB O:SER16 3.4 42.4 1.0
AL O:ALF5293 3.7 50.7 1.0
OD2 O:ASP125 4.1 45.4 1.0
OD2 O:ASP39 4.1 46.2 1.0
N O:SER16 4.2 40.1 1.0
O O:HOH5294 4.3 50.5 1.0
CA O:SER16 4.3 41.3 1.0
CG O:LYS15 4.4 42.4 1.0
O2A O:ADP5291 4.4 44.9 1.0
O3B O:ADP5291 4.4 37.0 1.0
OD1 O:ASP125 4.4 44.8 1.0
O3A O:ADP5291 4.4 42.8 1.0
OD2 O:ASP43 4.6 58.1 1.0
CG O:ASP125 4.6 44.3 1.0
NZ O:LYS41 4.7 52.6 1.0
O O:VAL126 4.7 40.7 1.0
OG O:SER44 4.8 57.0 1.0
OD1 O:ASP43 4.8 58.5 1.0
PA O:ADP5291 4.8 43.3 1.0
F1 O:ALF5293 4.9 52.5 1.0
NZ P:LYS10 5.0 42.3 1.0
CA O:LEU127 5.0 43.2 1.0

Magnesium binding site 8 out of 8 in 1m34

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Magnesium binding site 8 out of 8 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg5392

b:42.6
occ:1.00
 O P:HOH5396 2.1 34.8 1.0
O P:HOH5397 2.3 57.9 1.0
O P:HOH5398 2.3 53.7 1.0
F4 P:ALF5393 2.5 44.6 1.0
OG P:SER16 2.5 41.8 1.0
O1B P:ADP5391 2.5 46.4 1.0
O2B P:ADP5391 2.7 41.9 1.0
PB P:ADP5391 3.0 40.7 1.0
F2 P:ALF5393 3.1 47.3 1.0
CB P:SER16 3.6 39.4 1.0
AL P:ALF5393 3.7 48.5 1.0
OD2 P:ASP39 3.9 47.5 1.0
O3B P:ADP5391 4.1 41.4 1.0
O O:HOH5394 4.1 46.6 1.0
O3A P:ADP5391 4.2 44.3 1.0
O2A P:ADP5391 4.2 42.2 1.0
OD2 P:ASP43 4.4 58.4 1.0
N P:SER16 4.4 38.5 1.0
OD2 P:ASP125 4.5 45.9 1.0
CG P:LYS15 4.5 39.3 1.0
CA P:SER16 4.5 39.5 1.0
NZ P:LYS41 4.5 52.7 1.0
PA P:ADP5391 4.6 43.8 1.0
OD1 P:ASP125 4.7 46.8 1.0
OD1 P:ASP43 4.7 57.6 1.0
NZ P:LYS15 4.7 38.7 1.0
O1A P:ADP5391 4.7 45.4 1.0
F1 P:ALF5393 4.8 48.7 1.0
NZ O:LYS10 4.9 39.7 1.0
CG P:ASP43 4.9 56.8 1.0
CG P:ASP39 5.0 47.6 1.0
CG P:ASP125 5.0 46.0 1.0

Reference:

B.Schmid, O.Einsle, H.-J.Chiu, A.Willing, M.Yoshida, J.B.Howard, D.C.Rees. Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the Adp-ALF4 Stabilized Structure Biochemistry V. 41 15557 2002.
ISSN: ISSN 0006-2960
PubMed: 12501184
DOI: 10.1021/BI026642B
Page generated: Tue Aug 13 08:36:38 2024

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