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Magnesium in PDB 7qqa: Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii

Enzymatic activity of Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii

All present enzymatic activity of Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii:
1.18.6.1;

Protein crystallography data

The structure of Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii, PDB code: 7qqa was solved by C.Trncik, T.Mueller, P.Franke, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.48 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.677, 80.366, 80.024, 68.57, 75.85, 76.03
R / Rfree (%) 19.7 / 24.9

Other elements in 7qqa:

The structure of Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii (pdb code 7qqa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii, PDB code: 7qqa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7qqa

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Magnesium binding site 1 out of 4 in the Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii


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 Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:13.9
occ:1.00
 O A:HOH431 1.9 13.4 1.0
O3B A:ADP301 2.0 13.1 1.0
O A:HOH424 2.0 12.0 1.0
O A:HOH490 2.1 20.4 1.0
O A:HOH461 2.1 19.7 1.0
OG A:SER16 2.2 16.0 1.0
PB A:ADP301 3.2 14.0 1.0
CB A:SER16 3.2 16.8 1.0
O1B A:ADP301 3.5 12.1 1.0
OD2 A:ASP40 3.7 16.8 1.0
OD1 A:ASP44 3.8 22.6 1.0
N A:SER16 3.9 16.1 1.0
O1A A:ADP301 4.1 14.2 1.0
OD2 A:ASP125 4.1 16.1 1.0
CA A:SER16 4.1 16.7 1.0
OG A:SER45 4.2 20.3 1.0
O2B A:ADP301 4.3 12.7 1.0
O3A A:ADP301 4.3 13.6 1.0
OD1 A:ASP125 4.3 15.1 1.0
CG A:ASP40 4.4 15.9 1.0
PA A:ADP301 4.6 16.9 1.0
CG A:ASP125 4.6 15.1 1.0
CB A:LYS15 4.7 15.2 1.0
CB A:ASP40 4.7 15.4 1.0
O A:HOH512 4.8 19.4 1.0
O2A A:ADP301 4.8 15.7 1.0
O A:HOH406 4.8 17.2 1.0
CE A:LYS15 4.8 14.8 1.0
NZ A:LYS15 4.9 16.0 1.0
CG A:ASP44 4.9 22.2 1.0
C A:LYS15 4.9 14.9 1.0

Magnesium binding site 2 out of 4 in 7qqa

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Magnesium binding site 2 out of 4 in the Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii


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 Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:24.2
occ:1.00
 O B:HOH430 1.9 21.9 1.0
O B:HOH452 2.0 26.3 1.0
OG B:SER16 2.1 25.9 1.0
O B:HOH424 2.1 24.4 1.0
O1B B:ADP301 2.2 25.4 1.0
O B:HOH414 2.2 18.7 1.0
CB B:SER16 3.1 25.4 1.0
PB B:ADP301 3.3 27.6 1.0
O2B B:ADP301 3.4 28.3 1.0
OD1 B:ASP44 3.7 36.6 1.0
N B:SER16 3.9 29.1 1.0
OD2 B:ASP40 4.0 26.6 1.0
CA B:SER16 4.1 27.9 1.0
O2A B:ADP301 4.1 35.0 1.0
OG B:SER45 4.1 28.5 1.0
OD2 B:ASP125 4.1 24.4 1.0
O3A B:ADP301 4.3 28.1 1.0
O3B B:ADP301 4.5 27.5 1.0
OD1 B:ASP125 4.5 27.4 1.0
PA B:ADP301 4.5 31.4 1.0
O1A B:ADP301 4.6 28.8 1.0
CG B:ASP40 4.6 25.3 1.0
CG B:ASP125 4.7 24.2 1.0
O B:HOH476 4.7 35.8 1.0
CG B:ASP44 4.8 36.1 1.0
CB B:LYS15 4.8 28.3 1.0
O B:HOH425 4.9 32.0 1.0
CB B:ASP40 4.9 24.1 1.0
CA B:SER45 4.9 26.6 1.0

Magnesium binding site 3 out of 4 in 7qqa

Go back to Magnesium Binding Sites List in 7qqa
Magnesium binding site 3 out of 4 in the Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii


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 Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:16.2
occ:1.00
 O C:HOH410 2.0 21.5 1.0
O C:HOH483 2.0 10.8 1.0
O C:HOH441 2.1 17.0 1.0
OG C:SER16 2.1 18.6 1.0
O3B C:ADP301 2.1 18.0 1.0
O C:HOH478 2.2 21.1 1.0
CB C:SER16 3.1 19.0 1.0
PB C:ADP301 3.3 17.3 1.0
O1B C:ADP301 3.4 18.6 1.0
OD1 C:ASP44 3.5 32.5 1.0
O1A C:ADP301 3.9 21.9 1.0
N C:SER16 4.0 18.8 1.0
OD2 C:ASP40 4.0 16.7 1.0
CA C:SER16 4.1 18.5 1.0
O3A C:ADP301 4.2 18.2 1.0
OG C:SER45 4.2 23.1 1.0
OD2 C:ASP125 4.2 20.3 1.0
PA C:ADP301 4.4 19.7 1.0
O2B C:ADP301 4.5 17.2 1.0
OD1 C:ASP125 4.6 20.4 1.0
CG C:ASP44 4.6 31.0 1.0
O C:HOH523 4.6 23.9 1.0
CG C:ASP40 4.7 18.3 1.0
O2A C:ADP301 4.7 19.5 1.0
CG C:ASP125 4.8 18.9 1.0
O C:HOH412 4.9 21.4 1.0
CA C:SER45 5.0 22.1 1.0
CB C:LYS15 5.0 21.0 1.0
CB C:ASP40 5.0 17.5 1.0
OD2 C:ASP44 5.0 37.3 1.0

Magnesium binding site 4 out of 4 in 7qqa

Go back to Magnesium Binding Sites List in 7qqa
Magnesium binding site 4 out of 4 in the Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii


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 Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:19.3
occ:1.00
 O D:HOH461 2.0 14.2 1.0
O D:HOH477 2.0 14.9 1.0
O D:HOH479 2.1 16.1 1.0
O D:HOH431 2.1 18.9 1.0
O1B D:ADP301 2.1 14.7 1.0
OG D:SER16 2.1 17.6 1.0
CB D:SER16 3.2 17.0 1.0
PB D:ADP301 3.3 17.1 1.0
O2B D:ADP301 3.4 15.5 1.0
OD2 D:ASP40 3.7 16.6 1.0
OD1 D:ASP44 3.8 23.4 1.0
N D:SER16 3.9 17.1 1.0
O2A D:ADP301 4.0 17.3 1.0
OD2 D:ASP125 4.1 14.7 1.0
CA D:SER16 4.1 17.7 1.0
OG D:SER45 4.2 20.2 1.0
O3B D:ADP301 4.2 14.8 1.0
OD1 D:ASP125 4.3 16.6 1.0
O3A D:ADP301 4.3 16.4 1.0
CG D:ASP40 4.4 16.3 1.0
CG D:ASP125 4.6 15.7 1.0
O D:HOH428 4.6 19.4 1.0
PA D:ADP301 4.6 17.8 1.0
CB D:ASP40 4.7 17.0 1.0
CB D:LYS15 4.7 15.2 1.0
O1A D:ADP301 4.8 15.9 1.0
CE D:LYS15 4.9 15.8 1.0
NZ D:LYS15 4.9 15.7 1.0
CG D:ASP44 4.9 23.6 1.0
C D:LYS15 5.0 16.0 1.0

Reference:

C.Trncik, T.Mueller, P.Franke, O.Einsle. Mgadp-Bound Fe Protein of the Iron-Only Nitrogenase From Azotobacter Vinelandii Journal of Inorganic V. 227 2022BIOCHEMISTRY.
Page generated: Thu Apr 6 20:36:05 2023

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