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Magnesium in PDB 6q93: Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii

Enzymatic activity of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii

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

Protein crystallography data

The structure of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii, PDB code: 6q93 was solved by M.Rohde, S.Gerhardt, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.10 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 94.573, 176.857, 354.225, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 21.5

Other elements in 6q93:

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

Iron (Fe) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii (pdb code 6q93). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii, PDB code: 6q93:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6q93

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Magnesium binding site 1 out of 10 in the Mgadp-Bound Fe Protein of Vanadium 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 Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:42.9
occ:1.00
 OG A:SER17 1.9 41.7 1.0
O3B A:ADP1002 2.0 39.3 1.0
O A:HOH1104 2.0 42.0 1.0
O A:HOH1120 2.1 44.5 1.0
O A:HOH1135 2.1 39.2 1.0
O A:HOH1121 2.2 45.3 1.0
CB A:SER17 3.1 35.0 1.0
PB A:ADP1002 3.3 43.5 1.0
O1B A:ADP1002 3.5 45.7 1.0
OD2 A:ASP40 3.8 46.9 1.0
N A:SER17 3.9 33.5 1.0
OD1 A:ASP44 3.9 49.2 1.0
OD2 A:ASP126 4.0 49.4 1.0
CA A:SER17 4.0 33.3 1.0
O1A A:ADP1002 4.1 43.6 1.0
OD1 A:ASP126 4.2 36.3 1.0
OG A:SER45 4.2 48.5 1.0
O3A A:ADP1002 4.3 40.3 1.0
O2B A:ADP1002 4.3 43.4 1.0
CG A:ASP126 4.5 39.9 1.0
CG A:ASP40 4.5 47.0 1.0
PA A:ADP1002 4.6 43.0 1.0
O A:HOH1136 4.6 48.8 1.0
O2A A:ADP1002 4.7 44.1 1.0
CB A:LYS16 4.8 36.8 1.0
CE A:LYS16 4.9 34.9 1.0
CG A:ASP44 4.9 52.5 1.0
CB A:ASP40 4.9 38.1 1.0
C A:LYS16 4.9 38.0 1.0

Magnesium binding site 2 out of 10 in 6q93

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Magnesium binding site 2 out of 10 in the Mgadp-Bound Fe Protein of Vanadium 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 Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:87.5
occ:1.00
 O B:HOH405 2.0 94.9 1.0
OG B:SER17 2.1 88.2 1.0
O B:HOH406 2.3 68.6 1.0
O3B B:ADP301 2.4 75.2 1.0
O B:HOH402 2.6 61.1 1.0
CB B:SER17 3.2 79.2 1.0
OD2 B:ASP40 3.6 80.3 1.0
PB B:ADP301 3.7 76.2 1.0
OD1 B:ASP44 3.7 93.0 1.0
O2B B:ADP301 3.9 76.3 1.0
OG B:SER45 4.0 93.2 1.0
N B:SER17 4.0 73.1 1.0
OD2 B:ASP126 4.1 91.3 1.0
CG B:ASP40 4.1 71.4 1.0
CA B:SER17 4.2 74.8 1.0
CB B:ASP40 4.4 62.7 1.0
OD1 B:ASP126 4.5 82.4 1.0
O2A B:ADP301 4.6 70.1 1.0
O1B B:ADP301 4.7 71.7 1.0
O3A B:ADP301 4.7 76.9 1.0
CG B:ASP126 4.7 82.7 1.0
CB B:SER45 4.7 81.8 1.0
CA B:SER45 4.8 79.0 1.0
CB B:LYS16 4.8 70.0 1.0
N B:SER45 4.8 78.8 1.0
OD1 B:ASP40 4.9 69.7 1.0
CG B:ASP44 4.9 93.1 1.0
PA B:ADP301 5.0 72.7 1.0
CE B:LYS16 5.0 81.1 1.0

Magnesium binding site 3 out of 10 in 6q93

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Magnesium binding site 3 out of 10 in the Mgadp-Bound Fe Protein of Vanadium 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 Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:47.1
occ:1.00
 O C:HOH1102 2.0 36.6 1.0
O C:HOH1103 2.1 36.7 1.0
O3B C:ADP1002 2.1 41.2 1.0
OG C:SER17 2.1 42.5 1.0
O C:HOH1118 2.1 38.0 1.0
O C:HOH1121 2.2 40.6 1.0
CB C:SER17 3.2 41.3 1.0
PB C:ADP1002 3.3 41.6 1.0
O2B C:ADP1002 3.5 40.7 1.0
OD2 C:ASP40 3.6 47.2 1.0
OD1 C:ASP44 3.8 60.0 1.0
N C:SER17 4.0 37.5 1.0
OD2 C:ASP126 4.1 55.9 1.0
OG C:SER45 4.2 47.3 1.0
CA C:SER17 4.2 37.6 1.0
O2A C:ADP1002 4.2 42.1 1.0
CG C:ASP40 4.3 45.0 1.0
OD1 C:ASP126 4.3 42.2 1.0
O3A C:ADP1002 4.3 41.5 1.0
O1B C:ADP1002 4.3 43.2 1.0
CG C:ASP126 4.6 45.9 1.0
PA C:ADP1002 4.7 43.5 1.0
CB C:ASP40 4.7 38.4 1.0
O1A C:ADP1002 4.9 40.2 1.0
CE C:LYS16 4.9 35.3 1.0
CG C:ASP44 4.9 58.0 1.0
CD C:LYS42 4.9 50.9 1.0
CB C:LYS16 4.9 38.3 1.0

Magnesium binding site 4 out of 10 in 6q93

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Magnesium binding site 4 out of 10 in the Mgadp-Bound Fe Protein of Vanadium 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 Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1004

b:94.6
occ:1.00
 OE1 C:GLU113 3.1 0.8 1.0
OE2 C:GLU113 3.2 1.0 1.0
CD C:GLU113 3.5 0.8 1.0
O C:GLU69 3.6 99.8 1.0
O C:LEU71 3.6 77.7 1.0
OE1 C:GLU72 3.9 0.3 1.0
C C:GLU69 4.5 97.3 1.0
CD C:GLU72 4.6 0.7 1.0
C C:LEU71 4.8 76.8 1.0
CG C:GLU113 4.8 87.7 1.0
OE2 C:GLU72 4.9 0.2 1.0

Magnesium binding site 5 out of 10 in 6q93

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Magnesium binding site 5 out of 10 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:53.9
occ:1.00
 OG D:SER17 1.9 56.2 1.0
O D:HOH408 2.0 45.0 1.0
O3B D:ADP301 2.1 52.2 1.0
O D:HOH409 2.2 47.6 1.0
O D:HOH403 2.2 41.0 1.0
O D:HOH406 2.2 41.0 1.0
CB D:SER17 3.1 55.9 1.0
PB D:ADP301 3.4 52.8 1.0
O1B D:ADP301 3.6 53.8 1.0
OD1 D:ASP44 3.8 65.3 1.0
OD2 D:ASP40 3.8 62.0 1.0
N D:SER17 3.9 54.7 1.0
OD2 D:ASP126 4.0 64.2 1.0
CA D:SER17 4.1 54.4 1.0
O1A D:ADP301 4.2 58.9 1.0
OD1 D:ASP126 4.2 54.1 1.0
O3A D:ADP301 4.3 56.3 1.0
O2B D:ADP301 4.4 51.3 1.0
OG D:SER45 4.4 59.5 1.0
CG D:ASP40 4.5 58.6 1.0
CG D:ASP126 4.5 55.5 1.0
PA D:ADP301 4.6 55.9 1.0
O2A D:ADP301 4.7 52.3 1.0
CG D:ASP44 4.9 66.6 1.0
CB D:LYS16 4.9 54.5 1.0
CB D:ASP40 4.9 47.3 1.0
C D:LYS16 5.0 58.0 1.0
CE D:LYS16 5.0 46.7 1.0

Magnesium binding site 6 out of 10 in 6q93

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Magnesium binding site 6 out of 10 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1003

b:74.5
occ:1.00
 O E:HOH1108 2.0 66.8 1.0
O3B E:ADP1002 2.1 69.6 1.0
O E:HOH1105 2.2 62.0 1.0
O E:HOH1101 2.3 58.3 1.0
OG E:SER17 2.7 71.3 1.0
O2B E:ADP1002 3.0 63.5 1.0
PB E:ADP1002 3.1 67.0 1.0
OD2 E:ASP40 3.3 64.4 1.0
CB E:SER17 3.7 65.2 1.0
OD1 E:ASP44 3.8 81.6 1.0
CG E:ASP40 4.1 61.4 1.0
O3A E:ADP1002 4.1 65.7 1.0
O2A E:ADP1002 4.2 59.6 1.0
O1B E:ADP1002 4.2 63.8 1.0
NZ E:LYS16 4.4 92.0 1.0
N E:SER17 4.5 60.0 1.0
CD E:LYS42 4.5 79.3 1.0
OG E:SER45 4.6 75.2 1.0
PA E:ADP1002 4.6 61.0 1.0
CB E:ASP40 4.7 54.0 1.0
CB E:LYS42 4.7 60.3 1.0
CA E:SER17 4.7 61.2 1.0
OD1 E:ASP40 4.7 63.3 1.0
OD1 E:ASP126 4.7 67.4 1.0
OD2 E:ASP126 4.7 72.6 1.0
CG E:ASP44 5.0 82.2 1.0
O1A E:ADP1002 5.0 60.4 1.0
CE E:LYS16 5.0 67.0 1.0

Magnesium binding site 7 out of 10 in 6q93

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Magnesium binding site 7 out of 10 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:50.8
occ:1.00
 O F:HOH402 2.0 46.3 1.0
O F:HOH420 2.0 44.3 1.0
O3B F:ADP301 2.1 45.1 1.0
O F:HOH407 2.1 43.8 1.0
OG F:SER17 2.2 46.7 1.0
O F:HOH423 2.5 52.6 1.0
PB F:ADP301 3.3 47.9 1.0
CB F:SER17 3.4 40.8 1.0
O1B F:ADP301 3.4 47.2 1.0
OD2 F:ASP40 3.5 49.5 1.0
OD1 F:ASP44 3.9 57.8 1.0
N F:SER17 4.1 40.5 1.0
OD2 F:ASP126 4.2 48.9 1.0
OG F:SER45 4.2 48.4 1.0
CG F:ASP40 4.3 48.0 1.0
OD1 F:ASP126 4.3 44.0 1.0
O2B F:ADP301 4.3 47.9 1.0
O1A F:ADP301 4.3 49.1 1.0
CA F:SER17 4.3 39.7 1.0
O3A F:ADP301 4.3 47.2 1.0
O F:HOH438 4.5 53.0 1.0
CG F:ASP126 4.6 43.0 1.0
CB F:ASP40 4.7 38.0 1.0
PA F:ADP301 4.7 48.9 1.0
CE F:LYS16 4.8 40.3 1.0
O2A F:ADP301 4.9 49.3 1.0
CB F:LYS16 4.9 41.6 1.0
NZ F:LYS16 4.9 50.0 1.0
O F:HOH411 5.0 47.2 1.0
CG F:ASP44 5.0 60.4 1.0
CD F:LYS42 5.0 67.4 1.0

Magnesium binding site 8 out of 10 in 6q93

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Magnesium binding site 8 out of 10 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:95.1
occ:1.00
 O F:GLU69 3.2 61.3 1.0
OE2 F:GLU113 3.6 87.1 1.0
O F:LEU71 3.7 55.1 1.0
OE1 F:GLU72 3.9 89.4 1.0
C F:GLU69 4.3 60.0 1.0
CD F:GLU113 4.3 85.0 1.0
OE1 F:GLU113 4.4 83.7 1.0
CD F:GLU72 4.8 91.8 1.0
C F:LEU71 4.8 53.4 1.0

Magnesium binding site 9 out of 10 in 6q93

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Magnesium binding site 9 out of 10 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1003

b:54.0
occ:1.00
 O G:HOH1111 2.1 52.4 1.0
O3B G:ADP1002 2.1 51.2 1.0
O G:HOH1119 2.1 43.8 1.0
O G:HOH1117 2.1 44.3 1.0
OG G:SER17 2.1 53.5 1.0
O G:HOH1114 2.2 47.9 1.0
CB G:SER17 3.2 53.0 1.0
PB G:ADP1002 3.3 55.2 1.0
O1B G:ADP1002 3.5 52.9 1.0
OD2 G:ASP40 3.7 55.8 1.0
OD1 G:ASP44 3.7 70.0 1.0
OD2 G:ASP126 4.1 58.0 1.0
N G:SER17 4.1 52.2 1.0
O1A G:ADP1002 4.1 63.2 1.0
OG G:SER45 4.2 66.2 1.0
CA G:SER17 4.3 52.2 1.0
O3A G:ADP1002 4.3 59.0 1.0
O2B G:ADP1002 4.4 51.8 1.0
CG G:ASP40 4.4 54.3 1.0
OD1 G:ASP126 4.5 47.8 1.0
PA G:ADP1002 4.6 60.0 1.0
CG G:ASP126 4.7 50.7 1.0
O2A G:ADP1002 4.8 56.7 1.0
CB G:ASP40 4.8 47.6 1.0
CG G:ASP44 4.8 71.2 1.0
CE G:LYS16 4.9 50.8 1.0
CD G:LYS42 4.9 61.0 1.0
CB G:LYS16 5.0 51.5 1.0

Magnesium binding site 10 out of 10 in 6q93

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Magnesium binding site 10 out of 10 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:48.8
occ:1.00
 O H:HOH403 1.9 37.5 1.0
O H:HOH416 2.0 36.0 1.0
O H:HOH406 2.0 39.5 1.0
O3B H:ADP301 2.1 36.9 1.0
OG H:SER17 2.1 41.2 1.0
O H:HOH422 2.2 40.4 1.0
CB H:SER17 3.3 40.4 1.0
PB H:ADP301 3.4 42.2 1.0
OD2 H:ASP40 3.6 49.4 1.0
O2B H:ADP301 3.6 42.2 1.0
OD1 H:ASP44 3.8 57.6 1.0
OD2 H:ASP126 4.0 53.0 1.0
N H:SER17 4.0 40.4 1.0
OG H:SER45 4.1 51.3 1.0
CA H:SER17 4.3 39.3 1.0
CG H:ASP40 4.3 48.7 1.0
OD1 H:ASP126 4.3 40.1 1.0
O2A H:ADP301 4.3 44.7 1.0
O3A H:ADP301 4.4 43.6 1.0
O1B H:ADP301 4.4 44.4 1.0
CG H:ASP126 4.5 44.2 1.0
CB H:ASP40 4.6 42.6 1.0
PA H:ADP301 4.7 44.0 1.0
O H:HOH411 4.8 46.1 1.0
CE H:LYS16 4.8 36.6 1.0
CB H:LYS16 4.8 43.9 1.0
O1A H:ADP301 4.9 40.9 1.0
CG H:ASP44 4.9 57.0 1.0
CD H:LYS42 5.0 53.5 1.0

Reference:

M.Rohde, C.Trncik, D.Sippel, S.Gerhardt, O.Einsle. Crystal Structure of Vnfh, the Iron Protein Component of Vanadium Nitrogenase. J. Biol. Inorg. Chem. V. 23 1049 2018.
ISSN: ESSN 1432-1327
PubMed: 30141094
DOI: 10.1007/S00775-018-1602-4
Page generated: Tue Oct 1 15:25:47 2024

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