Atomistry » Magnesium » PDB 6q5a-6qin » 6q93
Atomistry »
  Magnesium »
    PDB 6q5a-6qin »
      6q93 »

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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Go back to Magnesium Binding Sites List in 6q93
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy