Iron 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:

Magnesium (Mg) 10 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 16 binding sites of Iron where determined in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii, PDB code: 6q93:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 6q93

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Iron binding site 1 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe1001

b:44.0
occ:1.00
FE1 A:SF41001 0.0 44.0 1.0
S4 A:SF41001 2.3 46.4 1.0
S3 A:SF41001 2.3 44.7 1.0
S2 A:SF41001 2.3 45.6 1.0
SG A:CYS98 2.3 46.1 1.0
FE2 A:SF41001 2.7 48.0 1.0
FE4 A:SF41001 2.7 45.2 1.0
FE3 A:SF41001 2.8 47.4 1.0
CB A:CYS98 3.3 42.9 1.0
CA A:CYS98 3.7 44.3 1.0
S1 A:SF41001 3.9 45.9 1.0
N A:ALA99 4.1 44.0 1.0
C A:CYS98 4.2 45.9 1.0
SG B:CYS133 4.5 57.0 1.0
N A:GLY100 4.6 40.8 1.0
CA A:GLY134 4.6 56.8 1.0
SG A:CYS133 4.8 56.1 1.0
N A:GLY134 4.9 56.3 1.0

Iron binding site 2 out of 16 in 6q93

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Iron binding site 2 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
A:Fe1001

b:48.0
occ:1.00
FE2 A:SF41001 0.0 48.0 1.0
S3 A:SF41001 2.3 44.7 1.0
S4 A:SF41001 2.3 46.4 1.0
S1 A:SF41001 2.3 45.9 1.0
SG A:CYS133 2.3 56.1 1.0
FE1 A:SF41001 2.7 44.0 1.0
FE3 A:SF41001 2.7 47.4 1.0
FE4 A:SF41001 2.8 45.2 1.0
CB A:CYS133 3.6 52.9 1.0
S2 A:SF41001 3.9 45.6 1.0
C A:CYS133 4.2 57.8 1.0
O A:CYS133 4.2 56.7 1.0
N B:ALA99 4.3 47.4 1.0
CG2 A:VAL131 4.3 58.2 1.0
CA A:CYS133 4.5 51.6 1.0
N A:GLY134 4.5 56.3 1.0
CB B:ALA99 4.7 48.5 1.0
SG A:CYS98 4.7 46.1 1.0
CA B:CYS98 4.8 45.2 1.0
SG B:CYS98 4.8 47.9 1.0
CB A:VAL131 4.8 60.0 1.0
SG B:CYS133 4.8 57.0 1.0
CA A:GLY134 4.9 56.8 1.0
CD2 A:PHE136 5.0 42.3 1.0

Iron binding site 3 out of 16 in 6q93

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Iron binding site 3 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
A:Fe1001

b:47.4
occ:1.00
FE3 A:SF41001 0.0 47.4 1.0
S2 A:SF41001 2.3 45.6 1.0
S1 A:SF41001 2.3 45.9 1.0
S4 A:SF41001 2.3 46.4 1.0
SG B:CYS98 2.4 47.9 1.0
FE4 A:SF41001 2.7 45.2 1.0
FE2 A:SF41001 2.7 48.0 1.0
FE1 A:SF41001 2.8 44.0 1.0
CB B:CYS98 3.3 43.6 1.0
CA B:CYS98 3.7 45.2 1.0
S3 A:SF41001 3.9 44.7 1.0
N B:ALA99 4.0 47.4 1.0
C B:CYS98 4.2 49.9 1.0
SG A:CYS133 4.5 56.1 1.0
N B:GLY100 4.5 50.1 1.0
CA B:GLY134 4.5 45.2 1.0
O B:HOH425 4.7 67.2 1.0
SG B:CYS133 4.7 57.0 1.0
N B:GLY134 4.9 46.8 1.0
SG A:CYS98 5.0 46.1 1.0

Iron binding site 4 out of 16 in 6q93

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Iron binding site 4 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
A:Fe1001

b:45.2
occ:1.00
FE4 A:SF41001 0.0 45.2 1.0
SG B:CYS133 2.2 57.0 1.0
S1 A:SF41001 2.3 45.9 1.0
S2 A:SF41001 2.3 45.6 1.0
S3 A:SF41001 2.3 44.7 1.0
FE3 A:SF41001 2.7 47.4 1.0
FE1 A:SF41001 2.7 44.0 1.0
FE2 A:SF41001 2.8 48.0 1.0
CB B:CYS133 3.4 52.9 1.0
S4 A:SF41001 3.9 46.4 1.0
CG1 B:VAL131 4.0 62.0 1.0
C B:CYS133 4.1 52.6 1.0
N A:ALA99 4.2 44.0 1.0
O B:CYS133 4.3 52.9 1.0
CA B:CYS133 4.4 52.2 1.0
N B:GLY134 4.4 46.8 1.0
SG A:CYS98 4.7 46.1 1.0
CG2 B:VAL131 4.7 62.8 1.0
CB A:ALA99 4.7 43.1 1.0
CA A:CYS98 4.7 44.3 1.0
SG B:CYS98 4.8 47.9 1.0
CA B:GLY134 4.9 45.2 1.0
N B:CYS133 4.9 53.9 1.0
CB B:VAL131 4.9 63.2 1.0
SG A:CYS133 5.0 56.1 1.0
C A:CYS98 5.0 45.9 1.0

Iron binding site 5 out of 16 in 6q93

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Iron binding site 5 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
C:Fe1001

b:44.5
occ:1.00
FE1 C:SF41001 0.0 44.5 1.0
SG C:CYS98 2.3 43.5 1.0
S4 C:SF41001 2.3 44.2 1.0
S3 C:SF41001 2.3 43.1 1.0
S2 C:SF41001 2.3 44.2 1.0
FE4 C:SF41001 2.7 44.7 1.0
FE3 C:SF41001 2.7 43.6 1.0
FE2 C:SF41001 2.7 45.4 1.0
CB C:CYS98 3.3 40.6 1.0
CA C:CYS98 3.7 40.6 1.0
S1 C:SF41001 3.9 44.1 1.0
N C:ALA99 4.0 40.0 1.0
C C:CYS98 4.2 44.3 1.0
SG D:CYS133 4.5 42.3 1.0
N C:GLY100 4.6 36.6 1.0
CA C:GLY134 4.6 44.3 1.0
SG C:CYS133 4.8 48.4 1.0
SG D:CYS98 4.9 42.9 1.0
N C:GLY134 4.9 45.4 1.0

Iron binding site 6 out of 16 in 6q93

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Iron binding site 6 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
C:Fe1001

b:45.4
occ:1.00
FE2 C:SF41001 0.0 45.4 1.0
S3 C:SF41001 2.3 43.1 1.0
SG C:CYS133 2.3 48.4 1.0
S1 C:SF41001 2.3 44.1 1.0
S4 C:SF41001 2.3 44.2 1.0
FE3 C:SF41001 2.7 43.6 1.0
FE4 C:SF41001 2.7 44.7 1.0
FE1 C:SF41001 2.7 44.5 1.0
CB C:CYS133 3.5 45.2 1.0
S2 C:SF41001 3.9 44.2 1.0
C C:CYS133 4.2 48.0 1.0
N D:ALA99 4.2 38.1 1.0
O C:CYS133 4.3 46.4 1.0
CG2 C:VAL131 4.4 42.4 1.0
CA C:CYS133 4.4 45.1 1.0
N C:GLY134 4.5 45.4 1.0
SG D:CYS98 4.5 42.9 1.0
CA D:CYS98 4.7 40.5 1.0
SG C:CYS98 4.7 43.5 1.0
CB D:ALA99 4.8 37.7 1.0
SG D:CYS133 4.9 42.3 1.0
CB C:VAL131 4.9 44.0 1.0
CA C:GLY134 4.9 44.3 1.0
C D:CYS98 4.9 41.8 1.0
N C:CYS133 5.0 43.9 1.0

Iron binding site 7 out of 16 in 6q93

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Iron binding site 7 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
C:Fe1001

b:43.6
occ:1.00
FE3 C:SF41001 0.0 43.6 1.0
SG D:CYS98 2.2 42.9 1.0
S2 C:SF41001 2.2 44.2 1.0
S4 C:SF41001 2.3 44.2 1.0
S1 C:SF41001 2.3 44.1 1.0
FE2 C:SF41001 2.7 45.4 1.0
FE4 C:SF41001 2.7 44.7 1.0
FE1 C:SF41001 2.7 44.5 1.0
CB D:CYS98 3.3 40.2 1.0
CA D:CYS98 3.7 40.5 1.0
S3 C:SF41001 3.9 43.1 1.0
N D:ALA99 4.1 38.1 1.0
C D:CYS98 4.2 41.8 1.0
SG C:CYS133 4.5 48.4 1.0
CA D:GLY134 4.5 37.5 1.0
N D:GLY100 4.6 39.6 1.0
SG D:CYS133 4.8 42.3 1.0
N D:GLY134 4.8 38.2 1.0
SG C:CYS98 4.9 43.5 1.0

Iron binding site 8 out of 16 in 6q93

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Iron binding site 8 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
C:Fe1001

b:44.7
occ:1.00
FE4 C:SF41001 0.0 44.7 1.0
S1 C:SF41001 2.3 44.1 1.0
SG D:CYS133 2.3 42.3 1.0
S2 C:SF41001 2.3 44.2 1.0
S3 C:SF41001 2.3 43.1 1.0
FE3 C:SF41001 2.7 43.6 1.0
FE1 C:SF41001 2.7 44.5 1.0
FE2 C:SF41001 2.7 45.4 1.0
CB D:CYS133 3.4 39.0 1.0
S4 C:SF41001 3.9 44.2 1.0
N C:ALA99 4.1 40.0 1.0
C D:CYS133 4.1 41.6 1.0
O D:CYS133 4.2 41.9 1.0
CA D:CYS133 4.4 38.2 1.0
CG2 D:VAL131 4.4 47.0 1.0
N D:GLY134 4.4 38.2 1.0
CB C:ALA99 4.6 40.0 1.0
SG C:CYS98 4.6 43.5 1.0
CA C:CYS98 4.7 40.6 1.0
SG D:CYS98 4.7 42.9 1.0
CB D:VAL131 4.8 47.4 1.0
SG C:CYS133 4.9 48.4 1.0
C C:CYS98 4.9 44.3 1.0
N D:CYS133 4.9 37.8 1.0
CA D:GLY134 5.0 37.5 1.0
CA C:ALA99 5.0 39.8 1.0

Iron binding site 9 out of 16 in 6q93

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Iron binding site 9 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
E:Fe1001

b:46.9
occ:1.00
FE1 E:SF41001 0.0 46.9 1.0
S4 E:SF41001 2.3 45.9 1.0
S3 E:SF41001 2.3 47.4 1.0
S2 E:SF41001 2.3 47.8 1.0
SG E:CYS98 2.4 50.4 1.0
FE2 E:SF41001 2.7 47.5 1.0
FE4 E:SF41001 2.8 50.0 1.0
FE3 E:SF41001 2.8 46.4 1.0
CB E:CYS98 3.4 47.7 1.0
CA E:CYS98 3.7 49.2 1.0
S1 E:SF41001 3.9 48.6 1.0
N E:ALA99 4.1 49.1 1.0
C E:CYS98 4.2 52.9 1.0
CA E:GLY134 4.5 45.3 1.0
N E:GLY100 4.6 43.6 1.0
SG F:CYS133 4.6 53.0 1.0
O E:HOH1129 4.6 71.9 1.0
SG E:CYS133 4.7 51.2 1.0
N E:GLY134 4.8 47.0 1.0
SG F:CYS98 5.0 49.8 1.0

Iron binding site 10 out of 16 in 6q93

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Iron binding site 10 out of 16 in the Mgadp-Bound Fe Protein of Vanadium Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
E:Fe1001

b:47.5
occ:1.00
FE2 E:SF41001 0.0 47.5 1.0
SG E:CYS133 2.2 51.2 1.0
S3 E:SF41001 2.3 47.4 1.0
S4 E:SF41001 2.3 45.9 1.0
S1 E:SF41001 2.3 48.6 1.0
FE1 E:SF41001 2.7 46.9 1.0
FE3 E:SF41001 2.7 46.4 1.0
FE4 E:SF41001 2.7 50.0 1.0
CB E:CYS133 3.4 46.7 1.0
S2 E:SF41001 3.9 47.8 1.0
CG1 E:VAL131 4.0 53.2 1.0
C E:CYS133 4.2 51.5 1.0
N F:ALA99 4.3 46.9 1.0
O E:CYS133 4.3 52.3 1.0
CA E:CYS133 4.4 45.8 1.0
N E:GLY134 4.4 47.0 1.0
CB F:ALA99 4.7 45.7 1.0
SG F:CYS98 4.7 49.8 1.0
CG2 E:VAL131 4.7 54.6 1.0
CA F:CYS98 4.8 46.9 1.0
SG E:CYS98 4.9 50.4 1.0
CA E:GLY134 4.9 45.3 1.0
N E:CYS133 4.9 45.8 1.0
CB E:VAL131 5.0 54.6 1.0
SG F:CYS133 5.0 53.0 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: Sun Dec 13 16:50:30 2020

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