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Iron 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:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 7qqa

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Iron binding site 1 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:22.1
occ:1.00
 FE1 A:SF4303 0.0 22.1 1.0
SG A:CYS132 2.2 21.6 1.0
S4 A:SF4303 2.3 24.9 1.0
S2 A:SF4303 2.3 20.8 1.0
S3 A:SF4303 2.3 22.2 1.0
FE4 A:SF4303 2.6 21.1 1.0
FE2 A:SF4303 2.7 21.8 1.0
FE3 A:SF4303 2.8 22.3 1.0
CB A:CYS132 3.5 20.2 1.0
S1 A:SF4303 3.9 21.8 1.0
CG2 A:VAL130 4.0 21.8 1.0
C A:CYS132 4.1 23.1 1.0
O A:CYS132 4.3 24.6 1.0
N B:ALA98 4.3 22.9 1.0
CA A:CYS132 4.3 21.5 1.0
N A:GLY133 4.4 23.0 1.0
SG B:CYS97 4.5 24.7 1.0
CA B:CYS97 4.6 23.9 1.0
CB A:VAL130 4.7 20.3 1.0
SG A:CYS97 4.7 20.1 1.0
SG B:CYS132 4.8 27.9 1.0
CB B:CYS97 4.8 23.9 1.0
N A:CYS132 4.9 22.9 1.0
CB B:ALA98 4.9 23.1 1.0
CA A:GLY133 4.9 21.2 1.0
C B:CYS97 5.0 23.8 1.0

Iron binding site 2 out of 8 in 7qqa

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Iron binding site 2 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:21.8
occ:1.00
 FE2 A:SF4303 0.0 21.8 1.0
SG A:CYS97 2.3 20.1 1.0
S3 A:SF4303 2.3 22.2 1.0
S4 A:SF4303 2.3 24.9 1.0
S1 A:SF4303 2.3 21.8 1.0
FE3 A:SF4303 2.7 22.3 1.0
FE1 A:SF4303 2.7 22.1 1.0
FE4 A:SF4303 2.8 21.1 1.0
CB A:CYS97 3.2 21.4 1.0
CA A:CYS97 3.7 23.6 1.0
S2 A:SF4303 3.9 20.8 1.0
N A:ALA98 4.1 21.7 1.0
C A:CYS97 4.2 22.4 1.0
SG B:CYS132 4.4 27.9 1.0
CA A:GLY133 4.5 21.2 1.0
N A:GLY99 4.6 20.1 1.0
O C:HOH525 4.7 39.5 1.0
SG A:CYS132 4.7 21.6 1.0
N A:GLY133 4.8 23.0 1.0
O C:HOH530 4.8 19.9 1.0
SG B:CYS97 5.0 24.7 1.0

Iron binding site 3 out of 8 in 7qqa

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Iron binding site 3 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:22.3
occ:1.00
 FE3 A:SF4303 0.0 22.3 1.0
SG B:CYS132 2.2 27.9 1.0
S4 A:SF4303 2.3 24.9 1.0
S2 A:SF4303 2.3 20.8 1.0
S1 A:SF4303 2.3 21.8 1.0
FE2 A:SF4303 2.7 21.8 1.0
FE4 A:SF4303 2.7 21.1 1.0
FE1 A:SF4303 2.8 22.1 1.0
CB B:CYS132 3.4 27.3 1.0
S3 A:SF4303 3.9 22.2 1.0
C B:CYS132 4.1 30.2 1.0
CG2 B:VAL130 4.2 22.9 1.0
N A:ALA98 4.2 21.7 1.0
O B:CYS132 4.3 29.3 1.0
CA B:CYS132 4.3 28.5 1.0
N B:GLY133 4.4 31.3 1.0
SG A:CYS97 4.5 20.1 1.0
CA A:CYS97 4.6 23.6 1.0
CB A:ALA98 4.8 21.6 1.0
SG B:CYS97 4.8 24.7 1.0
CB B:VAL130 4.9 22.5 1.0
SG A:CYS132 4.9 21.6 1.0
N B:CYS132 4.9 25.4 1.0
CA B:GLY133 4.9 31.7 1.0
C A:CYS97 5.0 22.4 1.0
CB A:CYS97 5.0 21.4 1.0

Iron binding site 4 out of 8 in 7qqa

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Iron binding site 4 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:21.1
occ:1.00
 FE4 A:SF4303 0.0 21.1 1.0
S1 A:SF4303 2.3 21.8 1.0
S3 A:SF4303 2.3 22.2 1.0
SG B:CYS97 2.3 24.7 1.0
S2 A:SF4303 2.3 20.8 1.0
FE1 A:SF4303 2.6 22.1 1.0
FE3 A:SF4303 2.7 22.3 1.0
FE2 A:SF4303 2.8 21.8 1.0
CB B:CYS97 3.2 23.9 1.0
O C:HOH592 3.6 33.3 1.0
CA B:CYS97 3.8 23.9 1.0
S4 A:SF4303 3.9 24.9 1.0
N B:ALA98 4.2 22.9 1.0
SG A:CYS132 4.2 21.6 1.0
C B:CYS97 4.3 23.8 1.0
CA B:GLY133 4.5 31.7 1.0
SG B:CYS132 4.7 27.9 1.0
N B:GLY99 4.7 23.9 1.0
N B:GLY133 4.8 31.3 1.0
O C:HOH525 4.9 39.5 1.0
SG A:CYS97 4.9 20.1 1.0

Iron binding site 5 out of 8 in 7qqa

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Iron binding site 5 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe303

b:19.4
occ:1.00
 FE1 C:SF4303 0.0 19.4 1.0
SG D:CYS132 2.2 24.6 1.0
S4 C:SF4303 2.3 19.8 1.0
S2 C:SF4303 2.3 18.6 1.0
S3 C:SF4303 2.3 19.6 1.0
FE2 C:SF4303 2.6 19.9 1.0
FE3 C:SF4303 2.7 18.7 1.0
FE4 C:SF4303 2.8 17.1 1.0
CB D:CYS132 3.3 22.0 1.0
S1 C:SF4303 3.9 18.5 1.0
N C:ALA98 4.2 17.3 1.0
CG2 D:VAL130 4.3 26.2 1.0
CB C:ALA98 4.4 21.0 1.0
C D:CYS132 4.4 24.0 1.0
CA D:CYS132 4.5 23.9 1.0
O D:CYS132 4.6 28.0 1.0
SG D:CYS97 4.6 19.4 1.0
N D:GLY133 4.7 22.2 1.0
SG C:CYS97 4.8 19.7 1.0
SG C:CYS132 4.8 19.0 1.0
CD2 D:PHE135 4.8 17.4 1.0
CA C:CYS97 4.9 21.8 1.0
CA C:ALA98 4.9 19.5 1.0
CE2 D:PHE135 5.0 18.6 1.0

Iron binding site 6 out of 8 in 7qqa

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Iron binding site 6 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe303

b:19.9
occ:1.00
 FE2 C:SF4303 0.0 19.9 1.0
S3 C:SF4303 2.3 19.6 1.0
S4 C:SF4303 2.3 19.8 1.0
S1 C:SF4303 2.3 18.5 1.0
SG D:CYS97 2.3 19.4 1.0
FE1 C:SF4303 2.6 19.4 1.0
FE3 C:SF4303 2.7 18.7 1.0
FE4 C:SF4303 2.7 17.1 1.0
CB D:CYS97 3.3 19.6 1.0
CA D:CYS97 3.6 21.9 1.0
S2 C:SF4303 3.9 18.6 1.0
N D:ALA98 4.0 18.7 1.0
C D:CYS97 4.1 20.7 1.0
N D:GLY99 4.5 22.3 1.0
SG D:CYS132 4.5 24.6 1.0
SG C:CYS132 4.8 19.0 1.0
CB C:CYS132 4.9 20.9 1.0
N D:CYS97 4.9 25.0 1.0
CA D:GLY133 5.0 20.9 1.0
SG C:CYS97 5.0 19.7 1.0
O D:HOH484 5.0 29.2 1.0

Iron binding site 7 out of 8 in 7qqa

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Iron binding site 7 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe303

b:18.7
occ:1.00
 FE3 C:SF4303 0.0 18.7 1.0
S4 C:SF4303 2.3 19.8 1.0
S2 C:SF4303 2.3 18.6 1.0
S1 C:SF4303 2.3 18.5 1.0
SG C:CYS132 2.3 19.0 1.0
FE2 C:SF4303 2.7 19.9 1.0
FE4 C:SF4303 2.7 17.1 1.0
FE1 C:SF4303 2.7 19.4 1.0
CB C:CYS132 3.2 20.9 1.0
S3 C:SF4303 3.9 19.6 1.0
N C:GLY134 4.1 24.3 1.0
CA C:GLY134 4.1 24.9 1.0
CG2 C:VAL130 4.3 24.1 1.0
CA C:CYS132 4.5 24.5 1.0
N D:ALA98 4.5 18.7 1.0
SG C:CYS97 4.7 19.7 1.0
SG D:CYS132 4.7 24.6 1.0
SG D:CYS97 4.8 19.4 1.0
CD2 C:PHE135 4.8 18.5 1.0
CA D:CYS97 4.8 21.9 1.0
C C:CYS132 4.9 26.8 1.0
N C:GLY133 5.0 24.5 1.0

Iron binding site 8 out of 8 in 7qqa

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Iron binding site 8 out of 8 in the Mgadp-Bound Fe Protein of the Iron-Only 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 the Iron-Only Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe303

b:17.1
occ:1.00
 FE4 C:SF4303 0.0 17.1 1.0
S1 C:SF4303 2.2 18.5 1.0
S3 C:SF4303 2.3 19.6 1.0
S2 C:SF4303 2.3 18.6 1.0
SG C:CYS97 2.3 19.7 1.0
FE3 C:SF4303 2.7 18.7 1.0
FE2 C:SF4303 2.7 19.9 1.0
FE1 C:SF4303 2.8 19.4 1.0
CB C:CYS97 3.4 21.7 1.0
CA C:CYS97 3.6 21.8 1.0
N C:ALA98 3.9 17.3 1.0
S4 C:SF4303 3.9 19.8 1.0
CA C:GLY134 4.0 24.9 1.0
C C:CYS97 4.1 19.4 1.0
N C:GLY134 4.4 24.3 1.0
N C:GLY99 4.5 17.8 1.0
SG D:CYS132 4.5 24.6 1.0
SG C:CYS132 4.6 19.0 1.0
SG D:CYS97 4.9 19.4 1.0
CB D:CYS132 4.9 22.0 1.0
N C:CYS97 4.9 23.2 1.0
CA C:ALA98 5.0 19.5 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 Aug 8 19:52:48 2024

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