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Iron in PDB 1fp6: The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp

Enzymatic activity of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp

All present enzymatic activity of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp:
1.18.6.1;

Protein crystallography data

The structure of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp, PDB code: 1fp6 was solved by S.B.Jang, L.C.Seefeldt, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.250, 119.530, 120.940, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.8

Other elements in 1fp6:

The structure of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp (pdb code 1fp6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp, PDB code: 1fp6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1fp6

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Iron binding site 1 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5290

b:29.5
occ:1.00
 FE1 A:SF45290 0.0 29.5 1.0
SG B:CYS97 2.1 30.2 1.0
S3 A:SF45290 2.3 31.8 1.0
S4 A:SF45290 2.3 30.1 1.0
S2 A:SF45290 2.3 32.3 1.0
FE4 A:SF45290 2.6 29.7 1.0
FE2 A:SF45290 2.7 29.1 1.0
FE3 A:SF45290 2.7 30.5 1.0
CB B:CYS97 3.2 27.4 1.0
CA B:CYS97 3.6 32.2 1.0
S1 A:SF45290 3.9 29.6 1.0
N B:ALA98 4.1 29.3 1.0
C B:CYS97 4.2 31.5 1.0
SG A:CYS132 4.2 30.8 1.0
O B:HOH6481 4.4 46.8 1.0
CA B:GLY133 4.5 29.6 1.0
N B:GLY99 4.7 29.8 1.0
SG B:CYS132 4.7 33.3 1.0
N B:GLY133 4.7 32.4 1.0
SG A:CYS97 4.8 29.8 1.0
N B:CYS97 5.0 32.2 1.0

Iron binding site 2 out of 8 in 1fp6

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Iron binding site 2 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5290

b:29.1
occ:1.00
 FE2 A:SF45290 0.0 29.1 1.0
S4 A:SF45290 2.2 30.1 1.0
SG A:CYS97 2.3 29.8 1.0
S3 A:SF45290 2.3 31.8 1.0
S1 A:SF45290 2.3 29.6 1.0
FE4 A:SF45290 2.6 29.7 1.0
FE3 A:SF45290 2.7 30.5 1.0
FE1 A:SF45290 2.7 29.5 1.0
CB A:CYS97 3.4 26.5 1.0
CA A:CYS97 3.8 28.2 1.0
S2 A:SF45290 3.9 32.3 1.0
N A:ALA98 4.2 25.1 1.0
C A:CYS97 4.3 26.3 1.0
CA A:GLY133 4.3 29.5 1.0
SG B:CYS132 4.4 33.3 1.0
N A:GLY133 4.6 29.1 1.0
SG A:CYS132 4.6 30.8 1.0
O A:HOH5564 4.6 60.9 1.0
N A:GLY99 4.6 32.3 1.0
SG B:CYS97 4.6 30.2 1.0

Iron binding site 3 out of 8 in 1fp6

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Iron binding site 3 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5290

b:30.5
occ:1.00
 FE3 A:SF45290 0.0 30.5 1.0
SG A:CYS132 2.1 30.8 1.0
S1 A:SF45290 2.3 29.6 1.0
S4 A:SF45290 2.3 30.1 1.0
S2 A:SF45290 2.3 32.3 1.0
FE2 A:SF45290 2.7 29.1 1.0
FE1 A:SF45290 2.7 29.5 1.0
FE4 A:SF45290 2.7 29.7 1.0
CB A:CYS132 3.5 28.4 1.0
CG1 A:VAL130 3.7 27.6 1.0
N A:GLY133 3.9 29.1 1.0
S3 A:SF45290 3.9 31.8 1.0
C A:CYS132 4.2 30.3 1.0
N B:ALA98 4.2 29.3 1.0
CA A:CYS132 4.3 28.5 1.0
SG B:CYS97 4.5 30.2 1.0
CA A:GLY133 4.5 29.5 1.0
CA B:CYS97 4.6 32.2 1.0
CB B:ALA98 4.7 28.9 1.0
SG A:CYS97 4.7 29.8 1.0
N A:CYS132 4.8 28.5 1.0
SG B:CYS132 4.8 33.3 1.0
C B:CYS97 4.9 31.5 1.0

Iron binding site 4 out of 8 in 1fp6

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Iron binding site 4 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5290

b:29.7
occ:1.00
 FE4 A:SF45290 0.0 29.7 1.0
SG B:CYS132 2.2 33.3 1.0
S2 A:SF45290 2.3 32.3 1.0
S3 A:SF45290 2.3 31.8 1.0
S1 A:SF45290 2.3 29.6 1.0
FE1 A:SF45290 2.6 29.5 1.0
FE2 A:SF45290 2.6 29.1 1.0
FE3 A:SF45290 2.7 30.5 1.0
CB B:CYS132 3.5 30.8 1.0
S4 A:SF45290 3.9 30.1 1.0
CG1 B:VAL130 4.1 26.0 1.0
N B:GLY133 4.1 32.4 1.0
N A:ALA98 4.4 25.1 1.0
C B:CYS132 4.4 36.0 1.0
CA B:CYS132 4.4 33.4 1.0
SG B:CYS97 4.5 30.2 1.0
SG A:CYS97 4.6 29.8 1.0
SG A:CYS132 4.6 30.8 1.0
CB A:ALA98 4.7 27.2 1.0
CA B:GLY133 4.7 29.6 1.0
CA A:CYS97 4.8 28.2 1.0
N B:CYS132 4.9 31.3 1.0
CG2 B:VAL130 4.9 25.3 1.0
CD1 B:PHE135 5.0 26.1 1.0

Iron binding site 5 out of 8 in 1fp6

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Iron binding site 5 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe7290

b:30.1
occ:1.00
 FE1 C:SF47290 0.0 30.1 1.0
SG D:CYS97 2.2 34.8 1.0
S3 C:SF47290 2.3 33.4 1.0
S2 C:SF47290 2.3 32.9 1.0
S4 C:SF47290 2.3 30.4 1.0
FE4 C:SF47290 2.6 29.4 1.0
FE3 C:SF47290 2.6 29.7 1.0
FE2 C:SF47290 2.7 30.6 1.0
CB D:CYS97 3.3 33.9 1.0
CA D:CYS97 3.7 32.1 1.0
S1 C:SF47290 3.9 30.8 1.0
N D:ALA98 4.0 28.7 1.0
C D:CYS97 4.2 31.0 1.0
O D:HOH8492 4.4 53.6 1.0
SG C:CYS132 4.4 37.1 1.0
SG D:CYS132 4.6 34.1 1.0
SG C:CYS97 4.6 33.3 1.0
N D:GLY99 4.6 30.7 1.0
CA D:GLY133 4.7 30.9 1.0
O D:HOH8319 4.8 38.8 1.0
N D:CYS97 5.0 30.9 1.0

Iron binding site 6 out of 8 in 1fp6

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Iron binding site 6 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe7290

b:30.6
occ:1.00
 FE2 C:SF47290 0.0 30.6 1.0
SG C:CYS97 2.1 33.3 1.0
S4 C:SF47290 2.3 30.4 1.0
S1 C:SF47290 2.3 30.8 1.0
S3 C:SF47290 2.3 33.4 1.0
FE4 C:SF47290 2.6 29.4 1.0
FE3 C:SF47290 2.6 29.7 1.0
FE1 C:SF47290 2.7 30.1 1.0
CB C:CYS97 3.3 37.1 1.0
CA C:CYS97 3.8 34.5 1.0
S2 C:SF47290 3.9 32.9 1.0
N C:ALA98 4.2 31.3 1.0
C C:CYS97 4.3 33.7 1.0
SG D:CYS132 4.4 34.1 1.0
O D:HOH8444 4.4 41.4 1.0
CA C:GLY133 4.6 31.7 1.0
SG C:CYS132 4.7 37.1 1.0
N C:GLY99 4.7 31.1 1.0
SG D:CYS97 4.7 34.8 1.0
O C:HOH7340 4.7 37.6 1.0
O D:HOH8492 4.8 53.6 1.0
N C:GLY133 4.9 33.7 1.0

Iron binding site 7 out of 8 in 1fp6

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Iron binding site 7 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe7290

b:29.7
occ:1.00
 FE3 C:SF47290 0.0 29.7 1.0
SG C:CYS132 2.2 37.1 1.0
S1 C:SF47290 2.2 30.8 1.0
S4 C:SF47290 2.3 30.4 1.0
S2 C:SF47290 2.3 32.9 1.0
FE4 C:SF47290 2.6 29.4 1.0
FE1 C:SF47290 2.6 30.1 1.0
FE2 C:SF47290 2.6 30.6 1.0
CB C:CYS132 3.4 35.2 1.0
S3 C:SF47290 3.9 33.4 1.0
C C:CYS132 4.0 35.1 1.0
O C:CYS132 4.1 33.6 1.0
N D:ALA98 4.2 28.7 1.0
CA C:CYS132 4.3 35.7 1.0
N C:GLY133 4.4 33.7 1.0
SG C:CYS97 4.5 33.3 1.0
SG D:CYS97 4.5 34.8 1.0
CG2 C:VAL130 4.6 31.2 1.0
CA D:CYS97 4.6 32.1 1.0
CB D:ALA98 4.7 23.4 1.0
SG D:CYS132 4.8 34.1 1.0
CA C:GLY133 4.8 31.7 1.0
CB C:VAL130 4.9 33.4 1.0
N C:CYS132 4.9 34.9 1.0
C D:CYS97 4.9 31.0 1.0

Iron binding site 8 out of 8 in 1fp6

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Iron binding site 8 out of 8 in the The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Nitrogenase Fe Protein From Azotobacter Vinelandii Complexed with Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe7290

b:29.4
occ:1.00
 FE4 C:SF47290 0.0 29.4 1.0
SG D:CYS132 2.2 34.1 1.0
S2 C:SF47290 2.3 32.9 1.0
S1 C:SF47290 2.3 30.8 1.0
S3 C:SF47290 2.3 33.4 1.0
FE1 C:SF47290 2.6 30.1 1.0
FE3 C:SF47290 2.6 29.7 1.0
FE2 C:SF47290 2.6 30.6 1.0
CB D:CYS132 3.7 32.0 1.0
S4 C:SF47290 3.8 30.4 1.0
O D:CYS132 4.2 35.1 1.0
C D:CYS132 4.2 32.0 1.0
CG2 D:VAL130 4.4 28.0 1.0
N C:ALA98 4.4 31.3 1.0
SG C:CYS97 4.4 33.3 1.0
CA D:CYS132 4.5 29.5 1.0
SG D:CYS97 4.6 34.8 1.0
N D:GLY133 4.6 30.5 1.0
SG C:CYS132 4.7 37.1 1.0
CA C:CYS97 4.8 34.5 1.0
CB D:VAL130 4.8 29.7 1.0
CB C:ALA98 4.9 28.3 1.0
CA D:GLY133 5.0 30.9 1.0

Reference:

S.B.Jang, L.C.Seefeldt, J.W.Peters. Insights Into Nucleotide Signal Transduction in Nitrogenase: Structure of An Iron Protein with Mgadp Bound. Biochemistry V. 39 14745 2000.
ISSN: ISSN 0006-2960
PubMed: 11101289
DOI: 10.1021/BI001705G
Page generated: Sat Aug 3 05:11:21 2024

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