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Iron in PDB 5c2v: Kuenenia Stuttgartiensis Hydrazine Synthase

Protein crystallography data

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase, PDB code: 5c2v was solved by A.Dietl, C.Ferousi, W.J.Maalcke, A.Menzel, S.De Vries, J.T.Keltjens, M.S.M.Jetten, B.Kartal, T.R.M.Barends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.70
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 464.540, 464.540, 145.750, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 27.1

Other elements in 5c2v:

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Calcium (Ca) 12 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Kuenenia Stuttgartiensis Hydrazine Synthase (pdb code 5c2v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Kuenenia Stuttgartiensis Hydrazine Synthase, PDB code: 5c2v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5c2v

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Iron binding site 1 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe905

b:43.4
occ:1.00
FE A:HEC905 0.0 43.4 1.0
OH A:TYR591 2.0 30.0 1.0
NC A:HEC905 2.1 35.0 1.0
NA A:HEC905 2.1 38.2 1.0
NB A:HEC905 2.1 40.9 1.0
ND A:HEC905 2.1 43.5 1.0
CZ A:TYR591 3.0 45.1 1.0
C4C A:HEC905 3.1 47.0 1.0
C1B A:HEC905 3.1 37.4 1.0
C4A A:HEC905 3.1 44.1 1.0
C4B A:HEC905 3.1 27.6 1.0
C1C A:HEC905 3.1 54.0 1.0
C1A A:HEC905 3.1 46.2 1.0
C1D A:HEC905 3.1 32.1 1.0
C4D A:HEC905 3.1 36.5 1.0
CHD A:HEC905 3.4 51.5 1.0
CHB A:HEC905 3.4 34.6 1.0
CHC A:HEC905 3.5 27.1 1.0
CHA A:HEC905 3.5 50.8 1.0
CE1 A:TYR591 3.7 36.7 1.0
CE2 A:TYR591 3.9 39.8 1.0
O A:HOH1123 4.1 52.2 1.0
C2B A:HEC905 4.2 39.9 1.0
C3B A:HEC905 4.3 46.5 1.0
CB A:ALA569 4.3 37.4 1.0
C3C A:HEC905 4.3 42.1 1.0
C3A A:HEC905 4.3 37.9 1.0
C2A A:HEC905 4.3 35.8 1.0
C2C A:HEC905 4.3 43.3 1.0
C2D A:HEC905 4.3 39.4 1.0
C3D A:HEC905 4.3 36.7 1.0
N A:HIS587 4.3 34.2 1.0
CA A:HIS587 4.7 41.5 1.0
CB A:HIS587 4.9 37.0 1.0
CD1 A:TYR591 5.0 38.6 1.0

Iron binding site 2 out of 8 in 5c2v

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Iron binding site 2 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe906

b:56.5
occ:1.00
FE A:HEC906 0.0 56.5 1.0
NA A:HEC906 2.0 52.5 1.0
NB A:HEC906 2.1 58.6 1.0
NC A:HEC906 2.1 54.6 1.0
ND A:HEC906 2.1 59.7 1.0
NE2 A:HIS689 2.1 35.9 1.0
NE2 A:HIS772 2.1 41.7 1.0
CE1 A:HIS689 2.9 49.9 1.0
CD2 A:HIS772 2.9 57.9 1.0
C1A A:HEC906 3.1 58.8 1.0
C4B A:HEC906 3.1 61.5 1.0
C4C A:HEC906 3.1 63.6 1.0
C1B A:HEC906 3.1 58.3 1.0
C1C A:HEC906 3.1 63.9 1.0
C4A A:HEC906 3.1 50.7 1.0
C4D A:HEC906 3.1 54.0 1.0
C1D A:HEC906 3.1 72.2 1.0
CE1 A:HIS772 3.2 56.7 1.0
CD2 A:HIS689 3.2 53.3 1.0
CHA A:HEC906 3.4 50.2 1.0
CHD A:HEC906 3.4 69.2 1.0
CHC A:HEC906 3.4 69.9 1.0
CHB A:HEC906 3.4 46.0 1.0
ND1 A:HIS689 4.1 60.1 1.0
CG A:HIS772 4.1 56.1 1.0
ND1 A:HIS772 4.2 50.9 1.0
C2A A:HEC906 4.3 46.2 1.0
CG A:HIS689 4.3 54.8 1.0
C3B A:HEC906 4.3 58.6 1.0
C2B A:HEC906 4.3 61.7 1.0
C2C A:HEC906 4.3 68.8 1.0
C3A A:HEC906 4.3 51.1 1.0
C3C A:HEC906 4.3 76.7 1.0
C3D A:HEC906 4.3 65.8 1.0
C2D A:HEC906 4.3 67.4 1.0
CE2 A:PHE775 5.0 66.0 1.0

Iron binding site 3 out of 8 in 5c2v

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Iron binding site 3 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe404

b:42.8
occ:1.00
FE C:HEC404 0.0 42.8 1.0
NE2 C:HIS106 2.0 48.9 1.0
NA C:HEC404 2.1 52.3 1.0
NC C:HEC404 2.1 53.1 1.0
NB C:HEC404 2.1 36.0 1.0
ND C:HEC404 2.1 26.8 1.0
O C:HOH564 2.1 37.1 1.0
CE1 C:HIS106 2.8 51.6 1.0
C1B C:HEC404 3.0 42.4 1.0
C4B C:HEC404 3.1 54.5 1.0
C4A C:HEC404 3.1 49.5 1.0
C1D C:HEC404 3.1 45.1 1.0
C4D C:HEC404 3.1 50.1 1.0
C4C C:HEC404 3.1 41.1 1.0
C1A C:HEC404 3.1 42.9 1.0
C1C C:HEC404 3.1 39.0 1.0
CD2 C:HIS106 3.1 45.2 1.0
CHB C:HEC404 3.4 64.7 1.0
CHD C:HEC404 3.4 51.7 1.0
CHA C:HEC404 3.4 53.2 1.0
CHC C:HEC404 3.5 42.5 1.0
ND1 C:HIS106 4.0 39.3 1.0
OD2 C:ASP168 4.2 54.9 1.0
CG C:HIS106 4.2 48.9 1.0
C2B C:HEC404 4.2 43.3 1.0
C3B C:HEC404 4.2 52.0 1.0
C2D C:HEC404 4.3 43.5 1.0
C3D C:HEC404 4.3 34.7 1.0
C3A C:HEC404 4.3 61.5 1.0
C2C C:HEC404 4.3 41.9 1.0
C3C C:HEC404 4.3 41.8 1.0
C2A C:HEC404 4.3 60.2 1.0

Iron binding site 4 out of 8 in 5c2v

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Iron binding site 4 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe405

b:58.2
occ:1.00
FE C:HEC405 0.0 58.2 1.0
NE2 C:HIS332 2.0 39.3 1.0
NC C:HEC405 2.0 69.6 1.0
NA C:HEC405 2.0 62.9 1.0
NB C:HEC405 2.1 61.5 1.0
ND C:HEC405 2.1 51.7 1.0
NE2 C:HIS229 2.2 58.1 1.0
CD2 C:HIS229 2.9 62.3 1.0
CE1 C:HIS332 2.9 46.0 1.0
CD2 C:HIS332 3.0 44.4 1.0
C4C C:HEC405 3.1 62.5 1.0
C1B C:HEC405 3.1 62.8 1.0
C4A C:HEC405 3.1 59.5 1.0
C1A C:HEC405 3.1 63.0 1.0
C4B C:HEC405 3.1 53.5 1.0
C1D C:HEC405 3.1 63.9 1.0
C1C C:HEC405 3.1 68.6 1.0
C4D C:HEC405 3.1 59.8 1.0
CE1 C:HIS229 3.3 62.5 1.0
CHD C:HEC405 3.4 67.5 1.0
CHB C:HEC405 3.4 75.3 1.0
CHA C:HEC405 3.4 57.5 1.0
CHC C:HEC405 3.4 62.7 1.0
ND1 C:HIS332 4.0 45.5 1.0
CG C:HIS332 4.1 51.4 1.0
CG C:HIS229 4.1 66.2 1.0
C2B C:HEC405 4.3 53.7 1.0
C3B C:HEC405 4.3 67.3 1.0
C3A C:HEC405 4.3 67.3 1.0
C3C C:HEC405 4.3 70.8 1.0
C2A C:HEC405 4.3 69.1 1.0
C2C C:HEC405 4.3 68.7 1.0
ND1 C:HIS229 4.3 54.8 1.0
C2D C:HEC405 4.3 66.9 1.0
C3D C:HEC405 4.3 70.1 1.0

Iron binding site 5 out of 8 in 5c2v

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Iron binding site 5 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe905

b:48.5
occ:1.00
FE D:HEC905 0.0 48.5 1.0
NA D:HEC905 2.1 50.1 1.0
NC D:HEC905 2.1 46.9 1.0
NB D:HEC905 2.1 71.8 1.0
OH D:TYR591 2.1 45.2 1.0
ND D:HEC905 2.1 70.6 1.0
C1B D:HEC905 3.0 54.2 1.0
CZ D:TYR591 3.0 64.1 1.0
C4B D:HEC905 3.1 58.1 1.0
C4A D:HEC905 3.1 59.6 1.0
C4C D:HEC905 3.1 55.4 1.0
C1A D:HEC905 3.1 53.5 1.0
C1C D:HEC905 3.1 63.7 1.0
C1D D:HEC905 3.1 49.4 1.0
C4D D:HEC905 3.1 56.0 1.0
CHB D:HEC905 3.4 51.4 1.0
CHD D:HEC905 3.4 57.6 1.0
CHC D:HEC905 3.5 55.1 1.0
CHA D:HEC905 3.5 67.9 1.0
CE1 D:TYR591 3.8 58.7 1.0
CE2 D:TYR591 3.8 60.0 1.0
C2B D:HEC905 4.2 69.4 1.0
C3B D:HEC905 4.2 62.0 1.0
O D:HOH1083 4.3 55.6 1.0
C3C D:HEC905 4.3 52.5 1.0
C3A D:HEC905 4.3 61.4 1.0
C2A D:HEC905 4.3 53.2 1.0
CB D:ALA569 4.3 47.4 1.0
C2C D:HEC905 4.3 58.7 1.0
N D:HIS587 4.3 52.3 1.0
C2D D:HEC905 4.3 51.6 1.0
C3D D:HEC905 4.3 60.0 1.0
CA D:HIS587 4.7 47.6 1.0
CB D:HIS587 4.9 38.3 1.0

Iron binding site 6 out of 8 in 5c2v

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Iron binding site 6 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe906

b:45.3
occ:1.00
FE D:HEC906 0.0 45.3 1.0
NA D:HEC906 2.0 37.9 1.0
NC D:HEC906 2.1 46.6 1.0
NB D:HEC906 2.1 56.5 1.0
NE2 D:HIS772 2.1 38.0 1.0
ND D:HEC906 2.1 55.5 1.0
NE2 D:HIS689 2.1 46.1 1.0
CD2 D:HIS772 2.9 49.0 1.0
CE1 D:HIS689 2.9 56.9 1.0
C1A D:HEC906 3.1 51.5 1.0
C4A D:HEC906 3.1 46.0 1.0
C1B D:HEC906 3.1 49.2 1.0
C4C D:HEC906 3.1 54.6 1.0
C4B D:HEC906 3.1 47.7 1.0
C1C D:HEC906 3.1 58.6 1.0
C1D D:HEC906 3.1 49.0 1.0
C4D D:HEC906 3.1 46.6 1.0
CE1 D:HIS772 3.2 61.4 1.0
CD2 D:HIS689 3.2 61.4 1.0
CHB D:HEC906 3.4 52.3 1.0
CHA D:HEC906 3.4 38.3 1.0
CHD D:HEC906 3.4 54.0 1.0
CHC D:HEC906 3.5 58.5 1.0
ND1 D:HIS689 4.1 55.0 1.0
CG D:HIS772 4.1 46.7 1.0
ND1 D:HIS772 4.2 52.9 1.0
C2A D:HEC906 4.3 43.0 1.0
C3A D:HEC906 4.3 51.7 1.0
C2B D:HEC906 4.3 37.2 1.0
C3B D:HEC906 4.3 54.7 1.0
CG D:HIS689 4.3 60.3 1.0
C3C D:HEC906 4.3 56.3 1.0
C2C D:HEC906 4.3 57.8 1.0
C2D D:HEC906 4.3 58.0 1.0
C3D D:HEC906 4.4 62.1 1.0

Iron binding site 7 out of 8 in 5c2v

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Iron binding site 7 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe404

b:58.7
occ:1.00
FE F:HEC404 0.0 58.7 1.0
NA F:HEC404 2.1 69.7 1.0
NC F:HEC404 2.1 83.0 1.0
NE2 F:HIS106 2.1 45.2 1.0
NB F:HEC404 2.1 62.5 1.0
ND F:HEC404 2.1 51.1 1.0
O F:HOH536 2.1 37.8 1.0
CE1 F:HIS106 3.0 55.5 1.0
C1D F:HEC404 3.1 50.6 1.0
C1B F:HEC404 3.1 78.4 1.0
C4A F:HEC404 3.1 60.1 1.0
C4C F:HEC404 3.1 54.9 1.0
C4D F:HEC404 3.1 55.4 1.0
C1A F:HEC404 3.1 69.4 1.0
C4B F:HEC404 3.1 65.7 1.0
CD2 F:HIS106 3.1 54.7 1.0
C1C F:HEC404 3.1 65.4 1.0
CHD F:HEC404 3.4 54.2 1.0
CHB F:HEC404 3.4 60.7 1.0
CHA F:HEC404 3.4 66.9 1.0
CHC F:HEC404 3.5 73.5 1.0
ND1 F:HIS106 4.2 58.0 1.0
OD2 F:ASP168 4.2 68.4 1.0
CG F:HIS106 4.2 50.4 1.0
C2B F:HEC404 4.3 78.6 1.0
C2D F:HEC404 4.3 62.8 1.0
C3B F:HEC404 4.3 62.6 1.0
C3D F:HEC404 4.3 62.0 1.0
C3A F:HEC404 4.3 77.8 1.0
C3C F:HEC404 4.3 61.8 1.0
C2A F:HEC404 4.3 73.9 1.0
C2C F:HEC404 4.3 54.8 1.0
CG1 F:VAL164 4.8 77.5 1.0

Iron binding site 8 out of 8 in 5c2v

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Iron binding site 8 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe405

b:72.7
occ:1.00
FE F:HEC405 0.0 72.7 1.0
NA F:HEC405 2.0 82.7 1.0
NC F:HEC405 2.1 64.4 1.0
NB F:HEC405 2.1 70.5 1.0
ND F:HEC405 2.1 86.1 1.0
NE2 F:HIS229 2.2 74.8 1.0
NE2 F:HIS332 2.3 71.7 1.0
C1A F:HEC405 3.1 83.8 1.0
CE1 F:HIS332 3.1 61.8 1.0
C4D F:HEC405 3.1 74.0 1.0
C4A F:HEC405 3.1 81.8 1.0
C4C F:HEC405 3.1 71.2 1.0
C1D F:HEC405 3.1 86.2 1.0
C1C F:HEC405 3.1 73.0 1.0
C1B F:HEC405 3.1 74.6 1.0
C4B F:HEC405 3.1 69.8 1.0
CD2 F:HIS229 3.1 81.0 1.0
CE1 F:HIS229 3.2 78.3 1.0
CD2 F:HIS332 3.2 67.3 1.0
CHD F:HEC405 3.4 87.6 1.0
CHA F:HEC405 3.4 71.0 1.0
CHB F:HEC405 3.4 88.9 1.0
CHC F:HEC405 3.5 72.6 1.0
ND1 F:HIS332 4.1 55.0 1.0
CG F:HIS332 4.2 57.9 1.0
ND1 F:HIS229 4.3 82.1 1.0
C2A F:HEC405 4.3 86.6 1.0
C3A F:HEC405 4.3 86.0 1.0
C3D F:HEC405 4.3 82.7 1.0
C2D F:HEC405 4.3 77.3 1.0
CG F:HIS229 4.3 90.8 1.0
C2C F:HEC405 4.3 78.0 1.0
C3C F:HEC405 4.3 81.3 1.0
C2B F:HEC405 4.3 66.3 1.0
C3B F:HEC405 4.3 72.9 1.0

Reference:

A.Dietl, C.Ferousi, W.J.Maalcke, A.Menzel, S.De Vries, J.T.Keltjens, M.S.Jetten, B.Kartal, T.R.Barends. The Inner Workings of the Hydrazine Synthase Multiprotein Complex. Nature V. 527 394 2015.
ISSN: ESSN 1476-4687
PubMed: 26479033
DOI: 10.1038/NATURE15517
Page generated: Sun Dec 13 15:57:40 2020

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