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Iron in PDB 5c2w: Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon

Protein crystallography data

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon, PDB code: 5c2w 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) 48.50 / 3.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 464.120, 464.120, 145.450, 90.00, 90.00, 120.00
R / Rfree (%) 23.1 / 26.7

Other elements in 5c2w:

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Xenon (Xe) 4 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 Pressurized with 20 Bar Xenon (pdb code 5c2w). 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 Pressurized with 20 Bar Xenon, PDB code: 5c2w:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5c2w

Go back to Iron Binding Sites List in 5c2w
Iron binding site 1 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe907

b:40.9
occ:1.00
FE A:HEC907 0.0 40.9 1.0
OH A:TYR591 2.0 37.1 1.0
NA A:HEC907 2.1 52.8 1.0
NC A:HEC907 2.1 45.3 1.0
NB A:HEC907 2.1 38.6 1.0
ND A:HEC907 2.1 46.9 1.0
CZ A:TYR591 3.0 44.2 1.0
C1A A:HEC907 3.1 50.3 1.0
C1B A:HEC907 3.1 46.2 1.0
C4A A:HEC907 3.1 43.8 1.0
C4B A:HEC907 3.1 35.1 1.0
C1D A:HEC907 3.1 48.1 1.0
C4D A:HEC907 3.1 48.9 1.0
C4C A:HEC907 3.1 39.1 1.0
C1C A:HEC907 3.1 50.1 1.0
CHA A:HEC907 3.4 51.4 1.0
CHD A:HEC907 3.4 44.3 1.0
CHB A:HEC907 3.4 50.9 1.0
CHC A:HEC907 3.5 36.9 1.0
CE1 A:TYR591 3.8 46.9 1.0
CE2 A:TYR591 3.8 46.3 1.0
XE A:XE901 4.2 0.4 1.0
C2B A:HEC907 4.3 50.1 1.0
C3B A:HEC907 4.3 46.3 1.0
C2A A:HEC907 4.3 48.7 1.0
C3A A:HEC907 4.3 47.8 1.0
C2C A:HEC907 4.3 55.1 1.0
C2D A:HEC907 4.3 38.3 1.0
C3D A:HEC907 4.3 43.6 1.0
C3C A:HEC907 4.3 46.7 1.0
N A:HIS587 4.3 34.7 1.0
CB A:ALA569 4.4 47.0 1.0
CA A:HIS587 4.7 41.5 1.0
CB A:HIS587 5.0 45.8 1.0
CD1 A:TYR591 5.0 44.0 1.0

Iron binding site 2 out of 8 in 5c2w

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Iron binding site 2 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:53.7
occ:1.00
FE A:HEC908 0.0 53.7 1.0
NE2 A:HIS689 2.0 52.9 1.0
NA A:HEC908 2.0 56.8 1.0
NB A:HEC908 2.1 48.7 1.0
NC A:HEC908 2.1 57.0 1.0
ND A:HEC908 2.1 60.8 1.0
NE2 A:HIS772 2.2 52.6 1.0
CE1 A:HIS689 2.9 55.5 1.0
CD2 A:HIS772 2.9 54.3 1.0
C1A A:HEC908 3.1 54.5 1.0
C4A A:HEC908 3.1 57.5 1.0
C4D A:HEC908 3.1 60.3 1.0
C1D A:HEC908 3.1 68.9 1.0
C4C A:HEC908 3.1 59.1 1.0
C1B A:HEC908 3.1 50.1 1.0
C4B A:HEC908 3.1 60.0 1.0
C1C A:HEC908 3.1 63.3 1.0
CD2 A:HIS689 3.1 64.7 1.0
CE1 A:HIS772 3.3 58.3 1.0
CHA A:HEC908 3.4 56.5 1.0
CHD A:HEC908 3.4 67.3 1.0
CHB A:HEC908 3.4 49.9 1.0
CHC A:HEC908 3.5 65.9 1.0
ND1 A:HIS689 4.1 56.7 1.0
CG A:HIS772 4.2 64.4 1.0
CG A:HIS689 4.2 68.2 1.0
C2A A:HEC908 4.3 47.3 1.0
C3A A:HEC908 4.3 52.9 1.0
ND1 A:HIS772 4.3 61.0 1.0
C2B A:HEC908 4.3 60.0 1.0
C3B A:HEC908 4.3 57.5 1.0
C3C A:HEC908 4.3 68.2 1.0
C2C A:HEC908 4.3 69.5 1.0
C3D A:HEC908 4.3 57.5 1.0
C2D A:HEC908 4.3 65.2 1.0

Iron binding site 3 out of 8 in 5c2w

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Iron binding site 3 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe404

b:49.6
occ:1.00
FE C:HEC404 0.0 49.6 1.0
NA C:HEC404 2.0 61.0 1.0
NB C:HEC404 2.1 54.6 1.0
NC C:HEC404 2.1 49.7 1.0
O C:HOH552 2.1 42.8 1.0
ND C:HEC404 2.1 39.1 1.0
NE2 C:HIS106 2.2 47.0 1.0
CE1 C:HIS106 3.0 54.3 1.0
C1B C:HEC404 3.0 58.5 1.0
C4A C:HEC404 3.0 71.4 1.0
C1D C:HEC404 3.1 53.6 1.0
C4D C:HEC404 3.1 38.0 1.0
C4B C:HEC404 3.1 54.0 1.0
C4C C:HEC404 3.1 43.9 1.0
C1A C:HEC404 3.1 69.2 1.0
C1C C:HEC404 3.1 51.2 1.0
CD2 C:HIS106 3.3 48.0 1.0
CHB C:HEC404 3.4 68.5 1.0
CHD C:HEC404 3.4 52.5 1.0
CHA C:HEC404 3.4 64.4 1.0
CHC C:HEC404 3.5 53.2 1.0
OD2 C:ASP168 4.1 60.4 1.0
ND1 C:HIS106 4.2 68.8 1.0
C2B C:HEC404 4.2 62.2 1.0
C3B C:HEC404 4.3 52.8 1.0
C3A C:HEC404 4.3 62.7 1.0
C2D C:HEC404 4.3 50.9 1.0
C3D C:HEC404 4.3 39.4 1.0
C2A C:HEC404 4.3 61.4 1.0
C3C C:HEC404 4.3 50.7 1.0
C2C C:HEC404 4.3 48.6 1.0
CG C:HIS106 4.3 59.7 1.0
CG1 C:VAL164 5.0 54.1 1.0

Iron binding site 4 out of 8 in 5c2w

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Iron binding site 4 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe405

b:65.4
occ:1.00
FE C:HEC405 0.0 65.4 1.0
NE2 C:HIS332 2.0 48.7 1.0
NC C:HEC405 2.0 77.3 1.0
NA C:HEC405 2.0 62.1 1.0
ND C:HEC405 2.1 64.1 1.0
NB C:HEC405 2.1 67.1 1.0
NE2 C:HIS229 2.2 56.7 1.0
CE1 C:HIS332 2.9 58.0 1.0
CD2 C:HIS229 2.9 59.5 1.0
C4D C:HEC405 3.0 73.2 1.0
C4C C:HEC405 3.0 75.6 1.0
C1D C:HEC405 3.0 69.5 1.0
C1A C:HEC405 3.1 67.5 1.0
C4A C:HEC405 3.1 71.2 1.0
C1C C:HEC405 3.1 73.8 1.0
C1B C:HEC405 3.1 69.3 1.0
C4B C:HEC405 3.1 59.3 1.0
CD2 C:HIS332 3.1 56.2 1.0
CE1 C:HIS229 3.4 62.9 1.0
CHD C:HEC405 3.4 55.8 1.0
CHA C:HEC405 3.4 74.0 1.0
CHB C:HEC405 3.4 75.3 1.0
CHC C:HEC405 3.5 68.2 1.0
ND1 C:HIS332 4.0 60.5 1.0
CG C:HIS332 4.2 57.3 1.0
CG C:HIS229 4.2 63.1 1.0
C3D C:HEC405 4.3 73.9 1.0
C2D C:HEC405 4.3 72.6 1.0
C3C C:HEC405 4.3 79.1 1.0
C2A C:HEC405 4.3 76.8 1.0
C2C C:HEC405 4.3 71.0 1.0
C3A C:HEC405 4.3 73.5 1.0
C2B C:HEC405 4.3 67.6 1.0
C3B C:HEC405 4.3 74.7 1.0
ND1 C:HIS229 4.4 62.6 1.0

Iron binding site 5 out of 8 in 5c2w

Go back to Iron Binding Sites List in 5c2w
Iron binding site 5 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe907

b:62.3
occ:1.00
FE D:HEC907 0.0 62.3 1.0
NA D:HEC907 2.1 64.3 1.0
NB D:HEC907 2.1 76.5 1.0
NC D:HEC907 2.1 63.8 1.0
OH D:TYR591 2.1 56.3 1.0
ND D:HEC907 2.1 73.4 1.0
C1B D:HEC907 3.0 82.3 1.0
C4B D:HEC907 3.0 77.7 1.0
CZ D:TYR591 3.1 70.3 1.0
C1A D:HEC907 3.1 68.6 1.0
C1C D:HEC907 3.1 65.5 1.0
C4A D:HEC907 3.1 69.3 1.0
C4C D:HEC907 3.1 61.2 1.0
C4D D:HEC907 3.1 75.4 1.0
C1D D:HEC907 3.1 58.1 1.0
CHC D:HEC907 3.4 74.0 1.0
CHB D:HEC907 3.4 75.2 1.0
CHA D:HEC907 3.4 81.9 1.0
CHD D:HEC907 3.5 57.5 1.0
CE1 D:TYR591 3.8 82.5 1.0
CE2 D:TYR591 3.9 62.9 1.0
C2B D:HEC907 4.2 80.5 1.0
C3B D:HEC907 4.2 74.1 1.0
C2A D:HEC907 4.3 62.1 1.0
C3A D:HEC907 4.3 70.4 1.0
C2C D:HEC907 4.3 61.6 1.0
XE D:XE901 4.3 1.0 1.0
C3C D:HEC907 4.3 66.4 1.0
N D:HIS587 4.3 41.4 1.0
C3D D:HEC907 4.3 55.5 1.0
C2D D:HEC907 4.3 51.8 1.0
CB D:ALA569 4.4 51.4 1.0
CA D:HIS587 4.6 48.5 1.0
CB D:HIS587 4.8 50.0 1.0
CD2 D:HIS587 5.0 47.7 1.0

Iron binding site 6 out of 8 in 5c2w

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Iron binding site 6 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe908

b:51.1
occ:1.00
FE D:HEC908 0.0 51.1 1.0
NA D:HEC908 2.0 44.7 1.0
NC D:HEC908 2.1 60.0 1.0
ND D:HEC908 2.1 62.4 1.0
NB D:HEC908 2.1 51.2 1.0
NE2 D:HIS689 2.1 52.3 1.0
NE2 D:HIS772 2.1 51.9 1.0
CD2 D:HIS772 2.9 55.5 1.0
CE1 D:HIS689 2.9 60.9 1.0
C1A D:HEC908 3.0 58.0 1.0
C4A D:HEC908 3.1 43.9 1.0
C1D D:HEC908 3.1 67.1 1.0
C4D D:HEC908 3.1 64.9 1.0
C4C D:HEC908 3.1 59.2 1.0
C1B D:HEC908 3.1 48.9 1.0
C4B D:HEC908 3.1 59.2 1.0
C1C D:HEC908 3.1 64.3 1.0
CD2 D:HIS689 3.2 62.6 1.0
CE1 D:HIS772 3.3 57.8 1.0
CHA D:HEC908 3.4 63.1 1.0
CHD D:HEC908 3.4 67.9 1.0
CHB D:HEC908 3.4 56.7 1.0
CHC D:HEC908 3.5 59.9 1.0
ND1 D:HIS689 4.1 59.8 1.0
CG D:HIS772 4.1 64.7 1.0
C2A D:HEC908 4.3 59.7 1.0
C3A D:HEC908 4.3 53.1 1.0
CG D:HIS689 4.3 59.3 1.0
ND1 D:HIS772 4.3 61.1 1.0
C2B D:HEC908 4.3 46.1 1.0
C3B D:HEC908 4.3 58.3 1.0
C3C D:HEC908 4.3 62.7 1.0
C2D D:HEC908 4.3 57.5 1.0
C2C D:HEC908 4.3 66.4 1.0
C3D D:HEC908 4.3 68.9 1.0

Iron binding site 7 out of 8 in 5c2w

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Iron binding site 7 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe404

b:72.5
occ:1.00
FE F:HEC404 0.0 72.5 1.0
NA F:HEC404 2.0 77.8 1.0
ND F:HEC404 2.1 52.6 1.0
NC F:HEC404 2.1 86.1 1.0
NB F:HEC404 2.1 76.8 1.0
O F:HOH533 2.1 50.0 1.0
NE2 F:HIS106 2.2 61.5 1.0
C1D F:HEC404 3.0 63.9 1.0
C4D F:HEC404 3.0 53.5 1.0
C1B F:HEC404 3.1 88.4 1.0
C4A F:HEC404 3.1 77.2 1.0
C4C F:HEC404 3.1 72.7 1.0
C1A F:HEC404 3.1 82.0 1.0
C4B F:HEC404 3.1 77.0 1.0
C1C F:HEC404 3.1 88.0 1.0
CE1 F:HIS106 3.2 56.0 1.0
CD2 F:HIS106 3.2 76.7 1.0
CHD F:HEC404 3.4 59.3 1.0
CHA F:HEC404 3.4 76.0 1.0
CHB F:HEC404 3.4 74.0 1.0
CHC F:HEC404 3.5 85.2 1.0
OD2 F:ASP168 4.1 72.7 1.0
C2D F:HEC404 4.3 70.2 1.0
C3D F:HEC404 4.3 72.3 1.0
C2B F:HEC404 4.3 0.1 1.0
C3A F:HEC404 4.3 85.6 1.0
ND1 F:HIS106 4.3 71.0 1.0
C3B F:HEC404 4.3 74.6 1.0
C2A F:HEC404 4.3 79.0 1.0
C3C F:HEC404 4.3 78.4 1.0
C2C F:HEC404 4.3 85.7 1.0
CG F:HIS106 4.3 79.0 1.0
CG1 F:VAL164 4.8 93.5 1.0
CG F:ASP168 5.0 79.1 1.0

Iron binding site 8 out of 8 in 5c2w

Go back to Iron Binding Sites List in 5c2w
Iron binding site 8 out of 8 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe405

b:95.0
occ:1.00
FE F:HEC405 0.0 95.0 1.0
NC F:HEC405 2.0 62.1 1.0
NB F:HEC405 2.1 75.0 1.0
NA F:HEC405 2.1 88.1 1.0
ND F:HEC405 2.1 0.7 1.0
NE2 F:HIS332 2.2 80.2 1.0
NE2 F:HIS229 2.3 78.8 1.0
CE1 F:HIS332 3.0 76.6 1.0
C4C F:HEC405 3.0 80.0 1.0
C1C F:HEC405 3.1 74.7 1.0
C4B F:HEC405 3.1 76.5 1.0
C1B F:HEC405 3.1 85.7 1.0
C4A F:HEC405 3.1 96.4 1.0
C1D F:HEC405 3.1 98.2 1.0
C1A F:HEC405 3.1 93.2 1.0
C4D F:HEC405 3.1 89.8 1.0
CD2 F:HIS332 3.1 81.9 1.0
CD2 F:HIS229 3.2 95.1 1.0
CE1 F:HIS229 3.3 87.2 1.0
CHD F:HEC405 3.4 88.6 1.0
CHC F:HEC405 3.4 75.7 1.0
CHB F:HEC405 3.4 96.2 1.0
CHA F:HEC405 3.5 90.8 1.0
ND1 F:HIS332 4.1 79.5 1.0
CG F:HIS332 4.2 66.5 1.0
C3C F:HEC405 4.3 95.5 1.0
C2C F:HEC405 4.3 90.7 1.0
C3B F:HEC405 4.3 85.1 1.0
C2B F:HEC405 4.3 88.2 1.0
C3A F:HEC405 4.3 97.5 1.0
C2D F:HEC405 4.3 86.7 1.0
C2A F:HEC405 4.3 99.1 1.0
C3D F:HEC405 4.3 86.5 1.0
ND1 F:HIS229 4.3 0.2 1.0
CG F:HIS229 4.4 0.9 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 15:57:41 2020

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