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Iron in PDB 8d9m: Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens (pdb code 8d9m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens, PDB code: 8d9m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8d9m

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Iron binding site 1 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:115.8
occ:1.00
FE A:HEC601 0.0 115.8 1.0
NA A:HEC601 2.0 115.8 1.0
NC A:HEC601 2.0 115.8 1.0
NE2 A:HIS65 2.0 123.6 1.0
NE2 A:HIS93 2.0 116.9 1.0
NB A:HEC601 2.1 115.8 1.0
ND A:HEC601 2.1 115.8 1.0
CE1 A:HIS65 2.5 123.6 1.0
CD2 A:HIS93 2.9 116.9 1.0
C1A A:HEC601 3.0 115.8 1.0
C1C A:HEC601 3.0 115.8 1.0
C4A A:HEC601 3.0 115.8 1.0
C4C A:HEC601 3.0 115.8 1.0
CE1 A:HIS93 3.1 116.9 1.0
C1D A:HEC601 3.1 115.8 1.0
C4B A:HEC601 3.1 115.8 1.0
C4D A:HEC601 3.1 115.8 1.0
C1B A:HEC601 3.1 115.8 1.0
CD2 A:HIS65 3.2 123.6 1.0
CHA A:HEC601 3.4 115.8 1.0
CHC A:HEC601 3.4 115.8 1.0
CHD A:HEC601 3.4 115.8 1.0
CHB A:HEC601 3.4 115.8 1.0
ND1 A:HIS65 3.7 123.6 1.0
CG A:HIS65 4.1 123.6 1.0
CG A:HIS93 4.1 116.9 1.0
ND1 A:HIS93 4.1 116.9 1.0
C2A A:HEC601 4.2 115.8 1.0
C3A A:HEC601 4.2 115.8 1.0
C2C A:HEC601 4.3 115.8 1.0
C3C A:HEC601 4.3 115.8 1.0
C2D A:HEC601 4.3 115.8 1.0
C3B A:HEC601 4.3 115.8 1.0
C2B A:HEC601 4.3 115.8 1.0
C3D A:HEC601 4.3 115.8 1.0

Iron binding site 2 out of 8 in 8d9m

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Iron binding site 2 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:123.8
occ:1.00
FE A:HEC602 0.0 123.8 1.0
NA A:HEC602 2.0 123.8 1.0
NC A:HEC602 2.0 123.8 1.0
NE2 A:HIS115 2.0 128.0 1.0
NB A:HEC602 2.0 123.8 1.0
ND A:HEC602 2.1 123.8 1.0
NE2 A:HIS64 2.1 126.7 1.0
CE1 A:HIS115 2.9 128.0 1.0
CE1 A:HIS64 3.0 126.7 1.0
C1A A:HEC602 3.0 123.8 1.0
C1C A:HEC602 3.0 123.8 1.0
C4D A:HEC602 3.0 123.8 1.0
C4B A:HEC602 3.0 123.8 1.0
C4A A:HEC602 3.1 123.8 1.0
C4C A:HEC602 3.1 123.8 1.0
C1B A:HEC602 3.1 123.8 1.0
C1D A:HEC602 3.1 123.8 1.0
CD2 A:HIS64 3.1 126.7 1.0
CD2 A:HIS115 3.1 128.0 1.0
CHA A:HEC602 3.4 123.8 1.0
CHC A:HEC602 3.4 123.8 1.0
CHB A:HEC602 3.5 123.8 1.0
CHD A:HEC602 3.5 123.8 1.0
ND1 A:HIS115 4.0 128.0 1.0
ND1 A:HIS64 4.1 126.7 1.0
CG A:HIS115 4.2 128.0 1.0
CG A:HIS64 4.2 126.7 1.0
C2A A:HEC602 4.2 123.8 1.0
C3A A:HEC602 4.3 123.8 1.0
C2C A:HEC602 4.3 123.8 1.0
C3C A:HEC602 4.3 123.8 1.0
C3B A:HEC602 4.3 123.8 1.0
C3D A:HEC602 4.3 123.8 1.0
C2B A:HEC602 4.3 123.8 1.0
C2D A:HEC602 4.3 123.8 1.0
CMA A:HEC603 4.7 133.4 1.0
CMD A:HEC601 4.9 115.8 1.0

Iron binding site 3 out of 8 in 8d9m

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Iron binding site 3 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:133.4
occ:1.00
FE A:HEC603 0.0 133.4 1.0
NC A:HEC603 2.0 133.4 1.0
NA A:HEC603 2.0 133.4 1.0
NE2 A:HIS120 2.0 134.6 1.0
ND A:HEC603 2.0 133.4 1.0
NB A:HEC603 2.0 133.4 1.0
NE2 A:HIS54 2.0 146.0 1.0
CD2 A:HIS54 2.5 146.0 1.0
CD2 A:HIS120 2.5 134.6 1.0
C1A A:HEC603 3.0 133.4 1.0
C1C A:HEC603 3.0 133.4 1.0
C4B A:HEC603 3.0 133.4 1.0
C4D A:HEC603 3.0 133.4 1.0
C4C A:HEC603 3.1 133.4 1.0
C1D A:HEC603 3.1 133.4 1.0
C4A A:HEC603 3.1 133.4 1.0
C1B A:HEC603 3.1 133.4 1.0
CE1 A:HIS54 3.2 146.0 1.0
CE1 A:HIS120 3.3 134.6 1.0
CHA A:HEC603 3.4 133.4 1.0
CHC A:HEC603 3.4 133.4 1.0
CHD A:HEC603 3.4 133.4 1.0
CHB A:HEC603 3.5 133.4 1.0
CG A:HIS54 3.7 146.0 1.0
CG A:HIS120 3.8 134.6 1.0
ND1 A:HIS54 4.0 146.0 1.0
ND1 A:HIS120 4.1 134.6 1.0
C2A A:HEC603 4.2 133.4 1.0
C2C A:HEC603 4.3 133.4 1.0
C3C A:HEC603 4.3 133.4 1.0
C3A A:HEC603 4.3 133.4 1.0
C3B A:HEC603 4.3 133.4 1.0
C3D A:HEC603 4.3 133.4 1.0
C2D A:HEC603 4.3 133.4 1.0
C2B A:HEC603 4.3 133.4 1.0
CB A:HIS54 4.9 146.0 1.0

Iron binding site 4 out of 8 in 8d9m

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Iron binding site 4 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:130.3
occ:1.00
FE A:HEC604 0.0 130.3 1.0
NC A:HEC604 2.0 130.3 1.0
NB A:HEC604 2.0 130.3 1.0
NA A:HEC604 2.0 130.3 1.0
NE2 A:HIS121 2.0 131.1 1.0
ND A:HEC604 2.1 130.3 1.0
NE2 A:HIS135 2.1 136.3 1.0
CD2 A:HIS135 2.4 136.3 1.0
CD2 A:HIS121 2.9 131.1 1.0
CE1 A:HIS121 3.0 131.1 1.0
C1C A:HEC604 3.0 130.3 1.0
C4B A:HEC604 3.0 130.3 1.0
C1B A:HEC604 3.0 130.3 1.0
C4C A:HEC604 3.0 130.3 1.0
C4A A:HEC604 3.1 130.3 1.0
C1A A:HEC604 3.1 130.3 1.0
C1D A:HEC604 3.1 130.3 1.0
C4D A:HEC604 3.1 130.3 1.0
CE1 A:HIS135 3.2 136.3 1.0
CHC A:HEC604 3.4 130.3 1.0
CHD A:HEC604 3.4 130.3 1.0
CHB A:HEC604 3.4 130.3 1.0
CHA A:HEC604 3.4 130.3 1.0
CG A:HIS135 3.6 136.3 1.0
ND1 A:HIS135 3.9 136.3 1.0
CG A:HIS121 4.0 131.1 1.0
ND1 A:HIS121 4.1 131.1 1.0
C2B A:HEC604 4.3 130.3 1.0
C2A A:HEC604 4.3 130.3 1.0
C2C A:HEC604 4.3 130.3 1.0
C3B A:HEC604 4.3 130.3 1.0
C3A A:HEC604 4.3 130.3 1.0
C3C A:HEC604 4.3 130.3 1.0
C2D A:HEC604 4.3 130.3 1.0
C3D A:HEC604 4.3 130.3 1.0
CB A:HIS135 4.8 136.3 1.0

Iron binding site 5 out of 8 in 8d9m

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Iron binding site 5 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:130.7
occ:1.00
FE A:HEC605 0.0 130.7 1.0
NA A:HEC605 2.0 130.7 1.0
NE2 A:HIS206 2.0 135.1 1.0
NC A:HEC605 2.0 130.7 1.0
NE2 A:HIS233 2.0 131.9 1.0
ND A:HEC605 2.0 130.7 1.0
NB A:HEC605 2.1 130.7 1.0
CE1 A:HIS206 2.2 135.1 1.0
CE1 A:HIS233 3.0 131.9 1.0
CD2 A:HIS233 3.0 131.9 1.0
C1A A:HEC605 3.0 130.7 1.0
C4A A:HEC605 3.0 130.7 1.0
C1D A:HEC605 3.0 130.7 1.0
C4C A:HEC605 3.1 130.7 1.0
C4D A:HEC605 3.1 130.7 1.0
C1B A:HEC605 3.1 130.7 1.0
C1C A:HEC605 3.1 130.7 1.0
C4B A:HEC605 3.1 130.7 1.0
CD2 A:HIS206 3.3 135.1 1.0
CHA A:HEC605 3.4 130.7 1.0
CHD A:HEC605 3.4 130.7 1.0
CHB A:HEC605 3.4 130.7 1.0
ND1 A:HIS206 3.4 135.1 1.0
CHC A:HEC605 3.5 130.7 1.0
CG A:HIS206 4.0 135.1 1.0
ND1 A:HIS233 4.1 131.9 1.0
CG A:HIS233 4.1 131.9 1.0
C2A A:HEC605 4.3 130.7 1.0
C3A A:HEC605 4.3 130.7 1.0
C3C A:HEC605 4.3 130.7 1.0
C2D A:HEC605 4.3 130.7 1.0
C2C A:HEC605 4.3 130.7 1.0
C2B A:HEC605 4.3 130.7 1.0
C3B A:HEC605 4.3 130.7 1.0
C3D A:HEC605 4.3 130.7 1.0
CMB A:HEC607 4.6 124.4 1.0

Iron binding site 6 out of 8 in 8d9m

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Iron binding site 6 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:142.2
occ:1.00
FE A:HEC606 0.0 142.2 1.0
CE1 A:HIS207 1.7 134.0 1.0
NA A:HEC606 2.0 142.2 1.0
NE2 A:HIS218 2.0 147.0 1.0
NC A:HEC606 2.0 142.2 1.0
NE2 A:HIS207 2.0 134.0 1.0
NB A:HEC606 2.1 142.2 1.0
ND A:HEC606 2.1 142.2 1.0
CD2 A:HIS218 2.8 147.0 1.0
ND1 A:HIS207 2.9 134.0 1.0
C1A A:HEC606 3.0 142.2 1.0
C1C A:HEC606 3.1 142.2 1.0
C4D A:HEC606 3.1 142.2 1.0
C4C A:HEC606 3.1 142.2 1.0
C4A A:HEC606 3.1 142.2 1.0
C1D A:HEC606 3.1 142.2 1.0
C4B A:HEC606 3.1 142.2 1.0
C1B A:HEC606 3.1 142.2 1.0
CE1 A:HIS218 3.1 147.0 1.0
CD2 A:HIS207 3.3 134.0 1.0
CHA A:HEC606 3.4 142.2 1.0
CHC A:HEC606 3.4 142.2 1.0
CHD A:HEC606 3.4 142.2 1.0
CHB A:HEC606 3.5 142.2 1.0
CG A:HIS207 3.7 134.0 1.0
CG A:HIS218 4.0 147.0 1.0
ND1 A:HIS218 4.1 147.0 1.0
C2A A:HEC606 4.3 142.2 1.0
C3A A:HEC606 4.3 142.2 1.0
C2C A:HEC606 4.3 142.2 1.0
C3C A:HEC606 4.3 142.2 1.0
C3D A:HEC606 4.3 142.2 1.0
C2B A:HEC606 4.3 142.2 1.0
C3B A:HEC606 4.3 142.2 1.0
C2D A:HEC606 4.3 142.2 1.0
NE2 A:GLN203 4.9 133.9 1.0

Iron binding site 7 out of 8 in 8d9m

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Iron binding site 7 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe607

b:124.4
occ:1.00
FE A:HEC607 0.0 124.4 1.0
NC A:HEC607 2.0 124.4 1.0
NE2 A:HIS265 2.0 125.9 1.0
NA A:HEC607 2.0 124.4 1.0
NE2 A:HIS182 2.0 131.5 1.0
NB A:HEC607 2.1 124.4 1.0
ND A:HEC607 2.1 124.4 1.0
CE1 A:HIS265 2.6 125.9 1.0
CD2 A:HIS182 2.9 131.5 1.0
C4C A:HEC607 3.0 124.4 1.0
C1A A:HEC607 3.0 124.4 1.0
C1C A:HEC607 3.0 124.4 1.0
C4A A:HEC607 3.1 124.4 1.0
C1B A:HEC607 3.1 124.4 1.0
C1D A:HEC607 3.1 124.4 1.0
C4B A:HEC607 3.1 124.4 1.0
C4D A:HEC607 3.1 124.4 1.0
CE1 A:HIS182 3.1 131.5 1.0
CD2 A:HIS265 3.3 125.9 1.0
CHA A:HEC607 3.4 124.4 1.0
CHD A:HEC607 3.4 124.4 1.0
CHB A:HEC607 3.4 124.4 1.0
CHC A:HEC607 3.4 124.4 1.0
ND1 A:HIS265 3.9 125.9 1.0
CG A:HIS182 4.0 131.5 1.0
ND1 A:HIS182 4.1 131.5 1.0
CG A:HIS265 4.2 125.9 1.0
C3C A:HEC607 4.3 124.4 1.0
C2A A:HEC607 4.3 124.4 1.0
C2C A:HEC607 4.3 124.4 1.0
C3A A:HEC607 4.3 124.4 1.0
C2B A:HEC607 4.3 124.4 1.0
C3B A:HEC607 4.3 124.4 1.0
C2D A:HEC607 4.3 124.4 1.0
C3D A:HEC607 4.3 124.4 1.0
CAA A:HEC605 4.8 130.7 1.0
CD1 A:ILE241 5.0 116.7 1.0

Iron binding site 8 out of 8 in 8d9m

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Iron binding site 8 out of 8 in the Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em of the Omcz Nanowires From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe608

b:124.1
occ:1.00
FE A:HEC608 0.0 124.1 1.0
NC A:HEC608 2.0 124.1 1.0
NE2 A:HIS276 2.0 130.8 1.0
NB A:HEC608 2.0 124.1 1.0
NA A:HEC608 2.0 124.1 1.0
NE2 A:HIS239 2.0 123.3 1.0
ND A:HEC608 2.1 124.1 1.0
CD2 A:HIS276 2.4 130.8 1.0
CE1 A:HIS239 2.7 123.3 1.0
C4C A:HEC608 3.0 124.1 1.0
C1C A:HEC608 3.0 124.1 1.0
C4B A:HEC608 3.0 124.1 1.0
C1D A:HEC608 3.0 124.1 1.0
C1B A:HEC608 3.0 124.1 1.0
C4A A:HEC608 3.1 124.1 1.0
C4D A:HEC608 3.1 124.1 1.0
C1A A:HEC608 3.1 124.1 1.0
CE1 A:HIS276 3.2 130.8 1.0
CD2 A:HIS239 3.3 123.3 1.0
CHD A:HEC608 3.4 124.1 1.0
CHC A:HEC608 3.4 124.1 1.0
CHB A:HEC608 3.4 124.1 1.0
CHA A:HEC608 3.4 124.1 1.0
CG A:HIS276 3.7 130.8 1.0
ND1 A:HIS239 3.9 123.3 1.0
ND1 A:HIS276 4.0 130.8 1.0
CG A:HIS239 4.2 123.3 1.0
C3C A:HEC608 4.2 124.1 1.0
C2C A:HEC608 4.2 124.1 1.0
C3B A:HEC608 4.3 124.1 1.0
C2B A:HEC608 4.3 124.1 1.0
C3A A:HEC608 4.3 124.1 1.0
C2D A:HEC608 4.3 124.1 1.0
C2A A:HEC608 4.3 124.1 1.0
C3D A:HEC608 4.3 124.1 1.0
CB A:HIS276 4.9 130.8 1.0

Reference:

F.Wang, C.H.Chan, V.Suciu, K.Mustafa, M.Ammend, D.Si, A.I.Hochbaum, E.H.Egelman, D.R.Bond. Structure of Geobacter Omcz Filaments Suggests Extracellular Cytochrome Polymers Evolved Independently Multiple Times. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36062910
DOI: 10.7554/ELIFE.81551
Page generated: Fri Aug 9 23:27:33 2024

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