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Iron in PDB 7y6p: Cryo-Em Structure if Bacterioferritin Holoform

Enzymatic activity of Cryo-Em Structure if Bacterioferritin Holoform

All present enzymatic activity of Cryo-Em Structure if Bacterioferritin Holoform:
1.16.3.1;

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure if Bacterioferritin Holoform (pdb code 7y6p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 60 binding sites of Iron where determined in the Cryo-Em Structure if Bacterioferritin Holoform, PDB code: 7y6p:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 60 in 7y6p

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Iron binding site 1 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:19.5
occ:1.00
 OE1 A:GLU18 2.5 10.8 1.0
OE1 A:GLU51 2.5 11.6 1.0
OE2 A:GLU127 2.5 14.4 1.0
OE2 A:GLU18 2.7 10.8 1.0
ND1 A:HIS54 2.7 11.5 1.0
CD A:GLU18 2.9 10.8 1.0
CD A:GLU51 3.4 11.6 1.0
CD A:GLU127 3.6 14.4 1.0
CG A:HIS54 3.6 11.5 1.0
CE1 A:HIS54 3.6 11.5 1.0
OE2 A:GLU51 3.7 11.6 1.0
CB A:HIS54 3.8 11.5 1.0
OE1 A:GLU127 4.0 14.4 1.0
FE A:FE202 4.3 26.1 1.0
CG A:GLU18 4.4 10.8 1.0
CG2 A:ILE123 4.5 13.2 1.0
CA A:GLU51 4.6 11.6 1.0
CG A:GLU51 4.6 11.6 1.0
CB A:GLU51 4.8 11.6 1.0
NE2 A:HIS54 4.8 11.5 1.0
CD2 A:HIS54 4.8 11.5 1.0
CG A:GLU127 4.9 14.4 1.0

Iron binding site 2 out of 60 in 7y6p

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Iron binding site 2 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:26.1
occ:1.00
 OE2 A:GLU51 2.1 11.6 1.0
OE1 A:GLU127 3.2 14.4 1.0
CD A:GLU51 3.2 11.6 1.0
OE1 A:GLU47 3.4 10.9 1.0
OE2 A:GLU94 3.7 13.6 1.0
ND1 A:HIS130 3.8 12.6 1.0
OE1 A:GLU51 3.9 11.6 1.0
CD A:GLU127 4.1 14.4 1.0
CB A:HIS130 4.2 12.6 1.0
FE A:FE2201 4.3 19.5 1.0
OE2 A:GLU127 4.3 14.4 1.0
CG A:GLU51 4.3 11.6 1.0
CG A:HIS130 4.3 12.6 1.0
OE1 A:GLU94 4.4 13.6 1.0
CD A:GLU94 4.4 13.6 1.0
CD A:GLU47 4.6 10.9 1.0
CE2 A:TYR25 4.7 10.1 1.0
CE1 A:HIS130 4.7 12.6 1.0
CE1 A:HIS54 4.9 11.5 1.0
O A:ASP126 4.9 14.2 1.0
ND1 A:HIS54 5.0 11.5 1.0
OH A:TYR25 5.0 10.1 1.0

Iron binding site 3 out of 60 in 7y6p

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Iron binding site 3 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:13.1
occ:1.00
 FE A:HEM203 0.0 13.1 1.0
NC A:HEM203 2.0 13.1 1.0
NA A:HEM203 2.1 13.1 1.0
ND A:HEM203 2.1 13.1 1.0
NB A:HEM203 2.1 13.1 1.0
SD B:MET52 2.9 11.0 1.0
C1A A:HEM203 2.9 13.1 1.0
C4A A:HEM203 2.9 13.1 1.0
C1C A:HEM203 3.1 13.1 1.0
C4C A:HEM203 3.1 13.1 1.0
CE B:MET52 3.1 11.0 1.0
C1B A:HEM203 3.1 13.1 1.0
C4D A:HEM203 3.1 13.1 1.0
C1D A:HEM203 3.1 13.1 1.0
C4B A:HEM203 3.1 13.1 1.0
SD A:MET52 3.2 11.2 1.0
CHB A:HEM203 3.4 13.1 1.0
CHA A:HEM203 3.4 13.1 1.0
CHD A:HEM203 3.4 13.1 1.0
CHC A:HEM203 3.5 13.1 1.0
C2A A:HEM203 4.0 13.1 1.0
C3A A:HEM203 4.0 13.1 1.0
CE A:MET52 4.1 11.2 1.0
CG A:MET52 4.3 11.2 1.0
C2C A:HEM203 4.3 13.1 1.0
C3C A:HEM203 4.3 13.1 1.0
C3D A:HEM203 4.3 13.1 1.0
C2B A:HEM203 4.3 13.1 1.0
C2D A:HEM203 4.3 13.1 1.0
C3B A:HEM203 4.3 13.1 1.0
CE1 B:PHE49 4.4 10.6 1.0
CG B:MET52 4.5 11.0 1.0
CD1 B:PHE49 4.7 10.6 1.0
CB A:MET52 4.8 11.2 1.0

Iron binding site 4 out of 60 in 7y6p

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Iron binding site 4 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:20.4
occ:1.00
 OE1 B:GLU51 2.5 11.5 1.0
OE1 B:GLU18 2.5 10.5 1.0
OE2 B:GLU127 2.5 13.9 1.0
OE2 B:GLU18 2.6 10.5 1.0
ND1 B:HIS54 2.7 11.4 1.0
CD B:GLU18 2.9 10.5 1.0
CD B:GLU51 3.3 11.5 1.0
OE2 B:GLU51 3.5 11.5 1.0
CD B:GLU127 3.6 13.9 1.0
CG B:HIS54 3.6 11.4 1.0
CE1 B:HIS54 3.6 11.4 1.0
CB B:HIS54 3.8 11.4 1.0
OE1 B:GLU127 4.0 13.9 1.0
CG B:GLU18 4.4 10.5 1.0
FE B:FE202 4.4 29.7 1.0
CG2 B:ILE123 4.5 12.8 1.0
CA B:GLU51 4.6 11.5 1.0
CG B:GLU51 4.6 11.5 1.0
NE2 B:HIS54 4.8 11.4 1.0
CD2 B:HIS54 4.8 11.4 1.0
CB B:GLU51 4.9 11.5 1.0
CG B:GLU127 4.9 13.9 1.0

Iron binding site 5 out of 60 in 7y6p

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Iron binding site 5 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:29.7
occ:1.00
 OE2 B:GLU51 2.1 11.5 1.0
OE1 B:GLU47 3.3 10.9 1.0
CD B:GLU51 3.3 11.5 1.0
OE1 B:GLU127 3.5 13.9 1.0
ND1 B:HIS130 3.9 12.1 1.0
OE2 B:GLU94 4.0 13.2 1.0
OE1 B:GLU51 4.1 11.5 1.0
CB B:HIS130 4.3 12.1 1.0
CG B:HIS130 4.3 12.1 1.0
CG B:GLU51 4.3 11.5 1.0
CD B:GLU127 4.4 13.9 1.0
FE B:FE2201 4.4 20.4 1.0
OE2 B:GLU127 4.5 13.9 1.0
CD B:GLU47 4.5 10.9 1.0
OE1 B:GLU94 4.7 13.2 1.0
CE1 B:HIS130 4.7 12.1 1.0
CE2 B:TYR25 4.7 10.1 1.0
CD B:GLU94 4.7 13.2 1.0
CE1 B:HIS54 4.9 11.4 1.0
ND1 B:HIS54 5.0 11.4 1.0
O B:GLU47 5.0 10.9 1.0
O B:ASP126 5.0 13.8 1.0

Iron binding site 6 out of 60 in 7y6p

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Iron binding site 6 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:20.6
occ:1.00
 OE1 C:GLU18 2.5 11.4 1.0
OE2 C:GLU51 2.5 12.1 1.0
OE2 C:GLU127 2.5 14.5 1.0
OE2 C:GLU18 2.7 11.4 1.0
ND1 C:HIS54 2.7 12.0 1.0
CD C:GLU18 2.9 11.4 1.0
CD C:GLU51 3.4 12.1 1.0
CD C:GLU127 3.6 14.5 1.0
CG C:HIS54 3.6 12.0 1.0
CE1 C:HIS54 3.6 12.0 1.0
OE1 C:GLU51 3.7 12.1 1.0
CB C:HIS54 3.8 12.0 1.0
OE1 C:GLU127 4.0 14.5 1.0
FE C:FE202 4.3 30.7 1.0
CG C:GLU18 4.4 11.4 1.0
CG2 C:ILE123 4.5 13.2 1.0
CA C:GLU51 4.5 12.1 1.0
CG C:GLU51 4.7 12.1 1.0
NE2 C:HIS54 4.8 12.0 1.0
CD2 C:HIS54 4.8 12.0 1.0
CB C:GLU51 4.8 12.1 1.0
CG C:GLU127 4.9 14.5 1.0

Iron binding site 7 out of 60 in 7y6p

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Iron binding site 7 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:30.7
occ:1.00
 CB C:ALA97 3.6 13.8 1.0
CG1 C:VAL93 3.9 14.1 1.0
CB C:ALA21 4.0 9.9 1.0
OE2 C:GLU51 4.1 12.1 1.0
OE2 C:GLU127 4.2 14.5 1.0
FE C:FE2201 4.3 20.6 1.0
OE2 C:GLU94 4.3 13.8 1.0
OE1 C:GLU127 4.4 14.5 1.0
CD C:GLU127 4.5 14.5 1.0
O C:VAL93 4.5 14.1 1.0
OE2 C:GLU18 4.5 11.4 1.0
O C:ALA17 4.6 10.8 1.0
CD C:GLU94 4.7 13.8 1.0
OE1 C:GLU94 4.7 13.8 1.0
C C:VAL93 4.9 14.1 1.0
CD C:GLU51 4.9 12.1 1.0
C C:ALA17 5.0 10.8 1.0
NE2 C:GLN14 5.0 12.3 1.0
CD C:GLU18 5.0 11.4 1.0
CA C:ALA97 5.0 13.8 1.0

Iron binding site 8 out of 60 in 7y6p

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Iron binding site 8 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe203

b:13.0
occ:1.00
 FE C:HEM203 0.0 13.0 1.0
CE C:MET52 1.3 12.7 1.0
NA C:HEM203 2.0 13.0 1.0
NC C:HEM203 2.0 13.0 1.0
NB C:HEM203 2.1 13.0 1.0
ND C:HEM203 2.1 13.0 1.0
SD D:MET52 2.9 11.0 1.0
SD C:MET52 2.9 12.7 1.0
C4C C:HEM203 3.0 13.0 1.0
C4A C:HEM203 3.0 13.0 1.0
C1C C:HEM203 3.1 13.0 1.0
C1A C:HEM203 3.1 13.0 1.0
C1D C:HEM203 3.1 13.0 1.0
C4B C:HEM203 3.1 13.0 1.0
C1B C:HEM203 3.1 13.0 1.0
C4D C:HEM203 3.1 13.0 1.0
CHD C:HEM203 3.4 13.0 1.0
CHB C:HEM203 3.4 13.0 1.0
CHC C:HEM203 3.4 13.0 1.0
CHA C:HEM203 3.5 13.0 1.0
CE D:MET52 3.6 11.0 1.0
CG C:MET52 4.1 12.7 1.0
C3C C:HEM203 4.2 13.0 1.0
C3A C:HEM203 4.3 13.0 1.0
C2C C:HEM203 4.3 13.0 1.0
C2A C:HEM203 4.3 13.0 1.0
CG D:MET52 4.3 11.0 1.0
C2D C:HEM203 4.3 13.0 1.0
C3B C:HEM203 4.3 13.0 1.0
C2B C:HEM203 4.3 13.0 1.0
C3D C:HEM203 4.3 13.0 1.0
HHD C:HEM203 4.4 13.0 1.0
HHB C:HEM203 4.4 13.0 1.0
HHC C:HEM203 4.4 13.0 1.0
HHA C:HEM203 4.4 13.0 1.0
CE1 C:PHE49 4.9 11.4 1.0
CB D:MET52 5.0 11.0 1.0

Iron binding site 9 out of 60 in 7y6p

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Iron binding site 9 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:20.0
occ:1.00
 OE1 D:GLU51 2.5 11.4 1.0
OE2 D:GLU127 2.5 14.0 1.0
OE1 D:GLU18 2.5 10.6 1.0
OE2 D:GLU18 2.6 10.6 1.0
ND1 D:HIS54 2.7 11.2 1.0
CD D:GLU18 2.9 10.6 1.0
CD D:GLU51 3.5 11.4 1.0
CD D:GLU127 3.6 14.0 1.0
CG D:HIS54 3.6 11.2 1.0
CE1 D:HIS54 3.6 11.2 1.0
CB D:HIS54 3.8 11.2 1.0
OE2 D:GLU51 3.9 11.4 1.0
OE1 D:GLU127 4.0 14.0 1.0
CG2 D:ILE123 4.4 12.7 1.0
CG D:GLU18 4.4 10.6 1.0
FE D:FE202 4.5 28.4 1.0
CA D:GLU51 4.7 11.4 1.0
NE2 D:HIS54 4.7 11.2 1.0
CD2 D:HIS54 4.8 11.2 1.0
CG D:GLU51 4.8 11.4 1.0
CG D:GLU127 4.8 14.0 1.0
CB D:GLU51 4.9 11.4 1.0

Iron binding site 10 out of 60 in 7y6p

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Iron binding site 10 out of 60 in the Cryo-Em Structure if Bacterioferritin Holoform


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure if Bacterioferritin Holoform within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:28.4
occ:1.00
 OE2 D:GLU51 2.4 11.4 1.0
OE1 D:GLU47 3.0 11.1 1.0
CD D:GLU51 3.3 11.4 1.0
OE1 D:GLU127 3.7 14.0 1.0
OE1 D:GLU51 3.9 11.4 1.0
ND1 D:HIS130 3.9 12.3 1.0
OE2 D:GLU94 4.1 13.2 1.0
CG D:GLU51 4.2 11.4 1.0
CD D:GLU47 4.2 11.1 1.0
CB D:HIS130 4.3 12.3 1.0
CG D:HIS130 4.3 12.3 1.0
CD D:GLU127 4.5 14.0 1.0
FE D:FE2201 4.5 20.0 1.0
OE2 D:GLU127 4.7 14.0 1.0
CE1 D:HIS130 4.7 12.3 1.0
CE2 D:TYR25 4.7 10.1 1.0
OE1 D:GLU94 4.8 13.2 1.0
CD D:GLU94 4.8 13.2 1.0
CE1 D:HIS54 4.8 11.2 1.0
O D:GLU47 4.8 11.1 1.0
CB D:ASP50 4.8 11.4 1.0
OE2 D:GLU47 4.9 11.1 1.0
ND1 D:HIS54 4.9 11.2 1.0

Reference:

C.Jobichen, J.Sivaraman. Cryo-Em Structure if Bacterioferritin Holoform To Be Published.
Page generated: Thu Aug 7 10:16:08 2025

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