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Iron in PDB 7y6g: Cryo-Em Structure of Bacterioferritin Holoform 1A

Enzymatic activity of Cryo-Em Structure of Bacterioferritin Holoform 1A

All present enzymatic activity of Cryo-Em Structure of Bacterioferritin Holoform 1A:
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 - 59;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Bacterioferritin Holoform 1A (pdb code 7y6g). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 59 binding sites of Iron where determined in the Cryo-Em Structure of Bacterioferritin Holoform 1A, PDB code: 7y6g:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 59 in 7y6g

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Iron binding site 1 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:9.5
occ:1.00
 OE1 A:GLU51 2.5 5.3 1.0
OE2 A:GLU127 2.6 7.3 1.0
OE1 A:GLU18 2.6 5.1 1.0
OE2 A:GLU18 2.6 5.1 1.0
ND1 A:HIS54 2.7 5.7 1.0
CD A:GLU18 3.0 5.1 1.0
CD A:GLU51 3.4 5.3 1.0
OE2 A:GLU51 3.6 5.3 1.0
CG A:HIS54 3.6 5.7 1.0
CD A:GLU127 3.7 7.3 1.0
CE1 A:HIS54 3.7 5.7 1.0
CB A:HIS54 3.8 5.7 1.0
OE1 A:GLU127 4.1 7.3 1.0
FE A:FE202 4.2 30.0 1.0
CG A:GLU18 4.5 5.1 1.0
CG2 A:ILE123 4.6 6.9 1.0
CA A:GLU51 4.6 5.3 1.0
CG A:GLU51 4.6 5.3 1.0
CB A:GLU51 4.8 5.3 1.0
NE2 A:HIS54 4.8 5.7 1.0
CD2 A:HIS54 4.8 5.7 1.0
CG A:GLU127 4.9 7.3 1.0

Iron binding site 2 out of 59 in 7y6g

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Iron binding site 2 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:30.0
occ:1.00
 OE2 A:GLU51 2.2 5.3 1.0
OE2 A:GLU94 2.3 8.4 1.0
OE1 A:GLU127 2.6 7.3 1.0
CD A:GLU94 3.1 8.4 1.0
OE1 A:GLU94 3.3 8.4 1.0
CD A:GLU51 3.3 5.3 1.0
ND1 A:HIS130 3.5 6.6 1.0
CD A:GLU127 3.5 7.3 1.0
OH A:TYR25 3.8 4.8 1.0
OE1 A:GLU51 3.8 5.3 1.0
OE2 A:GLU127 3.8 7.3 1.0
CE1 A:TYR25 4.1 4.8 1.0
FE A:FE2201 4.2 9.5 1.0
CE1 A:HIS130 4.4 6.6 1.0
CG A:HIS130 4.4 6.6 1.0
CZ A:TYR25 4.4 4.8 1.0
CB A:HIS130 4.5 6.6 1.0
CG A:GLU94 4.6 8.4 1.0
CG A:GLU51 4.6 5.3 1.0
OE1 A:GLU47 4.7 5.1 1.0
CG A:GLU127 4.9 7.3 1.0
CA A:GLU127 4.9 7.3 1.0

Iron binding site 3 out of 59 in 7y6g

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Iron binding site 3 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:6.1
occ:1.00
 FE A:HEM203 0.0 6.1 1.0
NC A:HEM203 2.1 6.1 1.0
NA A:HEM203 2.1 6.1 1.0
ND A:HEM203 2.1 6.1 1.0
NB A:HEM203 2.1 6.1 1.0
SD B:MET52 2.7 5.1 1.0
C1A A:HEM203 2.9 6.1 1.0
C4A A:HEM203 2.9 6.1 1.0
C4D A:HEM203 3.1 6.1 1.0
C1C A:HEM203 3.1 6.1 1.0
C4C A:HEM203 3.1 6.1 1.0
C1B A:HEM203 3.1 6.1 1.0
C4B A:HEM203 3.1 6.1 1.0
C1D A:HEM203 3.1 6.1 1.0
CE B:MET52 3.1 5.1 1.0
SD A:MET52 3.1 5.4 1.0
CHA A:HEM203 3.4 6.1 1.0
CHB A:HEM203 3.4 6.1 1.0
CHC A:HEM203 3.4 6.1 1.0
CHD A:HEM203 3.5 6.1 1.0
C2A A:HEM203 4.0 6.1 1.0
C3A A:HEM203 4.0 6.1 1.0
CE A:MET52 4.2 5.4 1.0
C2C A:HEM203 4.3 6.1 1.0
C3C A:HEM203 4.3 6.1 1.0
C3D A:HEM203 4.3 6.1 1.0
C2B A:HEM203 4.3 6.1 1.0
C3B A:HEM203 4.3 6.1 1.0
C2D A:HEM203 4.3 6.1 1.0
CG B:MET52 4.4 5.1 1.0
CG A:MET52 4.4 5.4 1.0
CE1 B:PHE49 4.5 4.9 1.0
CD1 B:PHE49 4.7 4.9 1.0
CB A:MET52 5.0 5.4 1.0

Iron binding site 4 out of 59 in 7y6g

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Iron binding site 4 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:11.3
occ:1.00
 OE1 B:GLU127 2.5 7.2 1.0
OE1 B:GLU51 2.5 5.1 1.0
OE1 B:GLU18 2.6 4.9 1.0
OE2 B:GLU18 2.6 4.9 1.0
ND1 B:HIS54 2.7 5.3 1.0
CD B:GLU18 2.9 4.9 1.0
CD B:GLU51 3.4 5.1 1.0
OE2 B:GLU51 3.6 5.1 1.0
CD B:GLU127 3.6 7.2 1.0
CG B:HIS54 3.7 5.3 1.0
CE1 B:HIS54 3.7 5.3 1.0
CB B:HIS54 3.8 5.3 1.0
OE2 B:GLU127 4.1 7.2 1.0
CG B:GLU18 4.4 4.9 1.0
FE B:FE202 4.4 30.0 1.0
CG2 B:ILE123 4.5 6.7 1.0
CG B:GLU51 4.7 5.1 1.0
CA B:GLU51 4.8 5.1 1.0
NE2 B:HIS54 4.8 5.3 1.0
CD2 B:HIS54 4.8 5.3 1.0
CG B:GLU127 4.9 7.2 1.0

Iron binding site 5 out of 59 in 7y6g

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Iron binding site 5 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:30.0
occ:1.00
 OE2 B:GLU127 2.2 7.2 1.0
OE2 B:GLU94 2.4 8.2 1.0
OE2 B:GLU51 3.0 5.1 1.0
OE1 B:GLU94 3.1 8.2 1.0
CD B:GLU94 3.1 8.2 1.0
CD B:GLU127 3.3 7.2 1.0
ND1 B:HIS130 3.4 6.4 1.0
OE1 B:GLU127 3.7 7.2 1.0
CD B:GLU51 3.8 5.1 1.0
CB B:HIS130 4.0 6.4 1.0
CG B:HIS130 4.1 6.4 1.0
OE1 B:GLU51 4.1 5.1 1.0
OH B:TYR25 4.3 4.8 1.0
CA B:GLU127 4.4 7.2 1.0
CE1 B:HIS130 4.4 6.4 1.0
FE B:FE2201 4.4 11.3 1.0
CG B:GLU94 4.5 8.2 1.0
CG B:GLU127 4.5 7.2 1.0
CE1 B:TYR25 4.6 4.8 1.0
CB B:GLU127 4.7 7.2 1.0
OE1 B:GLU47 4.9 4.8 1.0
CZ B:TYR25 5.0 4.8 1.0

Iron binding site 6 out of 59 in 7y6g

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Iron binding site 6 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:8.8
occ:1.00
 OE1 C:GLU51 2.5 5.9 1.0
OE2 C:GLU127 2.5 7.2 1.0
OE1 C:GLU18 2.6 5.0 1.0
OE2 C:GLU18 2.6 5.0 1.0
ND1 C:HIS54 2.7 5.9 1.0
CD C:GLU18 2.9 5.0 1.0
CD C:GLU51 3.6 5.9 1.0
CG C:HIS54 3.6 5.9 1.0
CD C:GLU127 3.7 7.2 1.0
CE1 C:HIS54 3.7 5.9 1.0
CB C:HIS54 3.7 5.9 1.0
OE2 C:GLU51 4.1 5.9 1.0
OE1 C:GLU127 4.1 7.2 1.0
FE C:FE202 4.3 30.0 1.0
CG2 C:ILE123 4.4 6.6 1.0
CG C:GLU18 4.4 5.0 1.0
CA C:GLU51 4.6 5.9 1.0
CD2 C:HIS54 4.8 5.9 1.0
NE2 C:HIS54 4.8 5.9 1.0
CG C:GLU51 4.8 5.9 1.0
CB C:GLU51 4.9 5.9 1.0
CG C:GLU127 4.9 7.2 1.0
O C:GLU51 4.9 5.9 1.0

Iron binding site 7 out of 59 in 7y6g

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Iron binding site 7 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:30.0
occ:1.00
 CB C:ALA97 3.7 8.3 1.0
CB C:ALA21 4.0 4.5 1.0
O C:ALA17 4.1 5.0 1.0
CG1 C:VAL93 4.1 8.4 1.0
OE2 C:GLU127 4.2 7.2 1.0
OE2 C:GLU18 4.3 5.0 1.0
FE C:FE2201 4.3 8.8 1.0
C C:ALA17 4.4 5.0 1.0
CB C:ALA17 4.5 5.0 1.0
NE2 C:GLN14 4.5 5.7 1.0
OE1 C:GLU51 4.6 5.9 1.0
CD C:GLU18 4.6 5.0 1.0
N C:GLU18 4.7 5.0 1.0
CD C:GLU127 4.7 7.2 1.0
CA C:GLU18 4.8 5.0 1.0
O C:VAL93 4.8 8.4 1.0
OE1 C:GLU18 4.9 5.0 1.0
OE1 C:GLU127 4.9 7.2 1.0

Iron binding site 8 out of 59 in 7y6g

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Iron binding site 8 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe203

b:6.8
occ:1.00
 FE C:HEM203 0.0 6.8 1.0
CE C:MET52 1.6 6.5 1.0
NA C:HEM203 2.0 6.8 1.0
NC C:HEM203 2.0 6.8 1.0
NB C:HEM203 2.1 6.8 1.0
ND C:HEM203 2.1 6.8 1.0
C4C C:HEM203 3.0 6.8 1.0
C1C C:HEM203 3.0 6.8 1.0
C4A C:HEM203 3.0 6.8 1.0
C1A C:HEM203 3.1 6.8 1.0
SD D:MET52 3.1 5.6 1.0
C1D C:HEM203 3.1 6.8 1.0
C4B C:HEM203 3.1 6.8 1.0
C1B C:HEM203 3.1 6.8 1.0
C4D C:HEM203 3.1 6.8 1.0
SD C:MET52 3.2 6.5 1.0
CHD C:HEM203 3.4 6.8 1.0
CHC C:HEM203 3.4 6.8 1.0
CHB C:HEM203 3.4 6.8 1.0
CHA C:HEM203 3.5 6.8 1.0
CE D:MET52 4.1 5.6 1.0
C3C C:HEM203 4.2 6.8 1.0
C2C C:HEM203 4.2 6.8 1.0
C3A C:HEM203 4.3 6.8 1.0
C2A C:HEM203 4.3 6.8 1.0
C3B C:HEM203 4.3 6.8 1.0
C2D C:HEM203 4.3 6.8 1.0
C2B C:HEM203 4.3 6.8 1.0
C3D C:HEM203 4.4 6.8 1.0
HHD C:HEM203 4.4 6.8 1.0
HHA C:HEM203 4.4 6.8 1.0
HHC C:HEM203 4.4 6.8 1.0
HHB C:HEM203 4.4 6.8 1.0
CG C:MET52 4.5 6.5 1.0
CG D:MET52 4.5 5.6 1.0
CE1 C:PHE49 4.7 5.9 1.0
CD1 C:PHE49 4.9 5.9 1.0

Iron binding site 9 out of 59 in 7y6g

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Iron binding site 9 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:10.4
occ:1.00
 OE2 D:GLU51 2.5 5.5 1.0
OE2 D:GLU127 2.5 7.5 1.0
OE2 D:GLU18 2.6 5.2 1.0
OE1 D:GLU18 2.6 5.2 1.0
ND1 D:HIS54 2.7 5.8 1.0
CD D:GLU18 2.9 5.2 1.0
CD D:GLU51 3.5 5.5 1.0
CG D:HIS54 3.6 5.8 1.0
CD D:GLU127 3.6 7.5 1.0
CE1 D:HIS54 3.7 5.8 1.0
CB D:HIS54 3.8 5.8 1.0
OE1 D:GLU51 3.9 5.5 1.0
OE1 D:GLU127 4.1 7.5 1.0
FE D:FE202 4.3 30.0 1.0
CG2 D:ILE123 4.4 7.0 1.0
CG D:GLU18 4.4 5.2 1.0
CA D:GLU51 4.7 5.5 1.0
CD2 D:HIS54 4.8 5.8 1.0
NE2 D:HIS54 4.8 5.8 1.0
CG D:GLU51 4.8 5.5 1.0
CG D:GLU127 4.8 7.5 1.0
CB D:GLU51 5.0 5.5 1.0
NE2 D:GLN14 5.0 6.3 1.0

Iron binding site 10 out of 59 in 7y6g

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Iron binding site 10 out of 59 in the Cryo-Em Structure of Bacterioferritin Holoform 1A


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 of Bacterioferritin Holoform 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:30.0
occ:1.00
 OE1 D:GLU127 2.0 7.5 1.0
OE2 D:GLU94 2.6 8.6 1.0
OE1 D:GLU51 2.7 5.5 1.0
CD D:GLU127 3.1 7.5 1.0
OE1 D:GLU94 3.2 8.6 1.0
CD D:GLU94 3.2 8.6 1.0
OE2 D:GLU127 3.6 7.5 1.0
ND1 D:HIS130 3.6 6.7 1.0
CD D:GLU51 3.8 5.5 1.0
CB D:HIS130 4.1 6.7 1.0
OE2 D:GLU51 4.2 5.5 1.0
CG D:HIS130 4.2 6.7 1.0
CA D:GLU127 4.3 7.5 1.0
FE D:FE2201 4.3 10.4 1.0
CG D:GLU127 4.4 7.5 1.0
OH D:TYR25 4.5 5.0 1.0
OE2 D:GLU47 4.6 5.4 1.0
CE1 D:HIS130 4.6 6.7 1.0
CB D:GLU127 4.6 7.5 1.0
CG D:GLU94 4.7 8.6 1.0
CE1 D:TYR25 4.8 5.0 1.0
N D:GLU127 4.8 7.5 1.0
O D:ASP126 4.9 7.4 1.0

Reference:

C.Jobichen, J.Sivaraman. Cryo-Em Structure of Bacterioferritin Holoform 1A To Be Published.
Page generated: Fri Aug 9 11:20:08 2024

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