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Iron in PDB 8jax: Cryo-Em Structure of Holo Form of Scbfr with O Symmetry

Enzymatic activity of Cryo-Em Structure of Holo Form of Scbfr with O Symmetry

All present enzymatic activity of Cryo-Em Structure of Holo Form of Scbfr with O Symmetry:
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 - 36;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry (pdb code 8jax). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry, PDB code: 8jax:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in 8jax

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Iron binding site 1 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:167.3
occ:1.00
 OE1 A:GLU127 2.0 107.3 1.0
OE1 A:GLU51 2.0 96.9 1.0
OE2 A:GLU51 2.1 92.4 1.0
OE2 A:GLU127 2.2 102.7 1.0
OE2 A:GLU18 2.2 92.7 1.0
CD A:GLU127 2.3 101.1 1.0
OE1 A:GLU18 2.3 92.9 1.0
CD A:GLU51 2.3 94.1 1.0
CD A:GLU18 2.6 93.0 1.0
OE1 A:GLU94 2.6 112.4 1.0
ND1 A:HIS54 3.1 83.2 1.0
CE1 A:HIS54 3.4 85.8 1.0
CD A:GLU94 3.7 109.4 1.0
CG A:GLU127 3.7 96.3 1.0
CG A:GLU51 3.8 88.0 1.0
OE2 A:GLU94 4.0 108.6 1.0
CG A:GLU18 4.1 90.0 1.0
CG A:HIS54 4.4 80.8 1.0
CB A:GLU51 4.7 80.5 1.0
NE2 A:HIS54 4.7 80.9 1.0
CB A:GLU127 4.7 90.3 1.0

Iron binding site 2 out of 36 in 8jax

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Iron binding site 2 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:69.3
occ:0.04
 FE B:HEM201 0.0 69.3 0.0
CE B:MET52 1.6 78.3 1.0
NB B:HEM201 2.0 70.4 0.0
ND B:HEM201 2.0 70.5 0.0
NC B:HEM201 2.1 70.6 0.0
NA B:HEM201 2.1 70.7 0.0
SD A:MET52 3.0 105.2 1.0
C4B B:HEM201 3.0 70.6 0.0
C4D B:HEM201 3.0 70.4 0.0
C1A B:HEM201 3.0 70.7 0.0
SD B:MET52 3.0 104.9 1.0
C1C B:HEM201 3.1 70.5 0.0
C1D B:HEM201 3.1 70.5 0.0
C1B B:HEM201 3.1 70.5 0.0
C4A B:HEM201 3.1 70.7 0.0
C4C B:HEM201 3.1 70.9 0.0
CHC B:HEM201 3.3 70.7 0.0
CHA B:HEM201 3.4 70.6 0.0
CHD B:HEM201 3.5 70.7 0.0
CHB B:HEM201 3.5 70.8 0.0
CE A:MET52 3.5 81.3 1.0
C2A B:HEM201 4.2 70.5 0.0
C3B B:HEM201 4.2 69.9 0.0
C3D B:HEM201 4.2 70.4 0.0
C3A B:HEM201 4.3 70.4 0.0
C2B B:HEM201 4.3 70.1 0.0
C2D B:HEM201 4.3 70.5 0.0
C2C B:HEM201 4.3 70.2 0.0
C3C B:HEM201 4.3 70.5 0.0
CG B:MET52 4.3 83.9 1.0
CG A:MET52 4.3 85.0 1.0
CE1 B:PHE49 4.5 77.2 1.0
CD1 B:PHE49 4.9 73.0 1.0

Iron binding site 3 out of 36 in 8jax

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Iron binding site 3 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:174.4
occ:1.00
 OE2 B:GLU127 2.0 100.9 1.0
OE1 B:GLU51 2.0 93.7 1.0
OE2 B:GLU51 2.1 97.1 1.0
OE1 B:GLU127 2.1 104.0 1.0
OE2 B:GLU94 2.1 112.3 1.0
OE2 B:GLU18 2.2 100.6 1.0
CD B:GLU127 2.3 100.8 1.0
CD B:GLU51 2.3 95.1 1.0
OE1 B:GLU18 2.3 91.5 1.0
OE1 B:GLU94 2.6 112.3 1.0
CD B:GLU18 2.6 96.5 1.0
CD B:GLU94 2.7 111.8 1.0
ND1 B:HIS54 3.1 79.7 1.0
CE1 B:HIS54 3.3 80.8 1.0
CG B:GLU127 3.8 91.4 1.0
CG B:GLU51 3.8 89.5 1.0
CG B:GLU18 4.1 90.8 1.0
CG B:GLU94 4.2 107.0 1.0
CG B:HIS54 4.4 78.2 1.0
NE2 B:HIS54 4.6 79.0 1.0
CB B:GLU51 4.6 79.0 1.0
CB B:GLU127 4.7 85.1 1.0
CA B:GLU51 4.9 81.1 1.0

Iron binding site 4 out of 36 in 8jax

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Iron binding site 4 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:170.7
occ:1.00
 OE2 C:GLU127 2.1 113.4 1.0
OE1 C:GLU51 2.1 106.2 1.0
OE2 C:GLU51 2.1 100.5 1.0
OE2 C:GLU18 2.1 99.9 1.0
OE1 C:GLU18 2.2 104.8 1.0
OE1 C:GLU127 2.3 107.9 1.0
CD C:GLU51 2.4 100.3 1.0
CD C:GLU127 2.4 109.7 1.0
ND1 C:HIS54 2.4 85.8 1.0
CD C:GLU18 2.5 100.3 1.0
CE1 C:HIS54 3.1 87.3 1.0
CG C:HIS54 3.6 83.7 1.0
CG C:GLU127 3.7 101.5 1.0
CG C:GLU51 3.9 93.2 1.0
CG C:GLU18 4.0 95.0 1.0
CB C:HIS54 4.2 80.8 1.0
NE2 C:HIS54 4.3 87.5 1.0
CG2 C:ILE123 4.5 91.4 1.0
CD2 C:HIS54 4.6 85.4 1.0
CB C:GLU51 4.7 84.5 1.0
CA C:GLU51 4.7 86.8 1.0
CB C:GLU18 4.9 83.5 1.0
CB C:GLU127 4.9 93.0 1.0

Iron binding site 5 out of 36 in 8jax

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Iron binding site 5 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:86.8
occ:0.00
 FE D:HEM201 0.0 86.8 0.0
CE D:MET52 1.8 89.0 1.0
CE C:MET52 1.9 89.2 1.0
NC D:HEM201 2.0 86.8 0.0
NA D:HEM201 2.1 86.8 0.0
ND D:HEM201 2.1 86.8 0.0
NB D:HEM201 2.1 86.8 0.0
SD C:MET52 2.9 110.6 1.0
C4A D:HEM201 3.0 86.7 0.0
C1A D:HEM201 3.0 86.7 0.0
C4C D:HEM201 3.0 86.8 0.0
C1C D:HEM201 3.0 86.8 0.0
C1B D:HEM201 3.1 86.6 0.0
C4D D:HEM201 3.1 86.8 0.0
C1D D:HEM201 3.1 86.8 0.0
C4B D:HEM201 3.2 86.7 0.0
CHA D:HEM201 3.4 86.7 0.0
CHB D:HEM201 3.4 86.6 0.0
CHD D:HEM201 3.4 86.8 0.0
SD D:MET52 3.4 108.6 1.0
CHC D:HEM201 3.5 86.7 0.0
CG D:MET52 4.0 90.2 1.0
C3A D:HEM201 4.0 86.7 0.0
C2A D:HEM201 4.0 86.7 0.0
C3C D:HEM201 4.1 86.8 0.0
C2C D:HEM201 4.1 86.7 0.0
CG C:MET52 4.2 87.5 1.0
C2D D:HEM201 4.3 86.7 0.0
C3D D:HEM201 4.3 86.7 0.0
C2B D:HEM201 4.3 86.5 0.0
C3B D:HEM201 4.4 86.7 0.0
CE1 C:PHE49 4.8 82.7 1.0

Iron binding site 6 out of 36 in 8jax

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Iron binding site 6 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:173.6
occ:1.00
 OE1 D:GLU51 2.0 104.6 1.0
OE2 D:GLU51 2.1 108.3 1.0
OE2 D:GLU127 2.2 117.8 1.0
OE1 D:GLU18 2.2 99.9 1.0
OE2 D:GLU18 2.2 105.1 1.0
OE1 D:GLU127 2.2 117.9 1.0
CD D:GLU51 2.3 104.2 1.0
CD D:GLU127 2.3 114.3 1.0
CD D:GLU18 2.5 101.6 1.0
ND1 D:HIS54 2.6 83.5 1.0
CE1 D:HIS54 3.3 86.5 1.0
CG D:GLU127 3.6 104.7 1.0
CG D:GLU51 3.8 97.3 1.0
CG D:HIS54 3.8 84.4 1.0
CG D:GLU18 4.0 95.0 1.0
CG2 D:ILE123 4.2 85.8 1.0
CB D:HIS54 4.2 81.9 1.0
CB D:GLU51 4.4 88.2 1.0
CA D:GLU51 4.5 92.1 1.0
NE2 D:HIS54 4.5 88.8 1.0
CD2 D:HIS54 4.8 85.7 1.0
CB D:GLU127 4.9 97.0 1.0

Iron binding site 7 out of 36 in 8jax

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Iron binding site 7 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:194.2
occ:1.00
 CD F:GLU127 2.0 112.7 1.0
OE1 F:GLU127 2.0 115.1 1.0
OE1 F:GLU94 2.1 121.3 1.0
OE2 F:GLU51 2.1 102.7 1.0
OE1 F:GLU51 2.1 106.5 1.0
OE2 F:GLU18 2.2 105.1 1.0
OE2 F:GLU127 2.3 114.5 1.0
OE1 F:GLU18 2.3 105.4 1.0
CD F:GLU51 2.4 102.7 1.0
CD F:GLU18 2.6 102.7 1.0
OE2 F:GLU94 2.6 115.0 1.0
CD F:GLU94 2.7 119.4 1.0
CG F:GLU127 2.8 106.9 1.0
ND1 F:HIS54 3.1 94.0 1.0
CE1 F:HIS54 3.4 95.0 1.0
CG F:GLU51 3.8 96.8 1.0
CG F:GLU18 4.1 97.5 1.0
CB F:GLU127 4.1 97.6 1.0
CG F:GLU94 4.2 115.1 1.0
CG F:HIS54 4.4 88.8 1.0
NE2 F:HIS54 4.7 91.7 1.0
CB F:GLU51 4.8 89.7 1.0

Iron binding site 8 out of 36 in 8jax

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Iron binding site 8 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe202

b:87.2
occ:0.00
 FE F:HEM202 0.0 87.2 0.0
ND F:HEM202 2.1 87.1 0.0
NC F:HEM202 2.1 87.1 0.0
NA F:HEM202 2.1 87.4 0.0
NB F:HEM202 2.1 87.1 0.0
CE E:MET52 2.1 84.2 1.0
CE F:MET52 2.3 90.0 1.0
C4A F:HEM202 3.0 87.3 0.0
C1A F:HEM202 3.0 87.2 0.0
C4D F:HEM202 3.0 87.1 0.0
C1C F:HEM202 3.0 87.0 0.0
C1D F:HEM202 3.1 87.0 0.0
C1B F:HEM202 3.1 87.2 0.0
C4C F:HEM202 3.1 86.8 0.0
C4B F:HEM202 3.1 87.0 0.0
CHA F:HEM202 3.4 87.2 0.0
CHC F:HEM202 3.4 87.0 0.0
CHB F:HEM202 3.4 87.2 0.0
CHD F:HEM202 3.5 86.8 0.0
SD E:MET52 3.6 105.3 1.0
SD F:MET52 4.0 125.0 1.0
C3A F:HEM202 4.1 87.2 0.0
C2A F:HEM202 4.1 87.2 0.0
C3D F:HEM202 4.2 87.0 0.0
C2D F:HEM202 4.3 87.0 0.0
C2C F:HEM202 4.3 87.0 0.0
C3C F:HEM202 4.3 86.8 0.0
C2B F:HEM202 4.3 87.1 0.0
C3B F:HEM202 4.3 87.0 0.0
CG E:MET52 4.4 89.8 1.0
CG F:MET52 4.9 97.5 1.0

Iron binding site 9 out of 36 in 8jax

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Iron binding site 9 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:173.6
occ:1.00
 OE2 E:GLU18 2.1 104.2 1.0
OE1 E:GLU18 2.2 101.0 1.0
OE2 E:GLU127 2.2 113.4 1.0
OE2 E:GLU51 2.2 101.2 1.0
OE1 E:GLU51 2.2 106.9 1.0
OE1 E:GLU127 2.3 113.1 1.0
CD E:GLU127 2.4 110.7 1.0
CD E:GLU18 2.4 101.4 1.0
CD E:GLU51 2.5 102.6 1.0
CG E:GLU127 3.6 102.9 1.0
OE1 E:GLN14 3.9 93.2 1.0
CG E:GLU18 3.9 90.0 1.0
CG E:GLU51 4.1 98.6 1.0
CD2 E:HIS54 4.1 78.7 1.0
CG2 E:ILE123 4.4 86.3 1.0
CG E:HIS54 4.8 81.0 1.0
CB E:GLU18 4.9 78.6 1.0
CD E:GLN14 4.9 84.5 1.0
CB E:GLU127 4.9 92.9 1.0
OE1 E:GLU94 4.9 102.4 1.0
CB E:HIS54 4.9 75.0 1.0
CB E:GLU51 5.0 90.7 1.0

Iron binding site 10 out of 36 in 8jax

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Iron binding site 10 out of 36 in the Cryo-Em Structure of Holo Form of Scbfr with O Symmetry


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 Holo Form of Scbfr with O Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:162.1
occ:1.00
 OE1 G:GLU127 1.9 105.5 1.0
OE1 G:GLU51 2.0 98.7 1.0
OE2 G:GLU51 2.1 92.9 1.0
OE1 G:GLU18 2.2 93.7 1.0
OE2 G:GLU18 2.2 93.7 1.0
CD G:GLU51 2.3 95.3 1.0
OE2 G:GLU127 2.4 98.2 1.0
CD G:GLU127 2.5 101.6 1.0
ND1 G:HIS54 2.5 79.8 1.0
CD G:GLU18 2.5 92.7 1.0
CE1 G:HIS54 3.1 81.6 1.0
CG G:GLU51 3.7 89.2 1.0
CG G:HIS54 3.7 78.1 1.0
CG G:GLU127 4.0 94.9 1.0
CG G:GLU18 4.0 86.7 1.0
CB G:HIS54 4.3 74.1 1.0
CB G:GLU51 4.3 79.4 1.0
NE2 G:HIS54 4.4 80.5 1.0
CA G:GLU51 4.4 81.9 1.0
CG2 G:ILE123 4.7 80.7 1.0
CD2 G:HIS54 4.7 78.3 1.0

Reference:

C.Jobichen, T.Y.Chong, R.Rattinam, S.Basak, M.Srinivasan, Y.K.Choong, K.P.Pandey, T.B.Ngoc, J.Shi, J.Angayarkann, J.Sivaraman. Bacterioferritin Nanocage Structures Uncover the Bio-Mineralization Process in Ferritins PNAS Nexus 2023.
ISSN: ESSN 2752-6542
DOI: 10.1093/PNASNEXUS/PGAD235
Page generated: Sat Aug 10 06:39:01 2024

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