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Iron in PDB 6nbc: Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev

Iron Binding Sites:

The binding sites of Iron atom in the Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev (pdb code 6nbc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev, PDB code: 6nbc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6nbc

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Iron binding site 1 out of 4 in the Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:48.3
occ:1.00
FE A:HEM201 0.0 48.3 1.0
ND A:HEM201 2.0 48.3 1.0
NC A:HEM201 2.0 48.3 1.0
NB A:HEM201 2.0 48.3 1.0
NA A:HEM201 2.0 48.3 1.0
NE2 A:HIS87 2.1 47.9 1.0
CE1 A:HIS87 3.0 47.9 1.0
C1C A:HEM201 3.0 48.3 1.0
C1B A:HEM201 3.0 48.3 1.0
C1A A:HEM201 3.0 48.3 1.0
C4D A:HEM201 3.0 48.3 1.0
C4A A:HEM201 3.0 48.3 1.0
C1D A:HEM201 3.0 48.3 1.0
C4C A:HEM201 3.1 48.3 1.0
C4B A:HEM201 3.1 48.3 1.0
CD2 A:HIS87 3.1 47.9 1.0
CHC A:HEM201 3.4 48.3 1.0
CHA A:HEM201 3.4 48.3 1.0
CHB A:HEM201 3.4 48.3 1.0
CHD A:HEM201 3.4 48.3 1.0
ND1 A:HIS87 4.1 47.9 1.0
CG A:HIS87 4.2 47.9 1.0
NE2 A:HIS58 4.2 53.2 1.0
C3A A:HEM201 4.2 48.3 1.0
C2A A:HEM201 4.2 48.3 1.0
C2B A:HEM201 4.2 48.3 1.0
C3D A:HEM201 4.2 48.3 1.0
C2D A:HEM201 4.2 48.3 1.0
C2C A:HEM201 4.2 48.3 1.0
C3C A:HEM201 4.3 48.3 1.0
C3B A:HEM201 4.3 48.3 1.0
CE1 A:HIS58 4.6 53.2 1.0
CG2 A:VAL62 4.6 50.7 1.0

Iron binding site 2 out of 4 in 6nbc

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Iron binding site 2 out of 4 in the Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:49.5
occ:1.00
FE B:HEM201 0.0 49.5 1.0
NC B:HEM201 2.0 49.5 1.0
ND B:HEM201 2.0 49.5 1.0
NA B:HEM201 2.0 49.5 1.0
NB B:HEM201 2.0 49.5 1.0
NE2 B:HIS92 2.2 52.1 1.0
C1C B:HEM201 3.0 49.5 1.0
C4C B:HEM201 3.0 49.5 1.0
C1D B:HEM201 3.0 49.5 1.0
C4D B:HEM201 3.0 49.5 1.0
C4A B:HEM201 3.0 49.5 1.0
C1A B:HEM201 3.0 49.5 1.0
CD2 B:HIS92 3.0 52.1 1.0
C1B B:HEM201 3.1 49.5 1.0
C4B B:HEM201 3.1 49.5 1.0
CE1 B:HIS92 3.2 52.1 1.0
CHC B:HEM201 3.4 49.5 1.0
CHD B:HEM201 3.4 49.5 1.0
CHB B:HEM201 3.4 49.5 1.0
CHA B:HEM201 3.4 49.5 1.0
NE2 B:HIS63 4.1 52.7 1.0
C2C B:HEM201 4.2 49.5 1.0
CG B:HIS92 4.2 52.1 1.0
C3C B:HEM201 4.2 49.5 1.0
ND1 B:HIS92 4.2 52.1 1.0
C2D B:HEM201 4.2 49.5 1.0
C3D B:HEM201 4.2 49.5 1.0
C3A B:HEM201 4.3 49.5 1.0
C2A B:HEM201 4.3 49.5 1.0
C2B B:HEM201 4.3 49.5 1.0
C3B B:HEM201 4.3 49.5 1.0
CG2 B:VAL67 4.6 51.2 1.0
CE1 B:HIS63 4.8 52.7 1.0

Iron binding site 3 out of 4 in 6nbc

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Iron binding site 3 out of 4 in the Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:47.8
occ:1.00
FE C:HEM201 0.0 47.8 1.0
ND C:HEM201 2.0 47.8 1.0
NB C:HEM201 2.0 47.8 1.0
NA C:HEM201 2.0 47.8 1.0
NC C:HEM201 2.0 47.8 1.0
NE2 C:HIS87 2.1 47.2 1.0
C4B C:HEM201 3.0 47.8 1.0
C1A C:HEM201 3.0 47.8 1.0
C4D C:HEM201 3.0 47.8 1.0
CE1 C:HIS87 3.0 47.2 1.0
C1C C:HEM201 3.0 47.8 1.0
C1D C:HEM201 3.0 47.8 1.0
C1B C:HEM201 3.0 47.8 1.0
C4A C:HEM201 3.1 47.8 1.0
C4C C:HEM201 3.1 47.8 1.0
CD2 C:HIS87 3.1 47.2 1.0
CHC C:HEM201 3.4 47.8 1.0
CHA C:HEM201 3.4 47.8 1.0
CHD C:HEM201 3.4 47.8 1.0
CHB C:HEM201 3.4 47.8 1.0
ND1 C:HIS87 4.1 47.2 1.0
NE2 C:HIS58 4.2 52.2 1.0
CG C:HIS87 4.2 47.2 1.0
C2A C:HEM201 4.2 47.8 1.0
C3D C:HEM201 4.2 47.8 1.0
C3A C:HEM201 4.2 47.8 1.0
C2D C:HEM201 4.2 47.8 1.0
C3B C:HEM201 4.2 47.8 1.0
C2C C:HEM201 4.3 47.8 1.0
C2B C:HEM201 4.3 47.8 1.0
C3C C:HEM201 4.3 47.8 1.0
CE1 C:HIS58 4.6 52.2 1.0
CG2 C:VAL62 4.6 49.6 1.0

Iron binding site 4 out of 4 in 6nbc

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Iron binding site 4 out of 4 in the Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Methemoglobin State 1 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:48.3
occ:1.00
FE D:HEM201 0.0 48.3 1.0
NC D:HEM201 2.0 48.3 1.0
ND D:HEM201 2.0 48.3 1.0
NA D:HEM201 2.0 48.3 1.0
NB D:HEM201 2.0 48.3 1.0
NE2 D:HIS92 2.2 50.7 1.0
C1C D:HEM201 3.0 48.3 1.0
C1A D:HEM201 3.0 48.3 1.0
C4D D:HEM201 3.0 48.3 1.0
C4B D:HEM201 3.0 48.3 1.0
C4C D:HEM201 3.0 48.3 1.0
C1D D:HEM201 3.0 48.3 1.0
C4A D:HEM201 3.0 48.3 1.0
CD2 D:HIS92 3.1 50.7 1.0
C1B D:HEM201 3.1 48.3 1.0
CE1 D:HIS92 3.2 50.7 1.0
CHC D:HEM201 3.4 48.3 1.0
CHA D:HEM201 3.4 48.3 1.0
CHD D:HEM201 3.4 48.3 1.0
CHB D:HEM201 3.5 48.3 1.0
C2C D:HEM201 4.2 48.3 1.0
CG D:HIS92 4.2 50.7 1.0
C2A D:HEM201 4.2 48.3 1.0
NE2 D:HIS63 4.2 51.8 1.0
C3C D:HEM201 4.2 48.3 1.0
C3A D:HEM201 4.2 48.3 1.0
C3D D:HEM201 4.2 48.3 1.0
C2D D:HEM201 4.2 48.3 1.0
ND1 D:HIS92 4.2 50.7 1.0
C3B D:HEM201 4.3 48.3 1.0
C2B D:HEM201 4.3 48.3 1.0
CG2 D:VAL67 4.7 50.6 1.0
CE1 D:HIS63 4.9 51.8 1.0

Reference:

M.A.Herzik Jr., M.Wu, G.C.Lander. High-Resolution Structure Determination of Sub-100 kDa Complexes Using Conventional Cryo-Em. Nat Commun V. 10 1032 2019.
ISSN: ESSN 2041-1723
PubMed: 30833564
DOI: 10.1038/S41467-019-08991-8
Page generated: Wed Aug 7 02:53:47 2024

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