Iron in PDB 8s5i: Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction

Enzymatic activity of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction

All present enzymatic activity of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction:
4.2.1.22;

Iron Binding Sites:

The binding sites of Iron atom in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction (pdb code 8s5i). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction, PDB code: 8s5i:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8s5i

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Iron binding site 1 out of 6 in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:85.4
occ:1.00
 FE A:HEM601 0.0 85.4 1.0
NC A:HEM601 2.0 58.1 1.0
NA A:HEM601 2.0 62.7 1.0
NB A:HEM601 2.0 57.6 1.0
ND A:HEM601 2.0 57.9 1.0
HG A:CYS52 2.4 60.7 1.0
NE2 A:HIS65 2.7 49.5 1.0
C1D A:HEM601 3.0 57.4 1.0
C4C A:HEM601 3.0 51.8 1.0
C4A A:HEM601 3.0 61.0 1.0
C1B A:HEM601 3.0 56.1 1.0
C4D A:HEM601 3.0 58.6 1.0
C1A A:HEM601 3.0 59.4 1.0
C1C A:HEM601 3.0 54.3 1.0
C4B A:HEM601 3.1 58.5 1.0
SG A:CYS52 3.2 63.7 1.0
HB2 A:CYS52 3.3 59.5 1.0
CHB A:HEM601 3.4 58.2 1.0
CHD A:HEM601 3.4 55.5 1.0
HD2 A:HIS65 3.4 50.8 1.0
CHA A:HEM601 3.4 62.9 1.0
CHC A:HEM601 3.4 56.6 1.0
CD2 A:HIS65 3.4 46.3 1.0
CB A:CYS52 3.7 59.6 1.0
CE1 A:HIS65 3.8 53.8 1.0
HA A:CYS52 3.8 59.8 1.0
HE1 A:HIS65 4.0 51.4 1.0
C2D A:HEM601 4.2 55.4 1.0
C3D A:HEM601 4.2 54.8 1.0
C3A A:HEM601 4.2 58.6 1.0
HB2 A:TRP54 4.2 58.0 1.0
C2A A:HEM601 4.2 55.2 1.0
C3C A:HEM601 4.2 51.3 1.0
C2C A:HEM601 4.2 52.4 1.0
C2B A:HEM601 4.3 58.6 1.0
C3B A:HEM601 4.3 59.9 1.0
HD2 A:PRO64 4.3 57.0 1.0
HH12 A:ARG266 4.3 47.6 1.0
CA A:CYS52 4.4 59.6 1.0
HHB A:HEM601 4.4 57.9 1.0
H A:THR53 4.4 64.1 1.0
HHD A:HEM601 4.4 56.6 1.0
HHA A:HEM601 4.4 58.8 1.0
HHC A:HEM601 4.4 57.5 1.0
HB3 A:CYS52 4.6 60.9 1.0
CG A:HIS65 4.7 44.6 1.0
H A:TRP54 4.7 59.0 1.0
ND1 A:HIS65 4.8 53.1 1.0
N A:THR53 5.0 65.4 1.0
NH1 A:ARG266 5.0 50.0 1.0

Iron binding site 2 out of 6 in 8s5i

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Iron binding site 2 out of 6 in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:85.4
occ:1.00
 FE B:HEM601 0.0 85.4 1.0
NC B:HEM601 2.0 58.1 1.0
NA B:HEM601 2.0 62.7 1.0
NB B:HEM601 2.0 57.6 1.0
ND B:HEM601 2.0 57.9 1.0
HG B:CYS52 2.4 60.7 1.0
NE2 B:HIS65 2.7 49.5 1.0
C1D B:HEM601 3.0 57.4 1.0
C4C B:HEM601 3.0 51.8 1.0
C4A B:HEM601 3.0 61.0 1.0
C1B B:HEM601 3.0 56.1 1.0
C4D B:HEM601 3.0 58.6 1.0
C1C B:HEM601 3.0 54.3 1.0
C1A B:HEM601 3.0 59.4 1.0
C4B B:HEM601 3.1 58.5 1.0
SG B:CYS52 3.2 63.7 1.0
HB2 B:CYS52 3.3 59.5 1.0
CHB B:HEM601 3.4 58.2 1.0
CHD B:HEM601 3.4 55.5 1.0
HD2 B:HIS65 3.4 50.8 1.0
CHA B:HEM601 3.4 62.9 1.0
CHC B:HEM601 3.4 56.6 1.0
CD2 B:HIS65 3.4 46.3 1.0
CB B:CYS52 3.7 59.6 1.0
CE1 B:HIS65 3.8 53.8 1.0
HA B:CYS52 3.8 59.8 1.0
HE1 B:HIS65 4.0 51.4 1.0
C2D B:HEM601 4.2 55.4 1.0
C3D B:HEM601 4.2 54.8 1.0
C3A B:HEM601 4.2 58.6 1.0
HB2 B:TRP54 4.2 58.0 1.0
C2A B:HEM601 4.2 55.2 1.0
C3C B:HEM601 4.2 51.3 1.0
C2C B:HEM601 4.2 52.4 1.0
C2B B:HEM601 4.3 58.6 1.0
C3B B:HEM601 4.3 59.9 1.0
HD2 B:PRO64 4.3 57.0 1.0
HH12 B:ARG266 4.3 47.6 1.0
CA B:CYS52 4.3 59.6 1.0
HHB B:HEM601 4.4 57.9 1.0
H B:THR53 4.4 64.1 1.0
HHD B:HEM601 4.4 56.6 1.0
HHA B:HEM601 4.4 58.8 1.0
HHC B:HEM601 4.4 57.5 1.0
HB3 B:CYS52 4.6 60.9 1.0
CG B:HIS65 4.7 44.6 1.0
H B:TRP54 4.7 59.0 1.0
ND1 B:HIS65 4.8 53.1 1.0
N B:THR53 5.0 65.4 1.0
NH1 B:ARG266 5.0 50.0 1.0

Iron binding site 3 out of 6 in 8s5i

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Iron binding site 3 out of 6 in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:69.7
occ:1.00
 FE C:HEM601 0.0 69.7 1.0
NB C:HEM601 2.0 65.0 1.0
NA C:HEM601 2.0 69.7 1.0
NC C:HEM601 2.0 64.2 1.0
ND C:HEM601 2.0 69.0 1.0
HG C:CYS52 2.4 77.2 1.0
NE2 C:HIS65 2.8 61.7 1.0
C1A C:HEM601 3.0 67.6 1.0
C4A C:HEM601 3.0 67.5 1.0
C4D C:HEM601 3.0 66.2 1.0
C1D C:HEM601 3.0 65.8 1.0
C4C C:HEM601 3.1 55.5 1.0
C4B C:HEM601 3.1 65.4 1.0
C1B C:HEM601 3.1 63.0 1.0
C1C C:HEM601 3.1 62.6 1.0
HD2 C:HIS65 3.2 58.5 1.0
CD2 C:HIS65 3.4 58.5 1.0
CHA C:HEM601 3.4 68.0 1.0
CHB C:HEM601 3.4 62.3 1.0
CHC C:HEM601 3.4 63.7 1.0
CHD C:HEM601 3.4 57.2 1.0
SG C:CYS52 3.5 77.2 1.0
HD2 C:PRO64 3.6 60.9 1.0
HA C:CYS52 3.8 71.2 1.0
CE1 C:HIS65 4.0 57.0 1.0
HB2 C:CYS52 4.0 70.0 1.0
HB2 C:TRP54 4.1 64.7 1.0
H C:THR53 4.1 75.4 1.0
C2A C:HEM601 4.2 64.4 1.0
CB C:CYS52 4.2 70.0 1.0
C3A C:HEM601 4.2 65.9 1.0
C3D C:HEM601 4.2 63.7 1.0
C2D C:HEM601 4.3 64.9 1.0
C3C C:HEM601 4.3 57.2 1.0
C3B C:HEM601 4.3 67.9 1.0
C2C C:HEM601 4.3 61.7 1.0
C2B C:HEM601 4.3 66.3 1.0
HE1 C:HIS65 4.3 57.0 1.0
HH12 C:ARG266 4.3 49.9 1.0
HHA C:HEM601 4.4 68.0 1.0
HHB C:HEM601 4.4 62.3 1.0
HHC C:HEM601 4.4 63.7 1.0
HHD C:HEM601 4.4 57.2 1.0
CD C:PRO64 4.4 60.9 1.0
HD3 C:PRO64 4.5 60.9 1.0
H C:TRP54 4.5 67.3 1.0
CA C:CYS52 4.5 71.2 1.0
OG C:SER63 4.6 76.8 1.0
CG C:HIS65 4.7 55.1 1.0
HG2 C:PRO64 4.7 59.1 1.0
HG C:SER63 4.8 76.8 1.0
N C:THR53 4.8 75.4 1.0
CB C:TRP54 4.9 64.7 1.0
ND1 C:HIS65 4.9 54.5 1.0
HB3 C:TRP54 4.9 64.7 1.0
NH1 C:ARG266 5.0 49.9 1.0

Iron binding site 4 out of 6 in 8s5i

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Iron binding site 4 out of 6 in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:69.7
occ:1.00
 FE D:HEM601 0.0 69.7 1.0
NC D:HEM601 2.0 64.2 1.0
NA D:HEM601 2.0 69.7 1.0
ND D:HEM601 2.0 69.0 1.0
NB D:HEM601 2.0 65.0 1.0
HG D:CYS52 2.4 77.2 1.0
NE2 D:HIS65 2.8 61.7 1.0
C4D D:HEM601 3.0 66.2 1.0
C1D D:HEM601 3.0 65.8 1.0
C1A D:HEM601 3.0 67.6 1.0
C4C D:HEM601 3.0 55.5 1.0
C1C D:HEM601 3.0 62.6 1.0
C4A D:HEM601 3.0 67.5 1.0
C1B D:HEM601 3.0 63.0 1.0
C4B D:HEM601 3.1 65.4 1.0
SG D:CYS52 3.2 77.2 1.0
HD2 D:HIS65 3.2 58.5 1.0
CD2 D:HIS65 3.4 58.5 1.0
CHA D:HEM601 3.4 68.0 1.0
CHC D:HEM601 3.4 63.7 1.0
CHD D:HEM601 3.4 57.2 1.0
CHB D:HEM601 3.4 62.3 1.0
HB2 D:CYS52 3.5 70.0 1.0
HD2 D:PRO64 3.6 60.9 1.0
CB D:CYS52 3.9 70.0 1.0
CE1 D:HIS65 3.9 57.0 1.0
HH12 D:ARG266 4.0 49.9 1.0
HA D:CYS52 4.0 71.2 1.0
HB2 D:TRP54 4.2 64.7 1.0
C3D D:HEM601 4.2 63.7 1.0
C2D D:HEM601 4.2 64.9 1.0
C2A D:HEM601 4.2 64.4 1.0
C3A D:HEM601 4.2 65.9 1.0
C3C D:HEM601 4.3 57.2 1.0
C2B D:HEM601 4.3 66.3 1.0
C2C D:HEM601 4.3 61.7 1.0
HE1 D:HIS65 4.3 57.0 1.0
C3B D:HEM601 4.3 67.9 1.0
HHC D:HEM601 4.3 63.7 1.0
HHA D:HEM601 4.4 68.0 1.0
HHD D:HEM601 4.4 57.2 1.0
HHB D:HEM601 4.4 62.3 1.0
CD D:PRO64 4.4 60.9 1.0
HD3 D:PRO64 4.4 60.9 1.0
H D:THR53 4.5 75.4 1.0
CA D:CYS52 4.5 71.2 1.0
HG2 D:PRO64 4.6 59.1 1.0
CG D:HIS65 4.6 55.1 1.0
H D:TRP54 4.7 67.3 1.0
HB3 D:CYS52 4.7 70.0 1.0
NH1 D:ARG266 4.7 49.9 1.0
HH11 D:ARG266 4.8 49.9 1.0
ND1 D:HIS65 4.9 54.5 1.0

Iron binding site 5 out of 6 in 8s5i

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Iron binding site 5 out of 6 in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe601

b:69.7
occ:1.00
 FE E:HEM601 0.0 69.7 1.0
NC E:HEM601 2.0 64.2 1.0
NA E:HEM601 2.0 69.7 1.0
ND E:HEM601 2.0 69.0 1.0
NB E:HEM601 2.0 65.0 1.0
HG E:CYS52 2.4 77.2 1.0
NE2 E:HIS65 2.8 61.7 1.0
C1A E:HEM601 3.0 67.6 1.0
C4D E:HEM601 3.0 66.2 1.0
C1D E:HEM601 3.0 65.8 1.0
C4A E:HEM601 3.0 67.5 1.0
C1C E:HEM601 3.0 62.6 1.0
C4C E:HEM601 3.0 55.5 1.0
C1B E:HEM601 3.0 63.0 1.0
C4B E:HEM601 3.1 65.4 1.0
SG E:CYS52 3.2 77.2 1.0
HD2 E:HIS65 3.3 58.5 1.0
CHA E:HEM601 3.4 68.0 1.0
CHC E:HEM601 3.4 63.7 1.0
CD2 E:HIS65 3.4 58.5 1.0
CHB E:HEM601 3.4 62.3 1.0
CHD E:HEM601 3.4 57.2 1.0
HD2 E:PRO64 3.6 60.9 1.0
HB2 E:CYS52 3.8 70.0 1.0
CE1 E:HIS65 3.9 57.0 1.0
HH12 E:ARG266 4.0 49.9 1.0
CB E:CYS52 4.1 70.0 1.0
HA E:CYS52 4.2 71.2 1.0
C3D E:HEM601 4.2 63.7 1.0
HB2 E:TRP54 4.2 64.7 1.0
C2D E:HEM601 4.2 64.9 1.0
C2A E:HEM601 4.2 64.4 1.0
C3A E:HEM601 4.2 65.9 1.0
HE1 E:HIS65 4.2 57.0 1.0
C2B E:HEM601 4.3 66.3 1.0
C3C E:HEM601 4.3 57.2 1.0
C2C E:HEM601 4.3 61.7 1.0
C3B E:HEM601 4.3 67.9 1.0
HHC E:HEM601 4.3 63.7 1.0
HHA E:HEM601 4.4 68.0 1.0
HHB E:HEM601 4.4 62.3 1.0
CD E:PRO64 4.4 60.9 1.0
HHD E:HEM601 4.4 57.2 1.0
HD3 E:PRO64 4.4 60.9 1.0
H E:THR53 4.5 75.4 1.0
HG2 E:PRO64 4.5 59.1 1.0
CG E:HIS65 4.7 55.1 1.0
CA E:CYS52 4.7 71.2 1.0
NH1 E:ARG266 4.7 49.9 1.0
HH11 E:ARG266 4.8 49.9 1.0
H E:TRP54 4.9 67.3 1.0
ND1 E:HIS65 4.9 54.5 1.0
HB3 E:CYS52 4.9 70.0 1.0
OG E:SER63 5.0 76.8 1.0

Iron binding site 6 out of 6 in 8s5i

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Iron binding site 6 out of 6 in the Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Full-Length Human Cystathionine Beta-Synthase with C-Terminal 6XHIS- Tag, Basal State, Single Particle Reconstruction within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe601

b:69.7
occ:1.00
 FE F:HEM601 0.0 69.7 1.0
NC F:HEM601 2.0 64.2 1.0
NA F:HEM601 2.0 69.7 1.0
ND F:HEM601 2.0 69.0 1.0
NB F:HEM601 2.0 65.0 1.0
HG F:CYS52 2.4 77.2 1.0
C4A F:HEM601 3.0 67.5 1.0
C1A F:HEM601 3.0 67.6 1.0
NE2 F:HIS65 3.0 61.7 1.0
C1B F:HEM601 3.0 63.0 1.0
C4D F:HEM601 3.1 66.2 1.0
C4C F:HEM601 3.1 55.5 1.0
C1D F:HEM601 3.1 65.8 1.0
C1C F:HEM601 3.1 62.6 1.0
C4B F:HEM601 3.1 65.4 1.0
HD2 F:HIS65 3.3 58.5 1.0
CHB F:HEM601 3.4 62.3 1.0
CHA F:HEM601 3.4 68.0 1.0
CHC F:HEM601 3.4 63.7 1.0
CHD F:HEM601 3.4 57.2 1.0
CD2 F:HIS65 3.5 58.5 1.0
SG F:CYS52 3.5 77.2 1.0
HD2 F:PRO64 3.6 60.9 1.0
HA F:CYS52 3.8 71.2 1.0
HB2 F:CYS52 4.1 70.0 1.0
H F:THR53 4.2 75.4 1.0
CE1 F:HIS65 4.2 57.0 1.0
C3A F:HEM601 4.2 65.9 1.0
C2A F:HEM601 4.2 64.4 1.0
C2D F:HEM601 4.3 64.9 1.0
C3D F:HEM601 4.3 63.7 1.0
HB2 F:TRP54 4.3 64.7 1.0
C2B F:HEM601 4.3 66.3 1.0
C3C F:HEM601 4.3 57.2 1.0
C2C F:HEM601 4.3 61.7 1.0
C3B F:HEM601 4.3 67.9 1.0
CB F:CYS52 4.3 70.0 1.0
OG F:SER63 4.3 76.8 1.0
HH12 F:ARG266 4.3 49.9 1.0
HHB F:HEM601 4.4 62.3 1.0
HHA F:HEM601 4.4 68.0 1.0
HHC F:HEM601 4.4 63.7 1.0
HHD F:HEM601 4.4 57.2 1.0
CD F:PRO64 4.4 60.9 1.0
HD3 F:PRO64 4.5 60.9 1.0
HG F:SER63 4.5 76.8 1.0
HE1 F:HIS65 4.5 57.0 1.0
CA F:CYS52 4.5 71.2 1.0
HA F:SER63 4.7 73.7 1.0
CG F:HIS65 4.8 55.1 1.0
H F:TRP54 4.8 67.3 1.0
N F:THR53 4.9 75.4 1.0
HG2 F:PRO64 5.0 59.1 1.0

Reference:

T.J.Mccorvie, D.Adamoski, R.A.C.Machado, J.Tang, H.J.Bailey, D.S.M.Ferreira, C.Strain-Damerell, A.Basle, A.L.B.Ambrosio, S.M.G.Dias, W.W.Yue. Architecture and Regulation of Filamentous Human Cystathionine Beta-Synthase. Nat Commun V. 15 2931 2024.
ISSN: ESSN 2041-1723
PubMed: 38575566
DOI: 10.1038/S41467-024-46864-X
Page generated: Sat Aug 10 17:15:13 2024

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