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Iron in PDB 1jbq: Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein

Enzymatic activity of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein

All present enzymatic activity of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein:
4.2.1.22;

Protein crystallography data

The structure of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein, PDB code: 1jbq was solved by M.Meier, M.Janosik, V.Kery, J.P.Kraus, P.Burkhard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.34 / 2.60
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 144.520, 144.520, 108.160, 90.00, 90.00, 120.00
R / Rfree (%) 25.7 / 29.6

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein (pdb code 1jbq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein, PDB code: 1jbq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1jbq

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Iron binding site 1 out of 6 in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.0
occ:1.00
 FE A:HEM501 0.0 25.0 1.0
ND A:HEM501 2.0 26.4 1.0
NC A:HEM501 2.0 22.7 1.0
NB A:HEM501 2.0 27.4 1.0
NA A:HEM501 2.0 19.3 1.0
NE2 A:HIS65 2.2 30.4 1.0
SG A:CYS52 2.3 37.9 1.0
C1C A:HEM501 3.0 31.3 1.0
C1B A:HEM501 3.0 34.2 1.0
CD2 A:HIS65 3.0 37.3 1.0
C4D A:HEM501 3.0 28.2 1.0
C1D A:HEM501 3.0 35.7 1.0
C4C A:HEM501 3.1 32.1 1.0
C1A A:HEM501 3.1 22.9 1.0
C4B A:HEM501 3.1 31.7 1.0
C4A A:HEM501 3.1 18.3 1.0
CE1 A:HIS65 3.4 32.4 1.0
CHB A:HEM501 3.4 27.8 1.0
CHD A:HEM501 3.4 37.9 1.0
CHA A:HEM501 3.4 24.9 1.0
CHC A:HEM501 3.4 34.2 1.0
CB A:CYS52 3.6 32.7 1.0
CA A:CYS52 4.3 33.5 1.0
CG A:HIS65 4.3 41.5 1.0
C2D A:HEM501 4.3 39.3 1.0
C3D A:HEM501 4.3 32.7 1.0
C2B A:HEM501 4.3 39.3 1.0
C3B A:HEM501 4.3 35.8 1.0
C2C A:HEM501 4.3 31.9 1.0
C3C A:HEM501 4.3 33.0 1.0
C2A A:HEM501 4.3 22.1 1.0
C3A A:HEM501 4.3 32.1 1.0
ND1 A:HIS65 4.4 32.1 1.0
NH1 A:ARG266 4.6 24.9 1.0
N A:THR53 4.7 34.6 1.0
CB A:TRP54 4.9 24.5 1.0
C A:CYS52 4.9 36.8 1.0
N A:TRP54 5.0 25.1 1.0

Iron binding site 2 out of 6 in 1jbq

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Iron binding site 2 out of 6 in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:34.5
occ:1.00
 FE B:HEM501 0.0 34.5 1.0
ND B:HEM501 2.0 25.1 1.0
NC B:HEM501 2.0 37.6 1.0
NB B:HEM501 2.0 33.8 1.0
NA B:HEM501 2.0 39.8 1.0
NE2 B:HIS65 2.2 37.9 1.0
SG B:CYS52 2.3 45.8 1.0
C4D B:HEM501 3.0 35.4 1.0
CD2 B:HIS65 3.0 40.9 1.0
C1A B:HEM501 3.0 40.3 1.0
C1D B:HEM501 3.0 33.4 1.0
C1B B:HEM501 3.0 35.1 1.0
C1C B:HEM501 3.1 38.6 1.0
C4A B:HEM501 3.1 41.2 1.0
C4C B:HEM501 3.1 42.3 1.0
C4B B:HEM501 3.1 38.4 1.0
CE1 B:HIS65 3.3 36.6 1.0
CHA B:HEM501 3.4 31.4 1.0
CHB B:HEM501 3.4 40.7 1.0
CHD B:HEM501 3.4 40.9 1.0
CHC B:HEM501 3.4 39.7 1.0
CB B:CYS52 3.6 53.9 1.0
CA B:CYS52 4.2 53.3 1.0
CG B:HIS65 4.2 39.6 1.0
C2D B:HEM501 4.3 29.8 1.0
C3D B:HEM501 4.3 37.6 1.0
C2A B:HEM501 4.3 45.6 1.0
C3A B:HEM501 4.3 45.2 1.0
C2B B:HEM501 4.3 36.5 1.0
C3B B:HEM501 4.3 38.0 1.0
C2C B:HEM501 4.3 37.1 1.0
C3C B:HEM501 4.3 39.3 1.0
ND1 B:HIS65 4.3 34.0 1.0
NH1 B:ARG266 4.6 24.5 1.0
N B:THR53 4.7 53.4 1.0
C B:CYS52 4.9 52.0 1.0
CB B:TRP54 4.9 47.0 1.0

Iron binding site 3 out of 6 in 1jbq

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Iron binding site 3 out of 6 in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:38.6
occ:1.00
 FE C:HEM501 0.0 38.6 1.0
ND C:HEM501 2.0 30.5 1.0
NB C:HEM501 2.0 32.4 1.0
NA C:HEM501 2.0 30.7 1.0
NC C:HEM501 2.0 27.3 1.0
SG C:CYS52 2.2 28.7 1.0
NE2 C:HIS65 2.2 44.9 1.0
C1B C:HEM501 3.0 46.6 1.0
C4D C:HEM501 3.0 40.6 1.0
C1A C:HEM501 3.0 34.9 1.0
CD2 C:HIS65 3.0 45.1 1.0
C4A C:HEM501 3.0 33.3 1.0
C1D C:HEM501 3.1 39.2 1.0
C1C C:HEM501 3.1 20.5 1.0
C4B C:HEM501 3.1 34.8 1.0
C4C C:HEM501 3.1 32.4 1.0
CE1 C:HIS65 3.3 46.6 1.0
CHB C:HEM501 3.4 41.5 1.0
CHA C:HEM501 3.4 39.2 1.0
CHD C:HEM501 3.4 40.1 1.0
CHC C:HEM501 3.4 26.1 1.0
CB C:CYS52 3.6 40.0 1.0
CA C:CYS52 4.2 40.0 1.0
CG C:HIS65 4.3 51.5 1.0
C2A C:HEM501 4.3 37.0 1.0
C3A C:HEM501 4.3 40.8 1.0
C2B C:HEM501 4.3 44.2 1.0
C3D C:HEM501 4.3 38.7 1.0
C2D C:HEM501 4.3 36.9 1.0
C3B C:HEM501 4.3 37.9 1.0
C2C C:HEM501 4.3 21.7 1.0
C3C C:HEM501 4.3 29.6 1.0
ND1 C:HIS65 4.4 55.0 1.0
NH1 C:ARG266 4.6 41.9 1.0
N C:THR53 4.7 37.8 1.0
CB C:TRP54 4.9 43.0 1.0
C C:CYS52 4.9 41.0 1.0
N C:TRP54 5.0 44.4 1.0

Iron binding site 4 out of 6 in 1jbq

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Iron binding site 4 out of 6 in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:32.7
occ:1.00
 FE D:HEM501 0.0 32.7 1.0
ND D:HEM501 2.0 43.4 1.0
NC D:HEM501 2.0 40.6 1.0
NB D:HEM501 2.0 32.3 1.0
NA D:HEM501 2.0 45.2 1.0
NE2 D:HIS65 2.2 23.3 1.0
SG D:CYS52 2.4 35.3 1.0
CD2 D:HIS65 3.0 36.8 1.0
C4D D:HEM501 3.0 53.0 1.0
C1B D:HEM501 3.0 27.7 1.0
C1D D:HEM501 3.0 50.4 1.0
C1A D:HEM501 3.0 44.2 1.0
C1C D:HEM501 3.1 41.0 1.0
C4A D:HEM501 3.1 41.9 1.0
C4C D:HEM501 3.1 45.1 1.0
C4B D:HEM501 3.1 37.7 1.0
CE1 D:HIS65 3.3 26.9 1.0
CHA D:HEM501 3.4 48.1 1.0
CHB D:HEM501 3.4 39.7 1.0
CHD D:HEM501 3.4 50.6 1.0
CHC D:HEM501 3.4 42.0 1.0
CB D:CYS52 3.6 51.4 1.0
CG D:HIS65 4.2 38.9 1.0
CA D:CYS52 4.3 51.6 1.0
C3D D:HEM501 4.3 55.2 1.0
C2D D:HEM501 4.3 52.6 1.0
C2A D:HEM501 4.3 45.1 1.0
C3A D:HEM501 4.3 43.9 1.0
C2B D:HEM501 4.3 30.3 1.0
C3B D:HEM501 4.3 27.1 1.0
ND1 D:HIS65 4.3 30.9 1.0
C3C D:HEM501 4.3 51.7 1.0
C2C D:HEM501 4.3 47.5 1.0
NH1 D:ARG266 4.7 32.5 1.0
N D:THR53 4.7 51.1 1.0
CB D:TRP54 4.9 35.4 1.0
C D:CYS52 4.9 50.3 1.0

Iron binding site 5 out of 6 in 1jbq

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Iron binding site 5 out of 6 in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:14.0
occ:1.00
 FE E:HEM501 0.0 14.0 1.0
ND E:HEM501 2.0 27.7 1.0
NB E:HEM501 2.0 18.9 1.0
NA E:HEM501 2.0 19.9 1.0
NC E:HEM501 2.0 18.9 1.0
NE2 E:HIS65 2.2 37.7 1.0
SG E:CYS52 2.3 34.4 1.0
CD2 E:HIS65 3.0 37.8 1.0
C1B E:HEM501 3.0 27.2 1.0
C4D E:HEM501 3.0 35.0 1.0
C4A E:HEM501 3.0 24.9 1.0
C1A E:HEM501 3.0 24.5 1.0
C1C E:HEM501 3.0 15.7 1.0
C4B E:HEM501 3.1 23.6 1.0
C1D E:HEM501 3.1 29.1 1.0
C4C E:HEM501 3.1 20.9 1.0
CE1 E:HIS65 3.3 41.1 1.0
CHB E:HEM501 3.4 17.5 1.0
CHA E:HEM501 3.4 28.2 1.0
CHC E:HEM501 3.4 19.3 1.0
CHD E:HEM501 3.4 29.4 1.0
CB E:CYS52 3.6 44.6 1.0
CG E:HIS65 4.2 39.6 1.0
CA E:CYS52 4.3 39.0 1.0
C2B E:HEM501 4.3 30.3 1.0
C2A E:HEM501 4.3 31.9 1.0
C3A E:HEM501 4.3 30.9 1.0
C3B E:HEM501 4.3 25.4 1.0
C3D E:HEM501 4.3 35.2 1.0
C2D E:HEM501 4.3 27.8 1.0
C2C E:HEM501 4.3 14.5 1.0
ND1 E:HIS65 4.3 39.7 1.0
C3C E:HEM501 4.3 14.8 1.0
NH1 E:ARG266 4.7 17.1 1.0
N E:THR53 4.7 30.1 1.0
C E:CYS52 4.9 39.0 1.0
CB E:TRP54 4.9 30.9 1.0
CD E:PRO64 5.0 28.6 1.0
N E:TRP54 5.0 30.1 1.0

Iron binding site 6 out of 6 in 1jbq

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Iron binding site 6 out of 6 in the Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'- Phosphate Dependent Hemeprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:15.4
occ:1.00
 FE F:HEM501 0.0 15.4 1.0
ND F:HEM501 2.0 24.7 1.0
NB F:HEM501 2.0 16.8 1.0
NC F:HEM501 2.0 22.0 1.0
NA F:HEM501 2.0 24.9 1.0
NE2 F:HIS65 2.2 23.3 1.0
SG F:CYS52 2.3 22.8 1.0
C4D F:HEM501 3.0 30.3 1.0
C1B F:HEM501 3.0 20.9 1.0
CD2 F:HIS65 3.0 29.9 1.0
C1A F:HEM501 3.0 28.5 1.0
C1D F:HEM501 3.0 30.6 1.0
C4A F:HEM501 3.1 27.2 1.0
C1C F:HEM501 3.1 20.9 1.0
C4B F:HEM501 3.1 19.0 1.0
C4C F:HEM501 3.1 21.2 1.0
CE1 F:HIS65 3.3 32.6 1.0
CHA F:HEM501 3.4 27.7 1.0
CHB F:HEM501 3.4 24.0 1.0
CHD F:HEM501 3.4 36.8 1.0
CHC F:HEM501 3.4 20.1 1.0
CB F:CYS52 3.6 27.8 1.0
CA F:CYS52 4.2 28.2 1.0
CG F:HIS65 4.3 34.8 1.0
C2B F:HEM501 4.3 12.1 1.0
C2A F:HEM501 4.3 33.8 1.0
C3A F:HEM501 4.3 32.4 1.0
C3D F:HEM501 4.3 35.3 1.0
C2D F:HEM501 4.3 32.0 1.0
C3B F:HEM501 4.3 21.4 1.0
C2C F:HEM501 4.3 22.7 1.0
C3C F:HEM501 4.3 25.6 1.0
ND1 F:HIS65 4.4 23.1 1.0
NH1 F:ARG266 4.6 8.6 1.0
N F:THR53 4.7 22.5 1.0
CB F:TRP54 4.9 29.2 1.0
C F:CYS52 4.9 21.2 1.0
N F:TRP54 5.0 31.8 1.0

Reference:

M.Meier, M.Janosik, V.Kery, J.P.Kraus, P.Burkhard. Structure of Human Cystathionine Beta-Synthase: A Unique Pyridoxal 5'-Phosphate-Dependent Heme Protein. Embo J. V. 20 3910 2001.
ISSN: ISSN 0261-4189
PubMed: 11483494
DOI: 10.1093/EMBOJ/20.15.3910
Page generated: Sat Aug 3 08:26:51 2024

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