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Iron in PDB 4l28: Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag

Enzymatic activity of Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag

All present enzymatic activity of Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag:
4.2.1.22;

Protein crystallography data

The structure of Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag, PDB code: 4l28 was solved by J.Ereno, T.Majtan, I.Oyenarte, J.P.Kraus, L.A.Martinez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.39 / 2.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.482, 131.074, 207.065, 90.00, 90.00, 90.00
R / Rfree (%) 25.6 / 28.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag (pdb code 4l28). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag, PDB code: 4l28:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4l28

Go back to Iron Binding Sites List in 4l28
Iron binding site 1 out of 4 in the Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:72.2
occ:1.00
 FE A:HEM602 0.0 72.2 1.0
NC A:HEM602 2.0 72.1 1.0
NB A:HEM602 2.0 72.2 1.0
NA A:HEM602 2.0 72.3 1.0
ND A:HEM602 2.0 72.1 1.0
NE2 A:HIS65 2.1 62.6 1.0
SG A:CYS52 2.2 68.3 1.0
C4C A:HEM602 3.0 72.0 1.0
CE1 A:HIS65 3.0 62.7 1.0
C1C A:HEM602 3.0 72.0 1.0
C1A A:HEM602 3.0 72.2 1.0
C4B A:HEM602 3.0 72.2 1.0
C4A A:HEM602 3.0 72.3 1.0
C1B A:HEM602 3.0 72.3 1.0
C1D A:HEM602 3.0 72.0 1.0
C4D A:HEM602 3.0 72.1 1.0
CD2 A:HIS65 3.1 63.0 1.0
CHD A:HEM602 3.4 72.0 1.0
CHB A:HEM602 3.4 72.3 1.0
CHC A:HEM602 3.4 72.1 1.0
CHA A:HEM602 3.4 72.2 1.0
CB A:CYS52 3.5 68.4 1.0
ND1 A:HIS65 4.1 63.2 1.0
C3C A:HEM602 4.2 71.9 1.0
C2C A:HEM602 4.2 71.9 1.0
C3A A:HEM602 4.2 72.3 1.0
C2A A:HEM602 4.2 72.4 1.0
CG A:HIS65 4.2 63.9 1.0
C3B A:HEM602 4.2 72.2 1.0
C2B A:HEM602 4.2 72.3 1.0
CA A:CYS52 4.2 68.5 1.0
C2D A:HEM602 4.3 72.0 1.0
C3D A:HEM602 4.3 72.1 1.0
NH1 A:ARG266 4.7 67.8 1.0
N A:THR53 4.8 77.8 1.0
CB A:TRP54 4.9 60.3 1.0
C A:CYS52 5.0 67.7 1.0

Iron binding site 2 out of 4 in 4l28

Go back to Iron Binding Sites List in 4l28
Iron binding site 2 out of 4 in the Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:0.8
occ:1.00
 FE B:HEM602 0.0 0.8 1.0
NC B:HEM602 2.0 0.7 1.0
NB B:HEM602 2.0 0.1 1.0
NA B:HEM602 2.0 0.8 1.0
ND B:HEM602 2.1 0.7 1.0
NE2 B:HIS65 2.1 82.0 1.0
SG B:CYS52 2.2 97.5 1.0
C4B B:HEM602 3.0 0.0 1.0
C1C B:HEM602 3.0 0.6 1.0
CE1 B:HIS65 3.0 82.3 1.0
C1B B:HEM602 3.0 0.1 1.0
C4C B:HEM602 3.0 0.5 1.0
C1A B:HEM602 3.0 0.8 1.0
C4A B:HEM602 3.1 0.8 1.0
C1D B:HEM602 3.1 0.6 1.0
C4D B:HEM602 3.1 0.6 1.0
CD2 B:HIS65 3.1 82.7 1.0
CHC B:HEM602 3.4 0.8 1.0
CHA B:HEM602 3.4 0.7 1.0
CHD B:HEM602 3.4 0.5 1.0
CHB B:HEM602 3.4 0.0 1.0
CB B:CYS52 3.6 97.7 1.0
ND1 B:HIS65 4.2 83.0 1.0
C3B B:HEM602 4.2 0.2 1.0
C2C B:HEM602 4.2 0.5 1.0
C2B B:HEM602 4.2 0.3 1.0
C3C B:HEM602 4.2 0.5 1.0
CG B:HIS65 4.3 83.9 1.0
CA B:CYS52 4.3 97.7 1.0
C2A B:HEM602 4.3 0.8 1.0
C3A B:HEM602 4.3 0.8 1.0
C2D B:HEM602 4.3 0.6 1.0
C3D B:HEM602 4.3 0.6 1.0
NH1 B:ARG266 4.8 82.5 1.0
N B:THR53 4.8 0.1 1.0
CB B:TRP54 4.9 94.9 1.0

Iron binding site 3 out of 4 in 4l28

Go back to Iron Binding Sites List in 4l28
Iron binding site 3 out of 4 in the Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe602

b:91.2
occ:1.00
 FE C:HEM602 0.0 91.2 1.0
NB C:HEM602 2.0 91.5 1.0
NC C:HEM602 2.0 91.1 1.0
NA C:HEM602 2.0 91.3 1.0
ND C:HEM602 2.0 91.1 1.0
NE2 C:HIS65 2.1 71.9 1.0
SG C:CYS52 2.2 87.8 1.0
CE1 C:HIS65 3.0 72.1 1.0
C4B C:HEM602 3.0 91.5 1.0
C1C C:HEM602 3.0 91.0 1.0
C1B C:HEM602 3.0 91.6 1.0
C1A C:HEM602 3.0 91.2 1.0
C4C C:HEM602 3.0 90.9 1.0
C4A C:HEM602 3.0 91.3 1.0
C4D C:HEM602 3.0 91.0 1.0
C1D C:HEM602 3.1 90.9 1.0
CD2 C:HIS65 3.1 72.6 1.0
CHC C:HEM602 3.4 91.2 1.0
CHA C:HEM602 3.4 91.0 1.0
CHB C:HEM602 3.4 91.5 1.0
CHD C:HEM602 3.4 90.9 1.0
CB C:CYS52 3.5 88.0 1.0
ND1 C:HIS65 4.1 72.9 1.0
C3B C:HEM602 4.2 91.7 1.0
CG C:HIS65 4.2 73.8 1.0
C2C C:HEM602 4.2 90.8 1.0
C2B C:HEM602 4.2 91.8 1.0
CA C:CYS52 4.2 88.1 1.0
C3A C:HEM602 4.2 91.2 1.0
C2A C:HEM602 4.3 91.3 1.0
C3C C:HEM602 4.3 90.8 1.0
C2D C:HEM602 4.3 90.9 1.0
C3D C:HEM602 4.3 90.9 1.0
NH1 C:ARG266 4.7 69.4 1.0
N C:THR53 4.8 92.1 1.0
CB C:TRP54 4.9 92.2 1.0

Iron binding site 4 out of 4 in 4l28

Go back to Iron Binding Sites List in 4l28
Iron binding site 4 out of 4 in the Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of DELTA516-525 Human Cystathionine Beta-Synthase D444N Mutant Containing C-Terminal 6XHIS Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe602

b:74.8
occ:1.00
 FE D:HEM602 0.0 74.8 1.0
NC D:HEM602 2.0 74.7 1.0
NB D:HEM602 2.0 75.0 1.0
NA D:HEM602 2.0 74.9 1.0
ND D:HEM602 2.0 74.8 1.0
NE2 D:HIS65 2.1 64.0 1.0
SG D:CYS52 2.2 71.2 1.0
CE1 D:HIS65 3.0 64.1 1.0
C4B D:HEM602 3.0 75.0 1.0
C1C D:HEM602 3.0 74.7 1.0
C1A D:HEM602 3.0 74.8 1.0
C4C D:HEM602 3.0 74.6 1.0
C4D D:HEM602 3.0 74.7 1.0
C1D D:HEM602 3.0 74.6 1.0
C1B D:HEM602 3.0 75.1 1.0
C4A D:HEM602 3.1 74.9 1.0
CD2 D:HIS65 3.2 64.5 1.0
CHC D:HEM602 3.4 74.8 1.0
CHA D:HEM602 3.4 74.8 1.0
CHD D:HEM602 3.4 74.6 1.0
CHB D:HEM602 3.4 75.0 1.0
CB D:CYS52 3.6 71.3 1.0
ND1 D:HIS65 4.1 64.8 1.0
C2C D:HEM602 4.2 74.5 1.0
C3C D:HEM602 4.2 74.5 1.0
C2A D:HEM602 4.2 74.9 1.0
C3B D:HEM602 4.2 75.1 1.0
C2D D:HEM602 4.2 74.6 1.0
CA D:CYS52 4.2 71.3 1.0
C3D D:HEM602 4.2 74.6 1.0
C2B D:HEM602 4.2 75.2 1.0
C3A D:HEM602 4.2 74.9 1.0
CG D:HIS65 4.2 65.7 1.0
NH1 D:ARG266 4.7 66.0 1.0
N D:THR53 4.8 77.2 1.0
CB D:TRP54 4.9 63.1 1.0
C D:CYS52 5.0 71.0 1.0

Reference:

J.Ereno-Orbea, T.Majtan, I.Oyenarte, J.P.Kraus, L.A.Martinez-Cruz. Structural Basis of Regulation and Oligomerization of Human Cystathionine Beta-Synthase, the Central Enzyme of Transsulfuration. Proc.Natl.Acad.Sci.Usa V. 110 E3790 2013.
ISSN: ISSN 0027-8424
PubMed: 24043838
DOI: 10.1073/PNAS.1313683110
Page generated: Tue Aug 5 12:21:13 2025

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