Iron in PDB 8stw: K384N Human Cystathionine Beta-Synthase (Delta 411-551)

All present enzymatic activity of K384N Human Cystathionine Beta-Synthase (Delta 411-551):
4.2.1.22;

The structure of K384N Human Cystathionine Beta-Synthase (Delta 411-551), PDB code: 8stw was solved by R.Mascarenhas, J.Roman, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.11 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	89.462, 90.189, 104.224, 106.15, 105.49, 107.47
R / Rfree (%)	21 / 24.3

The binding sites of Iron atom in the K384N Human Cystathionine Beta-Synthase (Delta 411-551) (pdb code 8stw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the K384N Human Cystathionine Beta-Synthase (Delta 411-551), PDB code: 8stw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the K384N Human Cystathionine Beta-Synthase (Delta 411-551)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of K384N Human Cystathionine Beta-Synthase (Delta 411-551) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:24.9 occ:1.00 FE A:HEM502 0.0 24.9 1.0 ND A:HEM502 1.9 25.6 1.0 NA A:HEM502 2.0 28.6 1.0 NE2 A:HIS65 2.0 22.4 1.0 NC A:HEM502 2.1 24.9 1.0 NB A:HEM502 2.1 28.6 1.0 SG A:CYS52 2.3 27.5 1.0 CD2 A:HIS65 2.9 22.5 1.0 C4D A:HEM502 2.9 24.6 1.0 C1D A:HEM502 2.9 25.6 1.0 C1A A:HEM502 3.0 28.6 1.0 C4A A:HEM502 3.0 28.9 1.0 C1B A:HEM502 3.0 30.0 1.0 C4C A:HEM502 3.1 25.4 1.0 CE1 A:HIS65 3.1 23.9 1.0 C1C A:HEM502 3.1 24.7 1.0 C4B A:HEM502 3.1 29.2 1.0 CHA A:HEM502 3.3 27.7 1.0 CHB A:HEM502 3.4 31.9 1.0 CHD A:HEM502 3.4 23.7 1.0 CHC A:HEM502 3.5 26.6 1.0 CB A:CYS52 3.5 28.7 1.0 CG A:HIS65 4.1 23.9 1.0 ND1 A:HIS65 4.1 24.5 1.0 C3D A:HEM502 4.2 25.1 1.0 C2D A:HEM502 4.2 24.6 1.0 C2A A:HEM502 4.2 30.7 1.0 C3A A:HEM502 4.2 33.0 1.0 CA A:CYS52 4.2 27.6 1.0 C3C A:HEM502 4.3 25.1 1.0 C2C A:HEM502 4.3 24.4 1.0 C2B A:HEM502 4.3 30.5 1.0 C3B A:HEM502 4.4 29.8 1.0 NH1 A:ARG266 4.7 36.1 1.0 N A:THR53 4.9 29.3 1.0

Iron binding site 2 out of 6 in the K384N Human Cystathionine Beta-Synthase (Delta 411-551)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of K384N Human Cystathionine Beta-Synthase (Delta 411-551) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:32.7 occ:1.00 FE B:HEM502 0.0 32.7 1.0 ND B:HEM502 1.9 34.1 1.0 NA B:HEM502 2.0 34.7 1.0 NB B:HEM502 2.1 33.6 1.0 NC B:HEM502 2.1 31.9 1.0 NE2 B:HIS65 2.2 35.0 1.0 SG B:CYS52 2.4 37.8 1.0 C4D B:HEM502 2.9 37.0 1.0 C1D B:HEM502 2.9 31.7 1.0 C1A B:HEM502 3.0 41.3 1.0 CD2 B:HIS65 3.0 34.1 1.0 C4B B:HEM502 3.0 35.2 1.0 C4C B:HEM502 3.0 31.5 1.0 C1B B:HEM502 3.0 37.6 1.0 C1C B:HEM502 3.1 32.0 1.0 C4A B:HEM502 3.1 38.0 1.0 CE1 B:HIS65 3.2 34.8 1.0 CHA B:HEM502 3.3 41.4 1.0 CHD B:HEM502 3.4 30.9 1.0 CHC B:HEM502 3.4 35.5 1.0 CHB B:HEM502 3.5 38.8 1.0 CB B:CYS52 3.5 38.7 1.0 CA B:CYS52 4.1 38.8 1.0 C2D B:HEM502 4.2 33.9 1.0 CG B:HIS65 4.2 36.5 1.0 C3D B:HEM502 4.2 33.5 1.0 C2A B:HEM502 4.2 43.5 1.0 C3C B:HEM502 4.2 30.0 1.0 C2C B:HEM502 4.2 30.8 1.0 C3A B:HEM502 4.3 43.3 1.0 C2B B:HEM502 4.3 35.3 1.0 C3B B:HEM502 4.3 34.0 1.0 ND1 B:HIS65 4.3 35.6 1.0 NH1 B:ARG266 4.8 40.0 1.0 N B:THR53 4.8 43.0 1.0 C B:CYS52 4.9 41.0 1.0

Iron binding site 3 out of 6 in the K384N Human Cystathionine Beta-Synthase (Delta 411-551)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of K384N Human Cystathionine Beta-Synthase (Delta 411-551) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:24.7 occ:1.00 FE C:HEM502 0.0 24.7 1.0 ND C:HEM502 1.9 29.8 1.0 NE2 C:HIS65 2.0 25.2 1.0 NA C:HEM502 2.0 31.4 1.0 NC C:HEM502 2.0 25.5 1.0 NB C:HEM502 2.1 26.3 1.0 SG C:CYS52 2.4 27.5 1.0 C1D C:HEM502 2.9 29.1 1.0 C4D C:HEM502 2.9 30.9 1.0 CD2 C:HIS65 2.9 24.8 1.0 C1A C:HEM502 3.0 32.8 1.0 C4C C:HEM502 3.0 27.8 1.0 C4A C:HEM502 3.0 31.8 1.0 CE1 C:HIS65 3.0 23.4 1.0 C1C C:HEM502 3.1 27.1 1.0 C1B C:HEM502 3.1 24.7 1.0 C4B C:HEM502 3.1 24.8 1.0 CHD C:HEM502 3.3 28.3 1.0 CHA C:HEM502 3.3 32.3 1.0 CHB C:HEM502 3.4 26.7 1.0 CHC C:HEM502 3.5 25.3 1.0 CB C:CYS52 3.7 26.2 1.0 CG C:HIS65 4.1 23.8 1.0 ND1 C:HIS65 4.1 22.1 1.0 C2D C:HEM502 4.1 31.5 1.0 C3D C:HEM502 4.1 33.2 1.0 C2A C:HEM502 4.2 35.7 1.0 C3A C:HEM502 4.2 35.3 1.0 C3C C:HEM502 4.2 29.1 1.0 C2C C:HEM502 4.2 29.0 1.0 CA C:CYS52 4.3 27.8 1.0 C2B C:HEM502 4.3 23.9 1.0 C3B C:HEM502 4.4 22.1 1.0 NH1 C:ARG266 4.7 32.0 1.0 N C:THR53 4.8 28.9 1.0 CD C:PRO64 4.9 39.2 1.0 CG C:PRO64 4.9 40.0 1.0 N C:TRP54 5.0 28.8 1.0 C C:CYS52 5.0 26.3 1.0 CB C:TRP54 5.0 30.8 1.0

Iron binding site 4 out of 6 in the K384N Human Cystathionine Beta-Synthase (Delta 411-551)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of K384N Human Cystathionine Beta-Synthase (Delta 411-551) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:32.9 occ:1.00 FE D:HEM502 0.0 32.9 1.0 ND D:HEM502 1.9 31.3 1.0 NA D:HEM502 2.0 37.6 1.0 NB D:HEM502 2.1 31.4 1.0 NC D:HEM502 2.1 33.8 1.0 NE2 D:HIS65 2.1 27.8 1.0 SG D:CYS52 2.3 34.0 1.0 C1D D:HEM502 2.8 30.0 1.0 C4D D:HEM502 2.9 30.7 1.0 C1A D:HEM502 3.0 33.4 1.0 CD2 D:HIS65 3.0 30.2 1.0 C4C D:HEM502 3.0 33.3 1.0 C1B D:HEM502 3.0 35.4 1.0 C4B D:HEM502 3.0 32.8 1.0 C4A D:HEM502 3.1 33.8 1.0 C1C D:HEM502 3.1 33.3 1.0 CE1 D:HIS65 3.1 27.6 1.0 CHD D:HEM502 3.3 31.7 1.0 CHA D:HEM502 3.3 33.6 1.0 CHB D:HEM502 3.4 33.2 1.0 CHC D:HEM502 3.4 34.9 1.0 CB D:CYS52 3.5 36.3 1.0 C2D D:HEM502 4.1 26.4 1.0 C3D D:HEM502 4.1 28.6 1.0 C2A D:HEM502 4.2 35.5 1.0 CG D:HIS65 4.2 28.5 1.0 CA D:CYS52 4.2 34.9 1.0 C3A D:HEM502 4.2 37.4 1.0 ND1 D:HIS65 4.2 27.2 1.0 C3C D:HEM502 4.3 35.9 1.0 C2B D:HEM502 4.3 34.1 1.0 C2C D:HEM502 4.3 36.5 1.0 C3B D:HEM502 4.3 32.8 1.0 NH2 D:ARG266 4.6 51.1 1.0 N D:THR53 4.9 27.5 1.0 C D:CYS52 5.0 28.9 1.0

Iron binding site 5 out of 6 in the K384N Human Cystathionine Beta-Synthase (Delta 411-551)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of K384N Human Cystathionine Beta-Synthase (Delta 411-551) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe502 b:42.9 occ:1.00 FE E:HEM502 0.0 42.9 1.0 ND E:HEM502 1.9 55.8 1.0 NA E:HEM502 2.0 46.9 1.0 NC E:HEM502 2.1 50.9 1.0 NB E:HEM502 2.1 49.4 1.0 NE2 E:HIS65 2.1 31.6 1.0 SG E:CYS52 2.4 51.1 1.0 C4D E:HEM502 2.8 58.2 1.0 C1D E:HEM502 2.9 57.1 1.0 C1A E:HEM502 3.0 50.6 1.0 C4C E:HEM502 3.0 57.0 1.0 C4B E:HEM502 3.0 50.1 1.0 CD2 E:HIS65 3.0 33.1 1.0 C4A E:HEM502 3.1 42.0 1.0 C1B E:HEM502 3.1 46.4 1.0 C1C E:HEM502 3.1 53.1 1.0 CE1 E:HIS65 3.2 32.8 1.0 CHA E:HEM502 3.3 57.5 1.0 CHD E:HEM502 3.3 60.3 1.0 CHC E:HEM502 3.4 52.9 1.0 CHB E:HEM502 3.5 41.5 1.0 CB E:CYS52 3.6 51.0 1.0 C3D E:HEM502 4.1 62.9 1.0 C2D E:HEM502 4.1 57.8 1.0 C2A E:HEM502 4.2 42.5 1.0 CA E:CYS52 4.2 51.5 1.0 CG E:HIS65 4.2 38.3 1.0 C3A E:HEM502 4.2 41.0 1.0 ND1 E:HIS65 4.2 30.4 1.0 C3C E:HEM502 4.3 60.7 1.0 C3B E:HEM502 4.3 53.0 1.0 C2B E:HEM502 4.3 47.0 1.0 C2C E:HEM502 4.4 53.5 1.0 NH1 E:ARG266 4.8 38.5 1.0 N E:THR53 4.8 60.0 1.0 C E:CYS52 5.0 51.4 1.0

Iron binding site 6 out of 6 in the K384N Human Cystathionine Beta-Synthase (Delta 411-551)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of K384N Human Cystathionine Beta-Synthase (Delta 411-551) within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe502 b:29.0 occ:1.00 FE F:HEM502 0.0 29.0 1.0 ND F:HEM502 1.9 33.6 1.0 NA F:HEM502 2.0 39.5 1.0 NE2 F:HIS65 2.1 21.7 1.0 NB F:HEM502 2.1 38.9 1.0 NC F:HEM502 2.1 36.9 1.0 SG F:CYS52 2.3 28.9 1.0 C4D F:HEM502 2.9 34.5 1.0 C1D F:HEM502 2.9 31.2 1.0 C1A F:HEM502 3.0 40.1 1.0 CD2 F:HIS65 3.0 24.1 1.0 C4B F:HEM502 3.0 41.8 1.0 C4A F:HEM502 3.1 40.0 1.0 C1B F:HEM502 3.1 40.3 1.0 CE1 F:HIS65 3.1 23.1 1.0 C4C F:HEM502 3.1 32.0 1.0 C1C F:HEM502 3.1 38.7 1.0 CHA F:HEM502 3.3 39.9 1.0 CHD F:HEM502 3.4 32.9 1.0 CHC F:HEM502 3.5 40.6 1.0 CHB F:HEM502 3.5 40.2 1.0 CB F:CYS52 3.5 33.8 1.0 CA F:CYS52 4.1 34.9 1.0 C3D F:HEM502 4.1 31.1 1.0 C2D F:HEM502 4.2 30.0 1.0 C2A F:HEM502 4.2 49.3 1.0 ND1 F:HIS65 4.2 25.6 1.0 CG F:HIS65 4.2 25.4 1.0 C3A F:HEM502 4.2 49.1 1.0 C2B F:HEM502 4.3 42.6 1.0 C2C F:HEM502 4.3 35.1 1.0 C3B F:HEM502 4.3 41.2 1.0 C3C F:HEM502 4.3 34.2 1.0 NH1 F:ARG266 4.7 36.9 1.0 N F:THR53 4.7 29.5 1.0 C F:CYS52 4.9 30.6 1.0 N F:TRP54 5.0 35.9 1.0

J.V.Roman, R.Mascarenhas, K.Ceric, D.P.Ballou, R.Banerjee. Disease-Causing Cystathionine Beta-Synthase Linker Mutations Impair Allosteric Regulation. J.Biol.Chem. 05449 2023.
ISSN: ESSN 1083-351X
PubMed: 37949228
DOI: 10.1016/J.JBC.2023.105449