Iron in PDB 9hif: Crystal Structure of Human Cystathionine Beta-Synthase Variant R336C

All present enzymatic activity of Crystal Structure of Human Cystathionine Beta-Synthase Variant R336C:
4.2.1.22;

The structure of Crystal Structure of Human Cystathionine Beta-Synthase Variant R336C, PDB code: 9hif was solved by C.Conter, L.A.Martinez-Cruz, C.Fernandez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.70 / 3.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	126.089, 139.024, 169.902, 90, 90, 90
R / Rfree (%)	21.1 / 23.6

The binding sites of Iron atom in the Crystal Structure of Human Cystathionine Beta-Synthase Variant R336C (pdb code 9hif). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Human Cystathionine Beta-Synthase Variant R336C, PDB code: 9hif:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Human Cystathionine Beta-Synthase Variant R336C


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 Human Cystathionine Beta-Synthase Variant R336C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:104.1 occ:1.00 FE A:HEM601 0.0 104.1 1.0 NE2 A:HIS65 2.0 90.1 1.0 NA A:HEM601 2.0 108.2 1.0 ND A:HEM601 2.0 97.0 1.0 NC A:HEM601 2.0 99.6 1.0 NB A:HEM601 2.0 116.8 1.0 SG A:CYS52 2.6 115.0 1.0 CE1 A:HIS65 2.9 89.0 1.0 HE1 A:HIS65 3.0 73.3 1.0 C1A A:HEM601 3.0 104.2 1.0 C4D A:HEM601 3.0 97.8 1.0 C4A A:HEM601 3.0 119.2 1.0 C1D A:HEM601 3.0 86.8 1.0 C1C A:HEM601 3.0 104.7 1.0 C4C A:HEM601 3.0 96.4 1.0 C1B A:HEM601 3.1 127.6 1.0 CD2 A:HIS65 3.1 90.4 1.0 C4B A:HEM601 3.1 117.0 1.0 HD2 A:HIS65 3.3 73.6 1.0 CHA A:HEM601 3.4 100.0 1.0 CHD A:HEM601 3.4 85.3 1.0 CHB A:HEM601 3.4 130.2 1.0 CHC A:HEM601 3.4 109.4 1.0 HB2 A:CYS52 3.6 103.0 1.0 CB A:CYS52 3.7 116.1 1.0 HA A:CYS52 3.8 98.0 1.0 ND1 A:HIS65 4.0 88.5 1.0 HH12 A:ARG266 4.1 81.6 1.0 HB2 A:TRP54 4.1 96.9 1.0 CG A:HIS65 4.2 94.9 1.0 C3D A:HEM601 4.2 95.6 1.0 C2A A:HEM601 4.2 105.7 1.0 C2D A:HEM601 4.2 85.8 1.0 C3A A:HEM601 4.2 114.6 1.0 C2C A:HEM601 4.3 111.0 1.0 C3C A:HEM601 4.3 103.5 1.0 C2B A:HEM601 4.3 125.2 1.0 C3B A:HEM601 4.3 123.8 1.0 CA A:CYS52 4.3 112.3 1.0 HHA A:HEM601 4.3 123.8 1.0 HHD A:HEM601 4.4 111.8 1.0 HD2 A:PRO64 4.4 75.7 1.0 H A:TRP54 4.4 98.3 1.0 HHB A:HEM601 4.4 148.5 1.0 HHC A:HEM601 4.4 130.5 1.0 H A:THR53 4.4 101.0 1.0 HB3 A:CYS52 4.5 103.0 1.0 HG2 A:PRO64 4.6 75.3 1.0 HD1 A:HIS65 4.8 72.9 1.0 NH1 A:ARG266 4.8 99.0 1.0 HH11 A:ARG266 4.9 81.6 1.0 HB3 A:TRP54 4.9 96.9 1.0 N A:THR53 4.9 117.6 1.0 CB A:TRP54 4.9 117.3 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Human Cystathionine Beta-Synthase Variant R336C


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 Human Cystathionine Beta-Synthase Variant R336C within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:89.3 occ:1.00 FE B:HEM601 0.0 89.3 1.0 NE2 B:HIS65 2.0 86.0 1.0 NA B:HEM601 2.0 101.8 1.0 ND B:HEM601 2.0 101.6 1.0 NC B:HEM601 2.0 98.6 1.0 NB B:HEM601 2.0 94.0 1.0 SG B:CYS52 2.6 92.0 1.0 CE1 B:HIS65 2.9 88.4 1.0 HE1 B:HIS65 3.0 85.2 1.0 C1A B:HEM601 3.0 110.6 1.0 C4D B:HEM601 3.0 110.3 1.0 C4A B:HEM601 3.0 111.7 1.0 C1D B:HEM601 3.0 96.6 1.0 C1C B:HEM601 3.1 94.5 1.0 C4C B:HEM601 3.1 112.1 1.0 C1B B:HEM601 3.1 98.2 1.0 C4B B:HEM601 3.1 96.3 1.0 CD2 B:HIS65 3.1 87.0 1.0 HD2 B:HIS65 3.4 83.7 1.0 CHA B:HEM601 3.4 117.3 1.0 CHD B:HEM601 3.4 106.8 1.0 CHB B:HEM601 3.4 109.2 1.0 CHC B:HEM601 3.5 91.3 1.0 HB2 B:CYS52 3.7 93.5 1.0 CB B:CYS52 3.8 91.4 1.0 HA B:CYS52 3.9 94.8 1.0 ND1 B:HIS65 4.0 91.2 1.0 HB2 B:TRP54 4.1 79.7 1.0 HH12 B:ARG266 4.1 100.5 1.0 CG B:HIS65 4.2 92.2 1.0 C3D B:HEM601 4.2 97.0 1.0 C2A B:HEM601 4.2 113.1 1.0 C2D B:HEM601 4.2 89.9 1.0 C3A B:HEM601 4.2 115.4 1.0 C2C B:HEM601 4.3 105.1 1.0 C3C B:HEM601 4.3 116.2 1.0 C3B B:HEM601 4.3 96.2 1.0 C2B B:HEM601 4.3 94.4 1.0 HHA B:HEM601 4.3 155.3 1.0 HD2 B:PRO64 4.4 107.7 1.0 CA B:CYS52 4.4 93.8 1.0 HHD B:HEM601 4.4 147.9 1.0 HHB B:HEM601 4.4 144.5 1.0 HHC B:HEM601 4.4 129.3 1.0 H B:TRP54 4.4 84.2 1.0 H B:THR53 4.5 99.4 1.0 HB3 B:CYS52 4.6 93.5 1.0 HG2 B:PRO64 4.7 113.3 1.0 HD1 B:HIS65 4.8 87.6 1.0 NH1 B:ARG266 4.8 98.6 1.0 HH11 B:ARG266 4.9 100.5 1.0 HB3 B:TRP54 4.9 79.7 1.0 CB B:TRP54 4.9 87.4 1.0 N B:THR53 5.0 103.2 1.0

C.Conter, R.Nunez-Franco, D.W.Al-Sadeq, C.Fernandez-Rodriguez, N.Goikoetxea-Usandizaga, G.K.Nasrallah, M.Nomikos, M.L.Martinez-Chantar, A.Astegno, G.Jimenez-Oses, L.A.Martinez-Cruz. The Disease-Linked R336C Mutation in Cystathionine Beta-Synthase Disrupts Communication with the Plp Cofactor, Yet Maintains the Enzyme'S Overall Structural Integrity. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40327797
DOI: 10.1111/FEBS.70116