Iron in PDB 8hzy: The Crystal Structure of A Radical Sam Enzyme Desii

The structure of The Crystal Structure of A Radical Sam Enzyme Desii, PDB code: 8hzy was solved by X.L.Hou, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.98 / 2.04
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.088, 105.19, 118.248, 90, 90, 90
R / Rfree (%)	20.5 / 24.4

The binding sites of Iron atom in the The Crystal Structure of A Radical Sam Enzyme Desii (pdb code 8hzy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Crystal Structure of A Radical Sam Enzyme Desii, PDB code: 8hzy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:24.7 occ:1.00 FE1 A:SF4501 0.0 24.7 1.0 S2 A:SF4501 2.2 26.0 1.0 S4 A:SF4501 2.3 34.3 1.0 S3 A:SF4501 2.3 23.9 1.0 SG A:CYS141 2.5 31.6 1.0 FE2 A:SF4501 2.7 35.4 1.0 FE3 A:SF4501 2.7 40.1 1.0 FE4 A:SF4501 2.7 62.7 1.0 CB A:CYS141 3.1 28.2 1.0 S1 A:SF4501 3.9 47.1 1.0 CB A:PHE143 3.9 23.8 1.0 O A:PHE143 4.5 27.0 1.0 CG A:ARG150 4.5 38.5 1.0 N A:PHE143 4.5 26.6 1.0 CA A:CYS141 4.6 24.1 1.0 CA A:PHE143 4.6 26.4 1.0 C A:PHE143 4.6 29.5 1.0 ND2 A:ASN216 4.7 17.3 1.0 CG A:PHE143 4.9 22.7 1.0 C A:CYS141 5.0 24.7 1.0

Iron binding site 2 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:35.4 occ:1.00 FE2 A:SF4501 0.0 35.4 1.0 S1 A:SF4501 2.3 47.1 1.0 S4 A:SF4501 2.3 34.3 1.0 S3 A:SF4501 2.3 23.9 1.0 SG A:CYS145 2.7 29.2 1.0 FE1 A:SF4501 2.7 24.7 1.0 FE4 A:SF4501 2.7 62.7 1.0 FE3 A:SF4501 2.7 40.1 1.0 CB A:CYS145 3.2 36.0 1.0 S2 A:SF4501 3.8 26.0 1.0 N A:CYS145 4.0 38.3 1.0 O A:HOH625 4.0 33.7 1.0 CB A:PHE143 4.1 23.8 1.0 CA A:CYS145 4.2 43.4 1.0 OH A:TYR242 4.5 31.0 1.0 CZ A:TYR242 4.8 27.6 1.0 CD2 A:PHE143 4.8 21.6 1.0 CB A:CYS148 4.8 49.8 1.0 SG A:CYS141 4.9 31.6 1.0 N A:ARG144 5.0 28.9 1.0 CG A:PHE143 5.0 22.7 1.0 C A:PHE143 5.0 29.5 1.0

Iron binding site 3 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:40.1 occ:1.00 FE3 A:SF4501 0.0 40.1 1.0 S4 A:SF4501 2.2 34.3 1.0 S2 A:SF4501 2.3 26.0 1.0 S1 A:SF4501 2.3 47.1 1.0 SG A:CYS148 2.7 47.5 1.0 FE1 A:SF4501 2.7 24.7 1.0 FE2 A:SF4501 2.7 35.4 1.0 FE4 A:SF4501 2.8 62.7 1.0 CB A:CYS148 3.1 49.8 1.0 S3 A:SF4501 3.9 23.9 1.0 CG A:ARG150 4.2 38.5 1.0 CB A:ARG150 4.5 40.5 1.0 CE2 A:PHE411 4.5 19.9 1.0 CA A:CYS148 4.6 49.2 1.0 CB A:CYS145 4.7 36.0 1.0 O A:HOH764 4.7 32.8 1.0 O A:HOH625 4.9 33.7 1.0 CD2 A:LEU189 4.9 19.7 1.0 O A:GLY188 4.9 18.8 1.0

Iron binding site 4 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:62.7 occ:1.00 FE4 A:SF4501 0.0 62.7 1.0 S3 A:SF4501 2.2 23.9 1.0 S1 A:SF4501 2.3 47.1 1.0 S2 A:SF4501 2.3 26.0 1.0 O A:HOH625 2.7 33.7 1.0 FE2 A:SF4501 2.7 35.4 1.0 FE1 A:SF4501 2.7 24.7 1.0 FE3 A:SF4501 2.8 40.1 1.0 O A:HOH764 3.2 32.8 1.0 OH A:TYR242 3.8 31.0 1.0 S4 A:SF4501 3.9 34.3 1.0 O A:GLY188 4.0 18.8 1.0 SG A:CYS141 4.8 31.6 1.0 CZ A:TYR242 4.9 27.6 1.0

Iron binding site 5 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:35.1 occ:1.00 FE1 B:SF4502 0.0 35.1 1.0 S2 B:SF4502 2.2 27.7 1.0 S3 B:SF4502 2.3 25.4 1.0 S4 B:SF4502 2.3 28.6 1.0 SG B:CYS148 2.6 43.9 1.0 FE4 B:SF4502 2.7 26.6 1.0 FE3 B:SF4502 2.7 46.6 1.0 FE2 B:SF4502 2.7 31.3 1.0 CB B:CYS148 3.1 44.5 1.0 S1 B:SF4502 3.9 33.4 1.0 CB B:ARG150 4.2 39.7 1.0 O B:GLY188 4.4 21.1 1.0 CA B:CYS148 4.6 43.5 1.0 CB B:CYS145 4.7 35.3 1.0 CE2 B:PHE411 4.8 26.6 1.0 CG B:ARG150 4.9 38.3 1.0 CD2 B:LEU189 4.9 17.3 1.0 CE B:MET501 4.9 50.2 1.0

Iron binding site 6 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:31.3 occ:1.00 FE2 B:SF4502 0.0 31.3 1.0 S1 B:SF4502 2.3 33.4 1.0 S3 B:SF4502 2.3 25.4 1.0 S4 B:SF4502 2.3 28.6 1.0 SG B:CYS145 2.6 36.0 1.0 FE4 B:SF4502 2.7 26.6 1.0 FE3 B:SF4502 2.7 46.6 1.0 FE1 B:SF4502 2.7 35.1 1.0 CB B:CYS145 3.1 35.3 1.0 S2 B:SF4502 3.9 27.7 1.0 OH B:TYR242 4.0 31.3 1.0 CB B:PHE143 4.2 27.8 1.0 N B:CYS145 4.2 36.6 1.0 CA B:CYS145 4.3 38.0 1.0 CZ B:TYR242 4.3 28.6 1.0 CE2 B:TYR242 4.5 26.1 1.0 CD2 B:PHE143 4.6 27.6 1.0 CZ B:PHE147 4.7 41.7 1.0 CB B:CYS148 4.7 44.5 1.0 CE1 B:PHE147 4.8 40.8 1.0 CG B:PHE143 4.9 26.6 1.0 SG B:CYS141 4.9 31.2 1.0 SD B:MET501 5.0 51.4 1.0 CE1 B:TYR242 5.0 29.3 1.0

Iron binding site 7 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:46.6 occ:1.00 FE3 B:SF4502 0.0 46.6 1.0 S4 B:SF4502 2.2 28.6 1.0 S2 B:SF4502 2.3 27.7 1.0 S1 B:SF4502 2.3 33.4 1.0 FE2 B:SF4502 2.7 31.3 1.0 FE4 B:SF4502 2.7 26.6 1.0 FE1 B:SF4502 2.7 35.1 1.0 CA B:MET501 2.8 35.6 1.0 CB B:MET501 3.2 40.8 1.0 N B:MET501 3.3 31.8 1.0 SD B:MET501 3.4 51.4 1.0 CE B:MET501 3.5 50.2 1.0 OH B:TYR242 3.8 31.3 1.0 CG B:MET501 3.8 46.5 1.0 S3 B:SF4502 3.9 25.4 1.0 C B:MET501 3.9 37.9 1.0 O B:MET501 4.1 38.8 1.0 O B:GLY188 4.1 21.1 1.0 SG B:CYS141 4.7 31.2 1.0 CZ B:TYR242 4.7 28.6 1.0

Iron binding site 8 out of 8 in the The Crystal Structure of A Radical Sam Enzyme Desii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of A Radical Sam Enzyme Desii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:26.6 occ:1.00 FE4 B:SF4502 0.0 26.6 1.0 S3 B:SF4502 2.2 25.4 1.0 S1 B:SF4502 2.3 33.4 1.0 S2 B:SF4502 2.3 27.7 1.0 SG B:CYS141 2.5 31.2 1.0 FE2 B:SF4502 2.7 31.3 1.0 FE1 B:SF4502 2.7 35.1 1.0 FE3 B:SF4502 2.7 46.6 1.0 CB B:CYS141 3.1 26.3 1.0 S4 B:SF4502 3.8 28.6 1.0 CB B:PHE143 3.9 27.8 1.0 ND2 B:ASN216 4.4 22.8 1.0 O B:PHE143 4.5 32.9 1.0 N B:PHE143 4.5 24.6 1.0 N B:MET501 4.5 31.8 1.0 CA B:PHE143 4.6 30.4 1.0 CA B:CYS141 4.6 26.3 1.0 C B:PHE143 4.6 32.8 1.0 CG B:PHE143 4.7 26.6 1.0 CA B:MET501 4.8 35.6 1.0 CG B:ARG150 4.8 38.3 1.0 CD2 B:PHE143 4.8 27.6 1.0 CB B:GLU190 4.9 11.1 1.0 SG B:CYS145 4.9 36.0 1.0 CB B:ARG150 4.9 39.7 1.0 C B:CYS141 5.0 27.1 1.0

X.Hou, J.Feng, J.L.Franklin, R.Russo, Z.Guo, J.Zhou, J.M.Gao, H.W.Liu, B.Wang. Mechanistic Insights From the Crystal Structure and Computational Analysis of the Radical Sam Deaminase Desii. Adv Sci 03494 2024.
ISSN: ESSN 2198-3844
PubMed: 38943270
DOI: 10.1002/ADVS.202403494