Iron in PDB 8qml: (2R,4R)-Metda Bound Hyde Structure (Control Experiment)

The structure of (2R,4R)-Metda Bound Hyde Structure (Control Experiment), PDB code: 8qml was solved by J.Omeiri, L.Martin, A.Usclat, M.V.Cherrier, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.14 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.48, 79.22, 85.16, 90, 90, 90
R / Rfree (%)	15.4 / 19.3

The structure of (2R,4R)-Metda Bound Hyde Structure (Control Experiment) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the (2R,4R)-Metda Bound Hyde Structure (Control Experiment) (pdb code 8qml). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the (2R,4R)-Metda Bound Hyde Structure (Control Experiment), PDB code: 8qml:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the (2R,4R)-Metda Bound Hyde Structure (Control Experiment)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of (2R,4R)-Metda Bound Hyde Structure (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe408 b:28.0 occ:1.00 FE1 A:SF4408 0.0 28.0 1.0 SG A:CYS70 2.2 27.6 1.0 S3 A:SF4408 2.3 27.2 1.0 S2 A:SF4408 2.3 28.7 1.0 S4 A:SF4408 2.3 29.3 1.0 FE2 A:SF4408 2.7 27.4 1.0 FE3 A:SF4408 2.7 29.1 1.0 FE4 A:SF4408 2.8 30.8 1.0 CB A:CYS70 2.9 29.4 1.0 S1 A:SF4408 3.8 29.4 1.0 CB A:LEU72 4.3 27.6 1.0 CA A:CYS70 4.4 28.8 1.0 SD A:SAH401 4.5 28.1 0.7 CD2 A:LEU305 4.5 32.3 1.0 CG A:SAH401 4.6 29.1 0.3 SG A:CYS67 4.7 28.6 1.0 N A:ARG73 4.7 29.1 1.0 CB A:CYS67 4.8 26.9 1.0 N A:LEU72 4.8 27.0 1.0 N A:SAH401 4.8 25.8 1.0 SG A:CYS63 4.8 26.9 1.0 O A:SAH401 4.8 34.1 1.0 C A:LEU72 4.8 29.2 1.0 CA A:LEU72 4.9 30.1 1.0 C A:CYS70 4.9 27.4 1.0 CG A:LEU72 4.9 30.2 1.0

Iron binding site 2 out of 4 in the (2R,4R)-Metda Bound Hyde Structure (Control Experiment)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of (2R,4R)-Metda Bound Hyde Structure (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe408 b:27.4 occ:1.00 FE2 A:SF4408 0.0 27.4 1.0 SG A:CYS63 2.2 26.9 1.0 S3 A:SF4408 2.3 27.2 1.0 S4 A:SF4408 2.3 29.3 1.0 S1 A:SF4408 2.3 29.4 1.0 FE1 A:SF4408 2.7 28.0 1.0 FE3 A:SF4408 2.7 29.1 1.0 FE4 A:SF4408 2.8 30.8 1.0 CB A:CYS63 3.3 29.1 1.0 S2 A:SF4408 3.9 28.7 1.0 N A:SAH401 4.1 25.8 1.0 CB A:LYS65 4.3 27.0 1.0 N A:GLU110 4.3 25.5 1.0 CA A:GLY109 4.5 23.5 1.0 O A:LYS65 4.6 33.4 1.0 SG A:CYS70 4.7 27.6 1.0 CA A:CYS63 4.7 26.9 1.0 N A:LYS65 4.7 27.0 1.0 C A:LYS65 4.8 27.9 1.0 SG A:CYS67 4.8 28.6 1.0 CA A:LYS65 4.8 26.8 1.0 O A:SAH401 4.9 34.1 1.0 CB A:LEU72 4.9 27.6 1.0 O A:LEU72 4.9 29.4 1.0 C A:GLY109 5.0 22.8 1.0

Iron binding site 3 out of 4 in the (2R,4R)-Metda Bound Hyde Structure (Control Experiment)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of (2R,4R)-Metda Bound Hyde Structure (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe408 b:29.1 occ:1.00 FE3 A:SF4408 0.0 29.1 1.0 S1 A:SF4408 2.3 29.4 1.0 S4 A:SF4408 2.3 29.3 1.0 S2 A:SF4408 2.3 28.7 1.0 SG A:CYS67 2.3 28.6 1.0 FE1 A:SF4408 2.7 28.0 1.0 FE2 A:SF4408 2.7 27.4 1.0 FE4 A:SF4408 2.8 30.8 1.0 CB A:CYS67 3.2 26.9 1.0 O A:HOH594 3.8 33.0 1.0 S3 A:SF4408 3.9 27.2 1.0 O A:SAH401 4.1 34.1 1.0 N A:CYS67 4.2 31.7 1.0 CB A:CYS70 4.3 29.4 1.0 CA A:CYS67 4.3 28.1 1.0 CB A:LYS65 4.3 27.0 1.0 NH2 A:ARG172 4.5 26.3 1.0 SG A:CYS70 4.6 27.6 1.0 OH A:TYR69 4.6 27.2 1.0 SG A:CYS63 4.7 26.9 1.0 CE1 A:TYR69 4.8 24.3 1.0 O A:HOH561 4.8 31.3 1.0 CD A:LYS65 4.9 26.9 1.0 NE A:ARG172 5.0 26.1 1.0 N A:SAH401 5.0 25.8 1.0

Iron binding site 4 out of 4 in the (2R,4R)-Metda Bound Hyde Structure (Control Experiment)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of (2R,4R)-Metda Bound Hyde Structure (Control Experiment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe408 b:30.8 occ:1.00 FE4 A:SF4408 0.0 30.8 1.0 O A:SAH401 2.2 34.1 1.0 N A:SAH401 2.3 25.8 1.0 S2 A:SF4408 2.3 28.7 1.0 S1 A:SF4408 2.3 29.4 1.0 S3 A:SF4408 2.3 27.2 1.0 FE1 A:SF4408 2.8 28.0 1.0 FE2 A:SF4408 2.8 27.4 1.0 FE3 A:SF4408 2.8 29.1 1.0 CG A:SAH401 3.0 29.1 0.3 C A:SAH401 3.0 27.8 1.0 CA A:SAH401 3.1 28.2 1.0 SD A:SAH401 3.4 28.1 0.7 CB A:SAH401 3.6 27.3 0.3 CG A:SAH401 3.8 30.4 0.7 CB A:SAH401 4.0 25.6 0.7 O A:HOH594 4.0 33.0 1.0 S4 A:SF4408 4.0 29.3 1.0 O A:HOH561 4.1 31.3 1.0 OXT A:SAH401 4.2 29.9 1.0 SD A:SAH401 4.4 27.9 0.3 SG A:CYS63 4.7 26.9 1.0 SG A:CYS70 4.8 27.6 1.0

J.Omeiri, L.Martin, A.Usclat, M.V.Cherrier, Y.Nicolet. Maturation of the [Fefe]-Hydrogenase: Direct Transfer of the ( Kappa 3-Cysteinate)Feii(Cn)(Co)2 Complex-B From Hydg to Hyde. Angew.Chem.Int.Ed.Engl. 14819 2023.
ISSN: ESSN 1521-3773
PubMed: 37962296
DOI: 10.1002/ANIE.202314819