Iron in PDB 5h8w: Xpd Mechanism

All present enzymatic activity of Xpd Mechanism:
3.6.4.12;

The structure of Xpd Mechanism, PDB code: 5h8w was solved by J.H.Naismith, D.Constantinescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.22 / 2.20
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	78.569, 78.569, 177.832, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 24.3

The structure of Xpd Mechanism also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Iron atom in the Xpd Mechanism (pdb code 5h8w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Xpd Mechanism, PDB code: 5h8w:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Xpd Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.7 occ:1.00 FE1 A:SF4801 0.0 25.7 1.0 S3 A:SF4801 2.1 27.1 1.0 S2 A:SF4801 2.1 27.7 1.0 S4 A:SF4801 2.1 27.5 1.0 SG A:CYS164 2.3 28.1 1.0 FE2 A:SF4801 2.5 25.8 1.0 FE3 A:SF4801 2.5 24.2 1.0 FE4 A:SF4801 2.6 24.2 1.0 CB A:CYS164 3.3 28.4 1.0 S1 A:SF4801 3.5 25.7 1.0 CG A:GLU167 4.2 32.6 1.0 CA A:CYS164 4.4 28.0 1.0 SG A:CYS92 4.5 28.5 1.0 SG A:CYS128 4.5 31.8 1.0 SG A:CYS113 4.6 32.6 1.0 CA A:CYS92 4.6 27.9 1.0 CB A:CYS92 4.9 27.8 1.0 CB A:TYR166 4.9 28.6 1.0 N A:ILE93 5.0 28.5 1.0 N A:GLU167 5.0 31.6 1.0

Iron binding site 2 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Xpd Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.8 occ:1.00 FE2 A:SF4801 0.0 25.8 1.0 S3 A:SF4801 2.1 27.1 1.0 S1 A:SF4801 2.1 25.7 1.0 S4 A:SF4801 2.1 27.5 1.0 SG A:CYS113 2.3 32.6 1.0 FE1 A:SF4801 2.5 25.7 1.0 FE4 A:SF4801 2.6 24.2 1.0 FE3 A:SF4801 2.6 24.2 1.0 CB A:CYS113 3.3 32.1 1.0 S2 A:SF4801 3.6 27.7 1.0 CA A:CYS113 4.0 33.0 1.0 NE A:ARG88 4.3 28.7 1.0 SG A:CYS164 4.5 28.1 1.0 CG A:GLU167 4.5 32.6 1.0 O A:CYS113 4.6 35.7 1.0 SG A:CYS92 4.6 28.5 1.0 C A:CYS113 4.7 34.9 1.0 OE2 A:GLU167 4.7 33.1 1.0 CG A:LYS117 4.7 39.5 1.0 SG A:CYS128 4.8 31.8 1.0 CD A:LYS117 4.8 39.2 1.0 CD A:ARG88 4.8 28.1 1.0

Iron binding site 3 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Xpd Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:24.2 occ:1.00 FE3 A:SF4801 0.0 24.2 1.0 S2 A:SF4801 2.1 27.7 1.0 S1 A:SF4801 2.1 25.7 1.0 S4 A:SF4801 2.1 27.5 1.0 SG A:CYS92 2.3 28.5 1.0 FE1 A:SF4801 2.5 25.7 1.0 FE4 A:SF4801 2.6 24.2 1.0 FE2 A:SF4801 2.6 25.8 1.0 CB A:CYS92 3.4 27.8 1.0 S3 A:SF4801 3.6 27.1 1.0 CA A:CYS92 3.8 27.9 1.0 CB A:LEU94 4.0 31.5 1.0 N A:LEU94 4.2 30.4 1.0 N A:ILE93 4.3 28.5 1.0 C A:CYS92 4.3 28.1 1.0 SG A:CYS164 4.5 28.1 1.0 SG A:CYS113 4.6 32.6 1.0 SG A:CYS128 4.6 31.8 1.0 CA A:LEU94 4.7 31.3 1.0 CB A:CYS113 4.8 32.1 1.0 CE2 A:PHE112 4.9 28.9 1.0

Iron binding site 4 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Xpd Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:24.2 occ:1.00 FE4 A:SF4801 0.0 24.2 1.0 S1 A:SF4801 2.1 25.7 1.0 S2 A:SF4801 2.1 27.7 1.0 S3 A:SF4801 2.1 27.1 1.0 SG A:CYS128 2.3 31.8 1.0 FE3 A:SF4801 2.6 24.2 1.0 FE1 A:SF4801 2.6 25.7 1.0 FE2 A:SF4801 2.6 25.8 1.0 CB A:CYS128 3.5 32.3 1.0 S4 A:SF4801 3.6 27.5 1.0 CB A:LEU94 4.2 31.5 1.0 CD2 A:LEU94 4.4 33.2 1.0 SG A:CYS164 4.6 28.1 1.0 SG A:CYS92 4.7 28.5 1.0 CB A:TYR130 4.7 27.7 1.0 SG A:CYS113 4.7 32.6 1.0 CB A:PHE131 4.8 32.2 1.0 CA A:CYS128 4.8 32.4 1.0 N A:PHE131 4.9 30.7 1.0 CG A:LEU94 4.9 32.7 1.0 CB A:CYS164 4.9 28.4 1.0

D.Constantinescu-Aruxandei, B.Petrovic-Stojanovska, J.C.Penedo, M.F.White, J.H.Naismith. Mechanism of Dna Loading By the Dna Repair Helicase Xpd. Nucleic Acids Res. V. 44 2806 2016.
ISSN: ESSN 1362-4962
PubMed: 26896802
DOI: 10.1093/NAR/GKW102