Iron in PDB 5h8c: Truncated Xpd

The structure of Truncated Xpd, PDB code: 5h8c 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)	29.00 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.800, 77.800, 99.540, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.9

The binding sites of Iron atom in the Truncated Xpd (pdb code 5h8c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Truncated Xpd, PDB code: 5h8c:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Truncated Xpd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Truncated Xpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:63.1 occ:1.00 FE1 A:SF4601 0.0 63.1 1.0 S2 A:SF4601 2.1 61.7 1.0 S4 A:SF4601 2.1 61.1 1.0 S3 A:SF4601 2.1 67.1 1.0 SG A:CYS137 2.3 67.5 1.0 FE2 A:SF4601 2.5 64.9 1.0 FE3 A:SF4601 2.5 59.8 1.0 FE4 A:SF4601 2.6 61.8 1.0 CB A:CYS137 3.5 68.7 1.0 S1 A:SF4601 3.5 63.4 1.0 CA A:CYS137 4.3 66.8 1.0 SG A:CYS102 4.5 66.2 1.0 CD2 A:TYR140 4.6 72.4 1.0 SG A:CYS88 4.6 63.3 1.0 CE2 A:TYR140 4.7 73.1 1.0 SG A:CYS105 4.7 78.2 1.0 CA A:CYS88 4.7 59.9 1.0 CD A:PRO138 4.9 62.8 1.0 CB A:TYR139 4.9 58.9 1.0 CB A:CYS88 4.9 61.0 1.0 CB A:LEU107 5.0 76.1 1.0

Iron binding site 2 out of 4 in the Truncated Xpd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Truncated Xpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:64.9 occ:1.00 FE2 A:SF4601 0.0 64.9 1.0 S1 A:SF4601 2.1 63.4 1.0 S4 A:SF4601 2.1 61.1 1.0 S3 A:SF4601 2.1 67.1 1.0 SG A:CYS102 2.3 66.2 1.0 FE1 A:SF4601 2.5 63.1 1.0 FE4 A:SF4601 2.5 61.8 1.0 FE3 A:SF4601 2.6 59.8 1.0 CB A:CYS102 3.3 69.3 1.0 S2 A:SF4601 3.5 61.7 1.0 CA A:CYS102 3.6 70.4 1.0 CG2 A:ILE100 3.9 65.6 1.0 N A:CYS102 4.1 68.7 1.0 SG A:CYS137 4.4 67.5 1.0 CE2 A:TYR140 4.4 73.1 1.0 CB A:CYS105 4.5 76.8 1.0 SG A:CYS105 4.6 78.2 1.0 SG A:CYS88 4.6 63.3 1.0 C A:PRO101 4.9 70.3 1.0 C A:CYS102 5.0 75.4 1.0

Iron binding site 3 out of 4 in the Truncated Xpd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Truncated Xpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:59.8 occ:1.00 FE3 A:SF4601 0.0 59.8 1.0 S2 A:SF4601 2.1 61.7 1.0 S1 A:SF4601 2.1 63.4 1.0 S4 A:SF4601 2.1 61.1 1.0 SG A:CYS88 2.3 63.3 1.0 FE1 A:SF4601 2.5 63.1 1.0 FE2 A:SF4601 2.6 64.9 1.0 FE4 A:SF4601 2.6 61.8 1.0 CB A:CYS88 3.3 61.0 1.0 S3 A:SF4601 3.6 67.1 1.0 CA A:CYS88 3.7 59.9 1.0 CG2 A:ILE100 3.9 65.6 1.0 N A:LEU89 4.0 61.9 1.0 CD2 A:TYR90 4.2 73.5 1.0 C A:CYS88 4.3 61.4 1.0 SG A:CYS102 4.5 66.2 1.0 CE2 A:TYR90 4.5 76.6 1.0 SG A:CYS137 4.7 67.5 1.0 SG A:CYS105 4.8 78.2 1.0 N A:TYR90 5.0 66.7 1.0 N A:CYS88 5.0 59.9 1.0

Iron binding site 4 out of 4 in the Truncated Xpd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Truncated Xpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:61.8 occ:1.00 FE4 A:SF4601 0.0 61.8 1.0 S1 A:SF4601 2.1 63.4 1.0 S3 A:SF4601 2.1 67.1 1.0 S2 A:SF4601 2.1 61.7 1.0 SG A:CYS105 2.4 78.2 1.0 FE2 A:SF4601 2.5 64.9 1.0 FE1 A:SF4601 2.6 63.1 1.0 FE3 A:SF4601 2.6 59.8 1.0 CB A:CYS105 3.2 76.8 1.0 S4 A:SF4601 3.6 61.1 1.0 CE2 A:TYR90 4.1 76.6 1.0 CB A:LEU107 4.4 76.1 1.0 CD2 A:TYR90 4.5 73.5 1.0 SG A:CYS137 4.6 67.5 1.0 SG A:CYS88 4.7 63.3 1.0 SG A:CYS102 4.7 66.2 1.0 CA A:CYS105 4.7 80.7 1.0 CA A:CYS102 4.9 70.4 1.0 N A:LYS108 4.9 79.9 1.0 CD1 A:LEU107 5.0 75.3 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