Iron in PDB 3crv: XPD_HELICASE

The structure of XPD_HELICASE, PDB code: 3crv was solved by L.Fan, A.S.Arvai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.58 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.542, 70.222, 144.293, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26

The binding sites of Iron atom in the XPD_HELICASE (pdb code 3crv). 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_HELICASE, PDB code: 3crv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the XPD_HELICASE


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of XPD_HELICASE within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:38.3 occ:1.00 FE1 A:SF4600 0.0 38.3 1.0 SG A:CYS137 2.2 38.0 1.0 S2 A:SF4600 2.3 37.3 1.0 S3 A:SF4600 2.3 40.5 1.0 S4 A:SF4600 2.4 39.9 1.0 FE4 A:SF4600 2.6 39.5 1.0 FE2 A:SF4600 2.7 38.9 1.0 FE3 A:SF4600 2.8 37.0 1.0 CB A:CYS137 3.1 36.9 1.0 S1 A:SF4600 3.8 39.5 1.0 CA A:CYS137 4.1 35.8 1.0 CD1 A:TYR140 4.2 36.7 1.0 CE1 A:TYR140 4.4 38.5 1.0 SG A:CYS102 4.7 52.8 1.0 SG A:CYS88 4.8 37.2 1.0 SG A:CYS105 4.8 47.4 1.0 C A:CYS137 4.9 34.5 1.0 CA A:CYS88 4.9 37.8 1.0 CB A:TYR139 4.9 33.0 1.0 CB A:LEU107 5.0 49.8 1.0

Iron binding site 2 out of 4 in the XPD_HELICASE


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of XPD_HELICASE within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:38.9 occ:1.00 FE2 A:SF4600 0.0 38.9 1.0 S1 A:SF4600 2.2 39.5 1.0 S3 A:SF4600 2.3 40.5 1.0 S4 A:SF4600 2.3 39.9 1.0 SG A:CYS105 2.4 47.4 1.0 FE1 A:SF4600 2.7 38.3 1.0 FE4 A:SF4600 2.7 39.5 1.0 FE3 A:SF4600 2.7 37.0 1.0 CB A:CYS105 3.1 51.7 1.0 S2 A:SF4600 3.9 37.3 1.0 CB A:LEU107 4.2 49.8 1.0 CE1 A:TYR90 4.3 47.7 1.0 CD1 A:TYR90 4.4 47.7 1.0 CA A:CYS105 4.6 53.6 1.0 SG A:CYS137 4.8 38.0 1.0 N A:LYS108 4.8 48.9 1.0 CA A:CYS102 4.8 57.1 1.0 SG A:CYS88 4.8 37.2 1.0 C A:LEU107 4.9 49.3 1.0 SG A:CYS102 4.9 52.8 1.0 CD2 A:LEU107 4.9 48.0 1.0 CA A:LEU107 4.9 50.7 1.0 CB A:CYS137 4.9 36.9 1.0 N A:LEU107 4.9 51.5 1.0

Iron binding site 3 out of 4 in the XPD_HELICASE


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of XPD_HELICASE within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:37.0 occ:1.00 FE3 A:SF4600 0.0 37.0 1.0 S1 A:SF4600 2.2 39.5 1.0 SG A:CYS88 2.3 37.2 1.0 S4 A:SF4600 2.3 39.9 1.0 S2 A:SF4600 2.4 37.3 1.0 FE4 A:SF4600 2.7 39.5 1.0 FE2 A:SF4600 2.7 38.9 1.0 FE1 A:SF4600 2.8 38.3 1.0 CB A:CYS88 3.3 37.9 1.0 CA A:CYS88 3.7 37.8 1.0 CG2 A:ILE100 3.8 54.6 1.0 S3 A:SF4600 4.0 40.5 1.0 N A:LEU89 4.0 40.0 1.0 C A:CYS88 4.3 38.9 1.0 CD1 A:TYR90 4.4 47.7 1.0 N A:TYR90 4.7 44.1 1.0 SG A:CYS102 4.7 52.8 1.0 SG A:CYS137 4.8 38.0 1.0 SG A:CYS105 4.8 47.4 1.0 CE1 A:TYR90 4.9 47.7 1.0 N A:CYS88 5.0 36.1 1.0

Iron binding site 4 out of 4 in the XPD_HELICASE


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of XPD_HELICASE within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:39.5 occ:1.00 FE4 A:SF4600 0.0 39.5 1.0 S2 A:SF4600 2.2 37.3 1.0 S1 A:SF4600 2.3 39.5 1.0 S3 A:SF4600 2.3 40.5 1.0 SG A:CYS102 2.3 52.8 1.0 FE1 A:SF4600 2.6 38.3 1.0 FE3 A:SF4600 2.7 37.0 1.0 FE2 A:SF4600 2.7 38.9 1.0 CB A:CYS102 3.2 56.3 1.0 CA A:CYS102 3.5 57.1 1.0 CG2 A:ILE100 3.8 54.6 1.0 S4 A:SF4600 3.9 39.9 1.0 CE1 A:TYR140 4.2 38.5 1.0 N A:CYS102 4.2 56.0 1.0 SG A:CYS137 4.5 38.0 1.0 CB A:CYS105 4.6 51.7 1.0 SG A:CYS88 4.6 37.2 1.0 SG A:CYS105 4.7 47.4 1.0 C A:CYS102 4.8 58.6 1.0 CD1 A:TYR140 4.9 36.7 1.0 CD A:LYS84 4.9 47.1 1.0 O A:CYS102 5.0 59.1 1.0 CB A:ILE100 5.0 54.8 1.0

L.Fan, J.O.Fuss, Q.J.Cheng, A.S.Arvai, M.Hammel, V.A.Roberts, P.K.Cooper, J.A.Tainer. Xpd Helicase Structures and Activities: Insights Into the Cancer and Aging Phenotypes From Xpd Mutations. Cell(Cambridge,Mass.) V. 133 789 2008.
ISSN: ISSN 0092-8674
PubMed: 18510924
DOI: 10.1016/J.CELL.2008.04.030