Iron in PDB 4a15: Crystal Structure of An Xpd Dna Complex

All present enzymatic activity of Crystal Structure of An Xpd Dna Complex:
3.6.4.12;

The structure of Crystal Structure of An Xpd Dna Complex, PDB code: 4a15 was solved by J.Kuper, S.C.Wolski, G.Michels, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.53 / 2.20
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	79.060, 79.060, 175.690, 90.00, 90.00, 120.00
R / Rfree (%)	19.23 / 25.049

The structure of Crystal Structure of An Xpd Dna Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Crystal Structure of An Xpd Dna Complex (pdb code 4a15). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of An Xpd Dna Complex, PDB code: 4a15:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of An Xpd Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of An Xpd Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:21.3 occ:1.00 FE1 A:SF41616 0.0 21.3 1.0 S4 A:SF41616 2.1 24.1 1.0 S2 A:SF41616 2.1 23.5 1.0 S3 A:SF41616 2.2 24.2 1.0 SG A:CYS92 2.3 28.0 1.0 FE2 A:SF41616 2.5 23.8 1.0 FE3 A:SF41616 2.6 23.3 1.0 FE4 A:SF41616 2.6 22.1 1.0 CB A:CYS92 3.3 27.7 1.0 S1 A:SF41616 3.7 23.1 1.0 CA A:CYS92 3.8 26.4 1.0 CB A:LEU94 3.9 32.5 1.0 N A:LEU94 4.1 29.9 1.0 N A:ILE93 4.2 28.5 1.0 C A:CYS92 4.3 28.2 1.0 CA A:LEU94 4.6 32.3 1.0 SG A:CYS113 4.7 28.2 1.0 SG A:CYS128 4.7 25.4 1.0 SG A:CYS164 4.7 24.0 1.0 CD2 A:LEU94 4.8 31.5 1.0 CE2 A:PHE112 4.9 31.0 1.0 CB A:CYS113 4.9 27.3 1.0 CG A:LEU94 5.0 34.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure of An Xpd Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of An Xpd Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:23.3 occ:1.00 FE3 A:SF41616 0.0 23.3 1.0 S2 A:SF41616 2.1 23.5 1.0 S4 A:SF41616 2.1 24.1 1.0 S1 A:SF41616 2.2 23.1 1.0 SG A:CYS128 2.3 25.4 1.0 FE2 A:SF41616 2.5 23.8 1.0 FE1 A:SF41616 2.6 21.3 1.0 FE4 A:SF41616 2.6 22.1 1.0 CB A:CYS128 3.6 25.0 1.0 S3 A:SF41616 3.7 24.2 1.0 CB A:LEU94 4.0 32.5 1.0 CD2 A:LEU94 4.1 31.5 1.0 CB A:TYR130 4.6 25.3 1.0 SG A:CYS164 4.6 24.0 1.0 SG A:CYS92 4.7 28.0 1.0 CG A:LEU94 4.7 34.8 1.0 CB A:PHE131 4.8 29.5 1.0 SG A:CYS113 4.8 28.2 1.0 CB A:CYS164 4.9 23.6 1.0 CA A:CYS128 4.9 27.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of An Xpd Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of An Xpd Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:23.8 occ:1.00 FE2 A:SF41616 0.0 23.8 1.0 S3 A:SF41616 2.1 24.2 1.0 S4 A:SF41616 2.2 24.1 1.0 S1 A:SF41616 2.2 23.1 1.0 SG A:CYS113 2.5 28.2 1.0 FE4 A:SF41616 2.5 22.1 1.0 FE3 A:SF41616 2.5 23.3 1.0 FE1 A:SF41616 2.5 21.3 1.0 CB A:CYS113 3.5 27.3 1.0 S2 A:SF41616 3.6 23.5 1.0 CA A:CYS113 4.0 27.6 1.0 NE A:ARG88 4.3 27.4 1.0 SG A:CYS92 4.6 28.0 1.0 CG A:GLU167 4.6 25.0 1.0 SG A:CYS164 4.6 24.0 1.0 OE2 A:GLU167 4.6 27.1 1.0 O A:CYS113 4.6 28.5 1.0 SG A:CYS128 4.7 25.4 1.0 C A:CYS113 4.7 29.1 1.0 CG A:LYS117 4.9 34.5 1.0 CD A:LYS117 4.9 32.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of An Xpd Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of An Xpd Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1616 b:22.1 occ:1.00 FE4 A:SF41616 0.0 22.1 1.0 S2 A:SF41616 2.1 23.5 1.0 S1 A:SF41616 2.1 23.1 1.0 S3 A:SF41616 2.1 24.2 1.0 SG A:CYS164 2.3 24.0 1.0 FE2 A:SF41616 2.5 23.8 1.0 FE3 A:SF41616 2.6 23.3 1.0 FE1 A:SF41616 2.6 21.3 1.0 CB A:CYS164 3.3 23.6 1.0 S4 A:SF41616 3.6 24.1 1.0 CG A:GLU167 4.2 25.0 1.0 CA A:CYS164 4.5 23.7 1.0 SG A:CYS92 4.5 28.0 1.0 SG A:CYS128 4.6 25.4 1.0 CA A:CYS92 4.6 26.4 1.0 SG A:CYS113 4.7 28.2 1.0 CB A:TYR166 4.8 22.2 1.0 CB A:CYS92 4.8 27.7 1.0 N A:ILE93 4.9 28.5 1.0 N A:GLU167 5.0 22.9 1.0 CB A:TYR130 5.0 25.3 1.0

J.Kuper, S.C.Wolski, G.Michels, C.Kisker. Functional and Structural Studies of the Nucleotide Excision Repair Helicase Xpd Suggest A Polarity For Dna Translocation. Embo J. V. 31 494 2011.
ISSN: ISSN 0261-4189
PubMed: 22081108
DOI: 10.1038/EMBOJ.2011.374