Iron in PDB 7lw8: Human Exonuclease 5 Crystal Structure in Complex with A Ssdna

The structure of Human Exonuclease 5 Crystal Structure in Complex with A Ssdna, PDB code: 7lw8 was solved by C.L.Tsai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.18 / 2.88
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.17, 83.98, 96.355, 90, 90, 90
R / Rfree (%)	20.5 / 25.9

The binding sites of Iron atom in the Human Exonuclease 5 Crystal Structure in Complex with A Ssdna (pdb code 7lw8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Exonuclease 5 Crystal Structure in Complex with A Ssdna, PDB code: 7lw8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Exonuclease 5 Crystal Structure in Complex with A Ssdna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Exonuclease 5 Crystal Structure in Complex with A Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:30.4 occ:1.00 FE1 A:SF4401 0.0 30.4 1.0 SG A:CYS352 2.3 45.8 1.0 S4 A:SF4401 2.3 22.4 1.0 S2 A:SF4401 2.3 23.2 1.0 S3 A:SF4401 2.3 28.7 1.0 FE2 A:SF4401 2.7 25.0 1.0 FE4 A:SF4401 2.7 29.4 1.0 FE3 A:SF4401 2.7 25.1 1.0 CB A:CYS352 3.2 44.3 1.0 S1 A:SF4401 3.9 28.7 1.0 CA A:CYS352 4.6 41.5 1.0 CB A:ARG355 4.7 53.9 1.0 SG A:CYS343 4.7 38.1 1.0 CB A:TRP354 4.7 31.3 1.0 CD2 A:LEU94 4.7 27.3 1.0 CB A:LEU94 4.8 31.6 1.0 CG A:LEU94 4.8 30.6 1.0 SG A:CYS92 4.8 24.5 1.0 SG A:CYS346 4.9 28.0 1.0 O A:TYR348 4.9 33.6 1.0 CE2 A:TYR98 5.0 36.4 1.0 N A:ARG355 5.0 61.8 1.0

Iron binding site 2 out of 4 in the Human Exonuclease 5 Crystal Structure in Complex with A Ssdna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Exonuclease 5 Crystal Structure in Complex with A Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:25.0 occ:1.00 FE2 A:SF4401 0.0 25.0 1.0 SG A:CYS346 2.3 28.0 1.0 S4 A:SF4401 2.3 22.4 1.0 S3 A:SF4401 2.3 28.7 1.0 S1 A:SF4401 2.3 28.7 1.0 FE4 A:SF4401 2.7 29.4 1.0 FE1 A:SF4401 2.7 30.4 1.0 FE3 A:SF4401 2.7 25.1 1.0 CB A:CYS346 3.1 27.8 1.0 S2 A:SF4401 3.9 23.2 1.0 OE1 A:GLN95 4.1 22.6 1.0 CB A:GLN95 4.3 27.4 1.0 CA A:CYS346 4.6 35.2 1.0 CG A:GLN95 4.6 21.4 1.0 CA A:CYS343 4.6 39.8 1.0 SG A:CYS352 4.8 45.8 1.0 SG A:CYS92 4.8 24.5 1.0 SG A:CYS343 4.8 38.1 1.0 C A:TYR348 4.8 27.1 1.0 CA A:GLN95 4.8 28.6 1.0 CD A:GLN95 4.8 26.2 1.0 CB A:CYS343 4.9 35.4 1.0 O A:TYR348 4.9 33.6 1.0 N A:ALA349 4.9 27.5 1.0 CB A:CYS352 5.0 44.3 1.0

Iron binding site 3 out of 4 in the Human Exonuclease 5 Crystal Structure in Complex with A Ssdna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Exonuclease 5 Crystal Structure in Complex with A Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:25.1 occ:1.00 FE3 A:SF4401 0.0 25.1 1.0 SG A:CYS92 2.3 24.5 1.0 S1 A:SF4401 2.3 28.7 1.0 S4 A:SF4401 2.3 22.4 1.0 S2 A:SF4401 2.3 23.2 1.0 FE2 A:SF4401 2.7 25.0 1.0 FE4 A:SF4401 2.7 29.4 1.0 FE1 A:SF4401 2.7 30.4 1.0 CB A:CYS92 3.5 24.4 1.0 S3 A:SF4401 3.9 28.7 1.0 N A:GLN95 4.0 35.6 1.0 CB A:GLN95 4.0 27.4 1.0 CG1 A:VAL335 4.3 33.2 1.0 CB A:LEU94 4.3 31.6 1.0 CA A:GLN95 4.4 28.6 1.0 N A:VAL335 4.5 29.6 1.0 CA A:GLY334 4.6 19.3 1.0 C A:LEU94 4.7 28.4 1.0 SG A:CYS346 4.7 28.0 1.0 SG A:CYS352 4.7 45.8 1.0 SG A:CYS343 4.8 38.1 1.0 CA A:CYS92 4.9 26.4 1.0 CA A:LEU94 4.9 27.3 1.0 OE1 A:GLN95 5.0 22.6 1.0

Iron binding site 4 out of 4 in the Human Exonuclease 5 Crystal Structure in Complex with A Ssdna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Exonuclease 5 Crystal Structure in Complex with A Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:29.4 occ:1.00 FE4 A:SF4401 0.0 29.4 1.0 SG A:CYS343 2.3 38.1 1.0 S1 A:SF4401 2.3 28.7 1.0 S2 A:SF4401 2.3 23.2 1.0 S3 A:SF4401 2.3 28.7 1.0 FE2 A:SF4401 2.7 25.0 1.0 FE1 A:SF4401 2.7 30.4 1.0 FE3 A:SF4401 2.7 25.1 1.0 CB A:CYS343 3.1 35.4 1.0 CA A:CYS343 3.5 39.8 1.0 S4 A:SF4401 3.9 22.4 1.0 N A:CYS343 4.0 38.1 1.0 CG2 A:VAL335 4.4 25.8 1.0 SG A:CYS92 4.7 24.5 1.0 SG A:CYS346 4.7 28.0 1.0 CG1 A:VAL335 4.7 33.2 1.0 CB A:CYS346 4.8 27.8 1.0 C A:LYS342 4.8 35.8 1.0 CG A:ARG355 4.9 59.2 1.0 SG A:CYS352 4.9 45.8 1.0 C A:CYS343 4.9 42.3 1.0 CB A:ARG355 4.9 53.9 1.0

S.Hambarde, C.L.Tsai, R.K.Pandita, A.Bacolla, A.Maitra, V.Charaka, C.R.Hunt, R.Kumar, O.Limbo, R.Le Meur, W.J.Chazin, S.E.Tsutakawa, P.Russell, K.Schlacher, T.K.Pandita, J.A.Tainer. EXO5-Dna Structure and Blm Interactions Direct Dna Resection Critical For Atr-Dependent Replication Restart. Mol.Cell 2021.
ISSN: ISSN 1097-2765
PubMed: 34197737
DOI: 10.1016/J.MOLCEL.2021.05.027