Iron in PDB 7lwa: Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg

The structure of Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg, PDB code: 7lwa 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)	47.52 / 2.85
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.512, 84.722, 95.034, 90, 90, 90
R / Rfree (%)	20.3 / 25.1

The structure of Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg (pdb code 7lwa). 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 (T88E) in Complex with Ssdna and Mg, PDB code: 7lwa:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg


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 (T88E) in Complex with Ssdna and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:44.3 occ:1.00 FE1 A:SF4401 0.0 44.3 1.0 SG A:CYS346 2.3 47.2 1.0 S2 A:SF4401 2.3 40.2 1.0 S3 A:SF4401 2.3 43.5 1.0 S4 A:SF4401 2.3 49.4 1.0 FE2 A:SF4401 2.7 42.2 1.0 FE4 A:SF4401 2.7 41.6 1.0 FE3 A:SF4401 2.7 40.2 1.0 CB A:CYS346 3.1 43.5 1.0 S1 A:SF4401 3.9 40.9 1.0 CB A:GLN95 4.1 38.7 1.0 NE2 A:GLN95 4.2 29.8 1.0 CA A:CYS346 4.5 47.5 1.0 CB A:CYS343 4.6 52.1 1.0 N A:ALA349 4.6 51.0 1.0 SG A:CYS343 4.7 48.6 1.0 CA A:CYS343 4.7 52.7 1.0 C A:TYR348 4.7 50.8 1.0 CA A:GLN95 4.7 40.2 1.0 SG A:CYS92 4.7 40.4 1.0 CG A:GLN95 4.7 36.1 1.0 SG A:CYS352 4.8 44.5 1.0 CA A:ALA349 4.8 50.3 1.0 CB A:CYS352 4.8 50.1 1.0 O A:TYR348 4.9 54.9 1.0 N A:GLN95 5.0 40.9 1.0 CD A:GLN95 5.0 41.6 1.0

Iron binding site 2 out of 4 in the Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg


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 (T88E) in Complex with Ssdna and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:42.2 occ:1.00 FE2 A:SF4401 0.0 42.2 1.0 SG A:CYS343 2.3 48.6 1.0 S1 A:SF4401 2.3 40.9 1.0 S3 A:SF4401 2.3 43.5 1.0 S4 A:SF4401 2.3 49.4 1.0 FE4 A:SF4401 2.7 41.6 1.0 FE1 A:SF4401 2.7 44.3 1.0 FE3 A:SF4401 2.7 40.2 1.0 CB A:CYS343 3.1 52.1 1.0 CA A:CYS343 3.8 52.7 1.0 S2 A:SF4401 3.9 40.2 1.0 N A:CYS343 4.2 47.6 1.0 CG2 A:VAL335 4.3 42.2 1.0 CB A:CYS346 4.7 43.5 1.0 SG A:CYS92 4.7 40.4 1.0 SG A:CYS346 4.7 47.2 1.0 SG A:CYS352 4.7 44.5 1.0 CB A:ARG355 4.8 64.9 1.0 C A:LYS342 4.9 48.6 1.0 CG1 A:VAL335 4.9 51.5 1.0

Iron binding site 3 out of 4 in the Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg


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 (T88E) in Complex with Ssdna and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:40.2 occ:1.00 FE3 A:SF4401 0.0 40.2 1.0 SG A:CYS92 2.3 40.4 1.0 S4 A:SF4401 2.3 49.4 1.0 S2 A:SF4401 2.3 40.2 1.0 S1 A:SF4401 2.3 40.9 1.0 FE2 A:SF4401 2.7 42.2 1.0 FE4 A:SF4401 2.7 41.6 1.0 FE1 A:SF4401 2.7 44.3 1.0 CB A:CYS92 3.6 35.8 1.0 N A:GLN95 3.8 40.9 1.0 S3 A:SF4401 3.9 43.5 1.0 CB A:GLN95 3.9 38.7 1.0 CB A:LEU94 4.1 44.5 1.0 CA A:GLN95 4.3 40.2 1.0 CG1 A:VAL335 4.3 51.5 1.0 N A:VAL335 4.5 46.5 1.0 CA A:GLY334 4.5 38.5 1.0 C A:LEU94 4.6 45.5 1.0 SG A:CYS346 4.7 47.2 1.0 CA A:LEU94 4.8 45.8 1.0 SG A:CYS352 4.8 44.5 1.0 SG A:CYS343 4.9 48.6 1.0 CA A:CYS92 4.9 36.7 1.0 N A:LEU94 4.9 46.0 1.0

Iron binding site 4 out of 4 in the Human Exonuclease 5 Crystal Structure (T88E) in Complex with Ssdna and Mg


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 (T88E) in Complex with Ssdna and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:41.6 occ:1.00 FE4 A:SF4401 0.0 41.6 1.0 SG A:CYS352 2.3 44.5 1.0 S2 A:SF4401 2.3 40.2 1.0 S3 A:SF4401 2.3 43.5 1.0 S1 A:SF4401 2.3 40.9 1.0 FE2 A:SF4401 2.7 42.2 1.0 FE3 A:SF4401 2.7 40.2 1.0 FE1 A:SF4401 2.7 44.3 1.0 CB A:CYS352 3.2 50.1 1.0 S4 A:SF4401 3.9 49.4 1.0 CD2 A:LEU94 4.6 42.8 1.0 CB A:ARG355 4.6 64.9 1.0 CA A:CYS352 4.6 63.8 1.0 N A:ARG355 4.7 88.2 1.0 SG A:CYS343 4.7 48.6 1.0 CB A:LEU94 4.7 44.5 1.0 CB A:TRP354 4.8 44.8 1.0 CG A:LEU94 4.8 41.4 1.0 SG A:CYS346 4.9 47.2 1.0 SG A:CYS92 4.9 40.4 1.0 CE2 A:TYR98 5.0 45.1 1.0 O A:TYR348 5.0 54.9 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