Iron in PDB 7lw9: Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na

The structure of Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na, PDB code: 7lw9 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)	45.11 / 2.71
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.073, 83.664, 96.15, 90, 90, 90
R / Rfree (%)	19.4 / 25.3

The structure of Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Samarium	(Sm)	2 atoms

The binding sites of Iron atom in the Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na (pdb code 7lw9). 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 Ssdna, Sm, and Na, PDB code: 7lw9:
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 Ssdna, Sm, and Na


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 Ssdna, Sm, and Na within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:43.4 occ:1.00 FE1 A:SF4501 0.0 43.4 1.0 S3 A:SF4501 2.3 50.5 1.0 S2 A:SF4501 2.3 42.4 1.0 S4 A:SF4501 2.3 33.4 1.0 SG A:CYS346 2.7 56.5 1.0 FE3 A:SF4501 2.7 45.5 1.0 FE2 A:SF4501 2.7 42.8 1.0 FE4 A:SF4501 2.7 45.8 1.0 CB A:CYS346 3.2 55.3 1.0 S1 A:SF4501 3.9 39.6 1.0 NE2 A:GLN95 4.1 43.5 1.0 CB A:GLN95 4.5 43.8 1.0 CG A:GLN95 4.5 48.3 1.0 O A:TYR348 4.6 56.2 1.0 C A:TYR348 4.7 47.2 1.0 CA A:CYS346 4.7 56.9 1.0 CA A:CYS343 4.8 51.5 1.0 CD A:GLN95 4.9 43.5 1.0 N A:ALA349 4.9 57.6 1.0 CA A:ALA349 4.9 58.1 1.0 CB A:CYS343 5.0 47.6 1.0

Iron binding site 2 out of 4 in the Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na


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 Ssdna, Sm, and Na within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:42.8 occ:1.00 FE2 A:SF4501 0.0 42.8 1.0 S4 A:SF4501 2.3 33.4 1.0 S3 A:SF4501 2.3 50.5 1.0 S1 A:SF4501 2.3 39.6 1.0 FE1 A:SF4501 2.7 43.4 1.0 FE3 A:SF4501 2.7 45.5 1.0 FE4 A:SF4501 2.7 45.8 1.0 SG A:CYS343 2.9 67.8 1.0 CB A:CYS343 3.3 47.6 1.0 CA A:CYS343 3.7 51.5 1.0 S2 A:SF4501 3.9 42.4 1.0 CG2 A:VAL335 4.1 45.6 1.0 N A:CYS343 4.3 44.6 1.0 CG1 A:VAL335 4.6 40.9 1.0 CB A:ARG355 4.8 79.5 1.0 CB A:CYS346 4.9 55.3 1.0 C A:LYS342 4.9 43.8 1.0 CB A:VAL335 5.0 51.7 1.0

Iron binding site 3 out of 4 in the Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na


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 Ssdna, Sm, and Na within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:45.5 occ:1.00 FE3 A:SF4501 0.0 45.5 1.0 S1 A:SF4501 2.3 39.6 1.0 S2 A:SF4501 2.3 42.4 1.0 S4 A:SF4501 2.3 33.4 1.0 SG A:CYS92 2.7 46.2 1.0 FE1 A:SF4501 2.7 43.4 1.0 FE4 A:SF4501 2.7 45.8 1.0 FE2 A:SF4501 2.7 42.8 1.0 CB A:CYS92 3.7 38.5 1.0 S3 A:SF4501 3.9 50.5 1.0 N A:GLN95 4.1 40.6 1.0 CB A:LEU94 4.1 48.0 1.0 CG1 A:VAL335 4.2 40.9 1.0 CB A:GLN95 4.2 43.8 1.0 N A:VAL335 4.5 51.8 1.0 CA A:GLY334 4.6 32.8 1.0 CA A:GLN95 4.6 40.2 1.0 C A:LEU94 4.8 39.5 1.0 CG2 A:VAL335 4.9 45.6 1.0 CA A:LEU94 4.9 39.0 1.0 NE2 A:GLN95 5.0 43.5 1.0

Iron binding site 4 out of 4 in the Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na


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 Ssdna, Sm, and Na within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:45.8 occ:1.00 FE4 A:SF4501 0.0 45.8 1.0 S2 A:SF4501 2.3 42.4 1.0 S1 A:SF4501 2.3 39.6 1.0 S3 A:SF4501 2.3 50.5 1.0 FE3 A:SF4501 2.7 45.5 1.0 FE1 A:SF4501 2.7 43.4 1.0 FE2 A:SF4501 2.7 42.8 1.0 SG A:CYS352 2.9 73.2 1.0 CB A:CYS352 3.5 61.3 1.0 S4 A:SF4501 3.9 33.4 1.0 CD2 A:LEU94 4.6 47.1 1.0 CB A:TRP354 4.7 56.3 1.0 CB A:LEU94 4.7 48.0 1.0 CG A:LEU94 4.7 42.6 1.0 O A:TYR348 4.8 56.2 1.0 N A:ARG355 4.9 89.0 1.0 CE2 A:TYR98 4.9 53.9 1.0 CB A:ARG355 4.9 79.5 1.0 CA A:CYS352 5.0 76.8 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