Chlorine in PDB 4gyz: Mus Musculus TDP2 Bound to Damp and MG2+

The structure of Mus Musculus TDP2 Bound to Damp and MG2+, PDB code: 4gyz was solved by M.J.Schellenberg, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.98 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.347, 169.326, 184.959, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22

The structure of Mus Musculus TDP2 Bound to Damp and MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Chlorine atom in the Mus Musculus TDP2 Bound to Damp and MG2+ (pdb code 4gyz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Mus Musculus TDP2 Bound to Damp and MG2+, PDB code: 4gyz:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:49.5 occ:1.00 O C:HOH518 3.1 51.6 1.0 N C:GLY346 3.3 32.5 1.0 OH C:TYR153 3.5 39.8 1.0 N C:LEU347 3.6 32.6 1.0 CA C:VAL345 3.8 31.4 1.0 C C:VAL345 4.0 32.5 1.0 CE2 C:TYR153 4.1 36.0 1.0 SG C:CYS149 4.2 53.2 1.0 CA C:GLY346 4.2 31.7 1.0 CB C:LEU347 4.2 35.1 1.0 CB C:VAL345 4.3 32.4 1.0 CZ C:TYR153 4.3 37.8 1.0 O C:HOH530 4.3 47.7 1.0 C C:GLY346 4.4 32.8 1.0 CG C:LEU347 4.4 34.7 1.0 CA C:LEU347 4.4 32.9 1.0 N C:GLU348 4.6 31.8 1.0 O C:LEU344 4.6 26.0 1.0 CG1 C:VAL345 4.6 33.5 1.0 CD1 C:LEU347 4.7 35.6 1.0 N C:VAL345 5.0 27.7 1.0 C C:LEU347 5.0 32.5 1.0

Chlorine binding site 2 out of 3 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:74.9 occ:1.00 OH D:TYR153 3.3 42.0 1.0 N D:GLY346 3.3 41.3 1.0 N D:LEU347 3.7 54.1 1.0 SG D:CYS149 4.0 84.4 1.0 CA D:GLY346 4.0 41.9 1.0 CE2 D:TYR153 4.0 39.8 1.0 CZ D:TYR153 4.1 40.8 1.0 C D:VAL345 4.3 42.0 1.0 CG D:GLU348 4.3 92.1 1.0 CA D:VAL345 4.3 42.3 1.0 C D:GLY346 4.4 47.0 1.0 CB D:VAL345 4.5 42.2 1.0 N D:GLU348 4.6 76.0 1.0 CB D:LEU347 4.6 63.2 1.0 CA D:LEU347 4.7 62.9 1.0 CG D:LEU347 4.9 60.7 1.0 CD1 D:LEU347 4.9 60.2 1.0

Chlorine binding site 3 out of 3 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl401 b:68.0 occ:1.00 N I:LEU342 3.4 39.6 1.0 CE1 I:HIS302 3.5 44.2 1.0 O I:LEU342 3.6 31.7 1.0 NE2 I:HIS302 3.7 42.7 1.0 CA I:SER341 4.0 48.2 1.0 C I:SER341 4.2 43.4 1.0 CA I:LEU342 4.3 35.1 1.0 C I:LEU342 4.4 33.6 1.0 CB I:LEU342 4.4 34.4 1.0 CD1 I:LEU297 4.5 38.9 1.0 CG I:PRO300 4.5 39.9 1.0 CB I:SER341 4.5 49.4 1.0 CB I:PRO300 4.7 40.1 1.0 ND1 I:HIS302 4.8 43.6 1.0

M.J.Schellenberg, C.D.Appel, S.Adhikari, P.D.Robertson, D.A.Ramsden, R.S.Williams. Mechanism of Repair of 5'-Topoisomerase II-Dna Adducts By Mammalian Tyrosyl-Dna Phosphodiesterase 2. Nat.Struct.Mol.Biol. V. 19 1363 2012.
ISSN: ISSN 1545-9993
PubMed: 23104055
DOI: 10.1038/NSMB.2418