Magnesium in PDB 4f1h: Crystal Structure of TDP2 From Danio Rerio Complexed with A Single Strand Dna

The structure of Crystal Structure of TDP2 From Danio Rerio Complexed with A Single Strand Dna, PDB code: 4f1h was solved by K.Shi, K.Kurahashi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.87 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.918, 95.100, 104.732, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.3

The binding sites of Magnesium atom in the Crystal Structure of TDP2 From Danio Rerio Complexed with A Single Strand Dna (pdb code 4f1h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of TDP2 From Danio Rerio Complexed with A Single Strand Dna, PDB code: 4f1h:

Magnesium binding site 1 out of 1 in the Crystal Structure of TDP2 From Danio Rerio Complexed with A Single Strand Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of TDP2 From Danio Rerio Complexed with A Single Strand Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:48.9 occ:1.00 OP1 C:DT1 2.5 24.8 1.0 OE2 A:GLU161 2.7 26.0 1.0 O A:HOH678 2.8 44.3 1.0 O A:HOH531 2.8 23.4 1.0 P C:DT1 3.4 15.6 0.7 CD A:GLU161 3.5 21.9 1.0 O A:HOH761 3.6 41.5 1.0 OE1 A:GLU161 3.6 23.4 1.0 OP3 C:DT1 3.7 19.1 1.0 O5' C:DT1 3.8 21.0 1.0 C7 C:DT1 3.8 17.7 1.0 C6 C:DT1 4.0 21.1 1.0 C5' C:DT1 4.0 21.6 1.0 C5 C:DT1 4.2 23.9 1.0 ND2 A:ASN129 4.3 18.7 1.0 OD1 A:ASP131 4.3 29.7 1.0 OD2 A:ASP359 4.5 26.7 1.0 O4' C:DT1 4.5 20.9 1.0 O A:HOH587 4.6 35.8 1.0 OP2 C:DT1 4.7 23.9 1.0 NE2 A:HIS360 4.7 16.1 1.0 OD1 A:ASN129 4.8 15.3 1.0 NZ A:LYS314 4.8 44.8 1.0 CE1 A:HIS235 4.9 15.6 1.0 CG A:ASN129 4.9 16.0 1.0 OD1 A:ASP359 4.9 23.2 1.0 CG A:GLU161 4.9 26.4 1.0 NE2 A:HIS235 4.9 14.6 1.0 N1 C:DT1 5.0 19.8 1.0 C4' C:DT1 5.0 19.6 1.0

K.Shi, K.Kurahashi, R.Gao, S.E.Tsutakawa, J.A.Tainer, Y.Pommier, H.Aihara. Structural Basis For Recognition of 5'-Phosphotyrosine Adducts By TDP2. Nat.Struct.Mol.Biol. V. 19 1372 2012.
ISSN: ISSN 1545-9993
PubMed: 23104058
DOI: 10.1038/NSMB.2423