Magnesium in PDB 3sz5: Crystal Structure of Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4

The structure of Crystal Structure of Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4, PDB code: 3sz5 was solved by W.Yang, W.Y.Chen, H.Wang, Q.Zhang, W.Zhou, M.Bartlam, R.M.Watt, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	108.697, 108.697, 48.219, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4 (pdb code 3sz5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4, PDB code: 3sz5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4


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 Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg220 b:51.4 occ:1.00 OP1 B:DT211 1.9 0.5 1.0 O A:ILE113 2.2 56.2 1.0 OE2 A:GLU112 2.3 52.6 1.0 OD2 A:ASP102 2.5 61.6 1.0 P B:DT211 3.2 0.1 1.0 CD A:GLU112 3.3 54.2 1.0 C A:ILE113 3.3 55.8 1.0 CG A:ASP102 3.4 61.5 1.0 OD1 A:ASP102 3.6 61.0 1.0 N A:ILE113 3.7 55.6 1.0 OP2 B:DT211 3.7 0.6 1.0 OE1 A:GLU112 3.8 52.3 1.0 NZ A:LYS114 3.9 57.9 1.0 CA A:ILE113 4.0 55.7 1.0 MG A:MG221 4.0 70.0 1.0 CD A:LYS114 4.0 52.5 1.0 O5' B:DT211 4.0 0.2 1.0 C5' B:DT211 4.1 0.1 1.0 CB A:ILE113 4.3 55.6 1.0 O3' B:DT210 4.3 0.1 1.0 OP2 B:DT212 4.3 0.3 1.0 CE A:LYS114 4.4 54.4 1.0 OE1 A:GLU68 4.4 75.5 1.0 CG A:GLU112 4.4 54.0 1.0 N A:LYS114 4.4 55.9 1.0 C A:GLU112 4.7 55.7 1.0 CA A:LYS114 4.8 55.7 1.0 CG2 A:ILE113 4.8 56.1 1.0 CB A:ASP102 4.8 62.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Lhk-Exo in Complex with 5-Phosphorylated Oligothymidine (Dt)4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg221 b:70.0 occ:1.00 OD1 A:ASP102 2.6 61.0 1.0 O A:SER100 2.7 64.0 1.0 O3' B:DT210 3.1 0.1 1.0 OE1 A:GLU112 3.1 52.3 1.0 OP1 B:DT211 3.1 0.5 1.0 CG A:ASP102 3.3 61.5 1.0 OD2 A:ASP102 3.6 61.6 1.0 P B:DT211 3.6 0.1 1.0 OE2 A:GLU112 3.8 52.6 1.0 CD A:GLU112 3.9 54.2 1.0 C3' B:DT210 3.9 99.7 1.0 C A:SER100 3.9 63.3 1.0 N A:ASP102 3.9 62.6 1.0 MG A:MG220 4.0 51.4 1.0 C4' B:DT210 4.0 97.8 1.0 C A:PRO101 4.0 62.5 1.0 NE2 A:GLN137 4.2 56.4 1.0 OP2 B:DT211 4.2 0.6 1.0 CA A:PRO101 4.3 62.8 1.0 CA A:ASP102 4.4 62.4 1.0 CB A:ASP102 4.4 62.1 1.0 OE1 A:GLN141 4.4 65.8 1.0 O5' B:DT210 4.5 89.9 1.0 O A:PRO101 4.5 62.2 1.0 N A:PRO101 4.6 63.0 1.0 CB A:SER100 4.7 63.4 1.0 C5' B:DT210 4.9 94.2 1.0 CA A:SER100 4.9 63.3 1.0

W.Yang, W.Y.Chen, H.Wang, J.W.Ho, J.D.Huang, P.C.Woo, S.K.Lau, K.Y.Yuen, Q.Zhang, W.Zhou, M.Bartlam, R.M.Watt, Z.Rao. Structural and Functional Insight Into the Mechanism of An Alkaline Exonuclease From Laribacter Hongkongensis. Nucleic Acids Res. V. 39 9803 2011.
ISSN: ISSN 0305-1048
PubMed: 21893587
DOI: 10.1093/NAR/GKR660