Magnesium in PDB 3syy: Crystal Structure of An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis

The structure of Crystal Structure of An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis, PDB code: 3syy 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 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	108.939, 108.939, 47.647, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.1

The binding sites of Magnesium atom in the Crystal Structure of An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis (pdb code 3syy). 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 An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis, PDB code: 3syy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis


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 An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:29.5 occ:1.00 O A:HOH384 2.3 39.7 1.0 OE2 A:GLU112 2.3 29.7 1.0 O A:HOH383 2.3 38.8 1.0 OD2 A:ASP102 2.4 27.7 1.0 O A:ILE113 2.4 24.5 1.0 CD A:GLU112 3.3 27.8 1.0 CG A:ASP102 3.3 29.7 1.0 OD1 A:ASP102 3.5 29.2 1.0 C A:ILE113 3.6 26.1 1.0 MG A:MG401 3.7 39.6 1.0 OE1 A:GLU112 3.8 27.8 1.0 N A:ILE113 3.9 25.6 1.0 O A:HOH386 4.0 50.2 1.0 NZ A:LYS114 4.1 29.6 1.0 O A:HOH305 4.1 61.0 1.0 OE1 A:GLU68 4.1 44.1 1.0 CA A:ILE113 4.2 25.2 1.0 CD A:LYS114 4.3 25.5 1.0 CG A:GLU112 4.4 28.6 1.0 O A:HOH387 4.4 51.4 1.0 CB A:ILE113 4.5 25.1 1.0 N A:LYS114 4.7 25.8 1.0 CE A:LYS114 4.7 27.7 1.0 CB A:ASP102 4.7 30.1 1.0 O A:HOH340 4.8 44.5 1.0 C A:GLU112 4.8 26.6 1.0 CD A:GLU68 4.8 47.3 1.0 CA A:LYS114 5.0 25.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis


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 An Alkaline Exonuclease (Lhk-Exo) From Laribacter Hongkongensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:39.6 occ:1.00 O A:SER100 2.7 33.8 1.0 OE1 A:GLU112 2.7 27.8 1.0 O A:HOH387 2.7 51.4 1.0 O A:HOH388 3.1 30.0 1.0 OD1 A:ASP102 3.3 29.2 1.0 OE2 A:GLU112 3.3 29.7 1.0 CD A:GLU112 3.4 27.8 1.0 O A:HOH298 3.6 44.7 1.0 NE2 A:GLN137 3.6 26.5 1.0 MG A:MG400 3.7 29.5 1.0 CG A:ASP102 3.8 29.7 1.0 O A:HOH384 3.8 39.7 1.0 OD2 A:ASP102 3.8 27.7 1.0 OE1 A:GLN141 3.9 35.2 1.0 C A:SER100 3.9 34.5 1.0 O A:HOH386 4.0 50.2 1.0 N A:ASP102 4.2 30.2 1.0 C A:PRO101 4.3 31.3 1.0 CA A:PRO101 4.3 32.6 1.0 N A:PRO101 4.7 33.5 1.0 O A:HOH383 4.8 38.8 1.0 CD A:GLN137 4.8 27.4 1.0 CB A:SER100 4.8 36.8 1.0 CB A:ASP102 4.9 30.1 1.0 O A:PRO101 4.9 30.3 1.0 CA A:ASP102 4.9 29.6 1.0 CG A:GLU112 4.9 28.6 1.0 CA A:SER100 4.9 35.0 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