Magnesium in PDB 5ayr: The Crystal Structure of Saugi/Human Udg Complex

All present enzymatic activity of The Crystal Structure of Saugi/Human Udg Complex:
3.2.2.27;

The structure of The Crystal Structure of Saugi/Human Udg Complex, PDB code: 5ayr was solved by H.C.Wang, T.P.Ko, M.F.Huang, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.93 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.831, 52.853, 82.338, 90.00, 112.36, 90.00
R / Rfree (%)	16.5 / 19.8

The binding sites of Magnesium atom in the The Crystal Structure of Saugi/Human Udg Complex (pdb code 5ayr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of Saugi/Human Udg Complex, PDB code: 5ayr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of Saugi/Human Udg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Saugi/Human Udg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg900 b:56.3 occ:1.00 OD1 A:ASN215 1.9 44.0 1.0 OD2 A:ASP145 1.9 49.5 1.0 O A:HOH1009 2.0 42.0 1.0 O B:HOH1008 2.3 75.8 1.0 O A:HOH1006 2.5 36.2 1.0 CG A:ASP145 2.7 43.3 1.0 O A:HOH1071 2.8 40.6 1.0 OD1 A:ASP145 2.9 49.1 1.0 CG A:ASN215 3.2 42.9 1.0 OE1 A:GLN144 4.0 39.1 1.0 CB A:ASP145 4.1 39.5 1.0 N A:ASP145 4.1 31.9 1.0 ND2 A:ASN215 4.1 41.9 1.0 CB A:ASN215 4.2 36.8 1.0 NE2 B:GLN52 4.2 45.4 1.0 CB A:GLN144 4.2 30.4 1.0 CA A:ASN215 4.5 33.7 1.0 OE1 B:GLN52 4.6 49.9 1.0 O B:SER27 4.6 25.6 1.0 OE2 B:GLU29 4.6 47.7 1.0 CA A:ASP145 4.7 31.0 1.0 CD B:GLN52 4.8 48.1 1.0 C A:GLN144 4.8 31.4 1.0 N A:ASN215 4.9 32.9 1.0 CD A:GLN144 5.0 30.6 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of Saugi/Human Udg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Saugi/Human Udg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg900 b:49.0 occ:0.50 OD2 B:ASP88 1.9 58.4 1.0 O B:MET89 2.0 49.2 1.0 CG B:ASP88 2.7 61.6 1.0 OD1 B:ASP88 2.7 65.9 1.0 O B:HOH1027 2.8 42.5 1.0 O B:HOH1015 3.0 64.7 1.0 C B:MET89 3.2 46.2 1.0 N B:ASP90 4.0 43.0 1.0 CA B:ASP90 4.1 41.4 1.0 CB B:ASP88 4.1 57.4 1.0 N B:MET89 4.2 47.6 1.0 CA B:MET89 4.2 46.7 1.0 C B:ASP88 4.4 50.0 1.0 CA B:ASP88 4.7 54.0 1.0 OD1 B:ASP90 4.7 56.3 1.0 CG B:ASP90 4.8 51.0 1.0 CB B:ASP90 4.8 45.4 1.0 CB B:MET89 4.9 44.8 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of Saugi/Human Udg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Saugi/Human Udg Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg900 b:53.6 occ:1.00 OD1 C:ASN215 1.9 49.3 1.0 O C:HOH1029 1.9 56.5 1.0 OD2 C:ASP145 2.0 50.0 1.0 O C:HOH1009 2.2 65.1 1.0 O C:HOH1007 2.3 43.8 1.0 O C:HOH1071 2.7 30.1 1.0 CG C:ASP145 3.1 46.4 1.0 CG C:ASN215 3.1 45.3 1.0 OD1 C:ASP145 3.5 52.4 1.0 O C:HOH1002 3.9 62.2 1.0 OE1 C:GLN144 4.0 30.9 1.0 CB C:ASN215 4.0 38.0 1.0 NE2 D:GLN52 4.1 32.3 1.0 ND2 C:ASN215 4.1 42.8 1.0 OE1 D:GLN52 4.3 43.9 1.0 CB C:ASP145 4.3 42.3 1.0 N C:ASP145 4.4 31.3 1.0 CB C:GLN144 4.4 24.5 1.0 OE2 D:GLU29 4.5 50.1 1.0 CA C:ASN215 4.5 33.1 1.0 CD D:GLN52 4.5 40.1 1.0 O D:SER27 4.7 29.4 1.0 CG D:GLU29 4.7 41.9 1.0 N C:ASN215 4.9 32.0 1.0 O D:HOH1021 5.0 37.3 1.0 CD C:GLN144 5.0 30.9 1.0 C C:GLN144 5.0 26.6 1.0 CA C:ASP145 5.0 34.2 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of Saugi/Human Udg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Saugi/Human Udg Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg900 b:50.7 occ:0.50 OD2 D:ASP88 2.0 61.2 1.0 O D:MET89 2.0 49.0 1.0 O D:HOH1007 2.4 75.5 1.0 CG D:ASP88 2.7 60.8 1.0 OD1 D:ASP88 2.9 64.1 1.0 C D:MET89 3.2 45.3 1.0 N D:ASP90 4.0 43.0 1.0 N D:MET89 4.0 47.8 1.0 CA D:ASP90 4.1 44.9 1.0 CB D:ASP88 4.1 57.6 1.0 CA D:MET89 4.2 45.3 1.0 C D:ASP88 4.3 49.8 1.0 CA D:ASP88 4.6 54.4 1.0 OD1 D:ASP90 4.6 61.9 1.0 CG D:ASP90 4.7 55.7 1.0 CB D:ASP90 4.7 49.1 1.0 CB D:MET89 4.8 45.9 1.0

H.C.Wang, C.H.Ho, C.C.Chou, T.P.Ko, M.F.Huang, K.C.Hsu, A.H.Wang. Using Structural-Based Protein Engineering to Modulate the Differential Inhibition Effects of Saugi on Human and Hsv Uracil Dna Glycosylase. Nucleic Acids Res. V. 44 4440 2016.
ISSN: ESSN 1362-4962
PubMed: 26980279
DOI: 10.1093/NAR/GKW185