Magnesium in PDB 1w0h: Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp

The structure of Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp, PDB code: 1w0h was solved by Y.Cheng, D.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 1.59
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.600, 101.600, 100.400, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 20.2

The binding sites of Magnesium atom in the Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp (pdb code 1w0h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp, PDB code: 1w0h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:8.6 occ:1.00 O1P A:AMP1002 2.1 20.8 1.0 OD2 A:ASP234 2.1 20.8 1.0 O A:HOH2242 2.2 19.3 1.0 OD1 A:ASP134 2.2 17.5 1.0 O A:HOH2020 2.2 20.2 1.0 OD2 A:ASP134 2.4 18.1 1.0 CG A:ASP134 2.7 15.1 1.0 CG A:ASP234 3.0 21.9 1.0 MG A:MG1001 3.3 20.4 1.0 CB A:ASP234 3.4 18.0 1.0 P A:AMP1002 3.5 19.6 1.0 O3P A:AMP1002 4.1 21.6 1.0 CB A:ASP134 4.1 15.1 1.0 O A:HOH2365 4.2 23.1 1.0 O5' A:AMP1002 4.2 17.6 1.0 OD1 A:ASP234 4.2 22.2 1.0 C5' A:AMP1002 4.3 19.3 1.0 CA A:ASP234 4.3 17.2 1.0 OD2 A:ASP230 4.3 20.0 1.0 O A:PHE135 4.3 13.1 1.0 O2P A:AMP1002 4.5 20.2 1.0 O A:HOH2368 4.6 41.3 1.0 O A:ASP234 4.6 16.5 1.0 O A:HOH2253 4.6 38.6 1.0 CB A:ASP230 4.7 18.4 1.0 O A:HOH2019 4.7 16.7 1.0 CA A:ASP134 4.7 13.5 1.0 OD2 A:ASP298 4.8 18.5 1.0 C A:ASP234 4.9 16.4 1.0 C A:ASP134 5.0 13.9 1.0 CG A:ASP230 5.0 20.3 1.0

Magnesium binding site 2 out of 2 in the Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:20.4 occ:1.00 OE2 A:GLU136 2.2 16.0 1.0 OD2 A:ASP134 2.2 18.1 1.0 OD2 A:ASP298 2.2 18.5 1.0 O1P A:AMP1002 2.3 20.8 1.0 O2P A:AMP1002 2.8 20.2 1.0 P A:AMP1002 3.1 19.6 1.0 CG A:ASP298 3.2 18.5 1.0 CD A:GLU136 3.2 14.7 1.0 MG A:MG1000 3.3 8.6 1.0 CG A:ASP134 3.5 15.1 1.0 CB A:ASP298 3.5 15.3 1.0 OE1 A:GLU136 3.6 14.5 1.0 O A:PHE135 3.7 13.1 1.0 O A:HOH2242 3.9 19.3 1.0 O A:HOH2020 4.0 20.2 1.0 O3P A:AMP1002 4.0 21.6 1.0 OD1 A:ASP134 4.2 17.5 1.0 CA A:HIS293 4.3 18.7 1.0 OD1 A:ASP298 4.3 20.3 1.0 CA A:GLY295 4.4 16.1 1.0 O5' A:AMP1002 4.4 17.6 1.0 O A:HOH2365 4.4 23.1 1.0 CB A:ASP134 4.5 15.1 1.0 CG A:GLU136 4.5 14.1 1.0 C5' A:AMP1002 4.5 19.3 1.0 O A:CYS294 4.6 16.6 1.0 O A:ASP134 4.6 15.1 1.0 C A:PHE135 4.6 12.3 1.0 C A:HIS293 4.7 18.4 1.0 C A:ASP134 4.8 13.9 1.0 N A:GLY295 4.8 15.4 1.0 N A:HIS293 4.8 18.9 1.0 C A:CYS294 4.9 17.3 1.0 ND1 A:HIS293 4.9 22.2 1.0 O A:HIS293 4.9 18.1 1.0

Y.Cheng, D.Patel. Crystallographic Structure of the Nuclease Domain of 3'Hexo, A Deddh Family Member, Bound to Ramp J.Mol.Biol. V. 343 305 2004.
ISSN: ISSN 0022-2836
PubMed: 15451662
DOI: 10.1016/J.JMB.2004.08.055