Magnesium in PDB 2r7d: Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63

The structure of Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63, PDB code: 2r7d was solved by J.Seetharaman, H.Neely, F.Forouhar, D.Wang, Y.Fang, K.Cunningham, L.-C.Ma, R.Xia, J.Liu, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.68 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.762, 92.205, 92.345, 60.08, 89.57, 71.11
R / Rfree (%)	22.1 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63 (pdb code 2r7d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63, PDB code: 2r7d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63


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 Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:20.6 occ:1.00 O A:HOH1453 2.1 16.0 1.0 OD1 A:ASP93 2.2 12.6 1.0 OD2 A:ASP102 2.2 12.4 1.0 O A:HOH1001 2.2 26.7 1.0 O A:HOH1002 2.3 15.7 1.0 O A:HOH1026 2.4 17.7 1.0 CG A:ASP102 3.0 13.3 1.0 CG A:ASP93 3.1 18.0 1.0 OD1 A:ASP102 3.3 13.3 1.0 OD2 A:ASP93 3.5 12.4 1.0 O A:HOH1048 3.9 19.5 1.0 O A:ILE92 4.1 11.1 1.0 O A:HOH1024 4.2 23.2 1.0 O A:HOH1036 4.2 26.5 1.0 N A:ASP102 4.2 13.8 1.0 O A:HOH1013 4.2 23.0 1.0 O A:ASP102 4.3 14.2 1.0 O A:HOH1284 4.3 43.5 1.0 CB A:ASP102 4.3 14.1 1.0 CB A:ASP93 4.4 15.6 1.0 N A:ASP101 4.5 18.1 1.0 CA A:ASP102 4.7 12.6 1.0 C A:ILE92 4.8 12.1 1.0 C A:ASP102 4.8 13.2 1.0 O A:HOH1010 4.9 18.6 1.0 CA A:ASP93 4.9 15.6 1.0 O A:HOH1201 4.9 41.1 1.0 CA A:PRO100 5.0 22.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63


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 Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2000 b:19.6 occ:1.00 OD2 B:ASP102 2.2 19.9 1.0 OD1 B:ASP93 2.2 20.0 1.0 O B:HOH2132 2.3 24.5 1.0 O B:HOH2003 2.3 20.1 1.0 O B:HOH2009 2.3 22.0 1.0 O B:HOH2001 2.4 30.2 1.0 CG B:ASP102 3.1 24.1 1.0 CG B:ASP93 3.2 23.1 1.0 OD1 B:ASP102 3.4 22.3 1.0 OD2 B:ASP93 3.5 22.2 1.0 O B:HOH2007 4.0 25.1 1.0 N B:ASP102 4.1 22.3 1.0 O B:HOH2017 4.1 99.8 1.0 O B:ILE92 4.2 17.2 1.0 O B:HOH2087 4.2 37.7 1.0 O B:HOH2081 4.3 42.5 1.0 N B:ASP101 4.3 27.8 1.0 O B:ASP102 4.3 21.9 1.0 CB B:ASP102 4.3 21.3 1.0 O B:HOH2027 4.4 32.7 1.0 CB B:ASP93 4.5 20.9 1.0 CA B:ASP102 4.6 23.5 1.0 C B:ASP102 4.8 23.9 1.0 CA B:PRO100 4.9 32.5 1.0 C B:ILE92 4.9 20.1 1.0 O B:HOH2052 4.9 56.5 1.0 CB B:ASP101 4.9 27.6 1.0 CA B:ASP93 5.0 20.7 1.0 O B:HOH2012 5.0 24.0 1.0 O B:HOH2174 5.0 32.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3000 b:20.6 occ:1.00 OD1 C:ASP93 2.1 15.0 1.0 O C:HOH3002 2.2 20.9 1.0 OD2 C:ASP102 2.3 14.7 1.0 O C:HOH3001 2.3 19.2 1.0 O C:HOH3021 2.3 20.8 1.0 O C:HOH3017 2.3 19.0 1.0 CG C:ASP93 3.1 15.7 1.0 CG C:ASP102 3.2 18.8 1.0 OD2 C:ASP93 3.4 19.1 1.0 OD1 C:ASP102 3.5 16.4 1.0 O C:HOH3052 4.1 27.9 1.0 O C:ILE92 4.1 16.5 1.0 O C:HOH3039 4.2 34.0 1.0 O C:HOH3015 4.2 27.6 1.0 N C:ASP102 4.2 18.6 1.0 O C:HOH3027 4.3 30.8 1.0 O C:ASP102 4.3 15.0 1.0 O C:HOH3056 4.4 28.5 1.0 CB C:ASP93 4.4 18.8 1.0 N C:ASP101 4.4 21.3 1.0 CB C:ASP102 4.4 17.7 1.0 CA C:ASP102 4.7 18.1 1.0 C C:ILE92 4.8 14.8 1.0 CA C:PRO100 4.8 27.4 1.0 C C:ASP102 4.9 16.2 1.0 CA C:ASP93 4.9 18.4 1.0 O C:HOH3011 4.9 20.0 1.0 O C:HOH3196 4.9 34.3 1.0

B.J.Schmier, J.Seetharaman, M.P.Deutscher, J.F.Hunt, A.Malhotra. The Structure and Enzymatic Properties of A Novel Rnase II Family Enzyme From Deinococcus Radiodurans. J.Mol.Biol. V. 415 547 2012.
ISSN: ISSN 0022-2836
PubMed: 22133431
DOI: 10.1016/J.JMB.2011.11.031