Magnesium in PDB 3va0: Crystal Structure of Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site

The structure of Crystal Structure of Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site, PDB code: 3va0 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.39 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.688, 105.807, 47.074, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.3

The structure of Crystal Structure of Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site (pdb code 3va0). 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 Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site, PDB code: 3va0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site


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 Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:22.3 occ:1.00 O C:HOH102 2.2 22.5 1.0 O A:HOH402 2.2 16.1 1.0 O A:HOH403 2.2 21.6 1.0 O A:HOH401 2.2 21.7 1.0 O C:HOH101 2.2 23.3 1.0 OD1 A:ASP23 2.5 22.1 1.0 H1 C:HOH102 2.8 27.0 1.0 H1 A:HOH402 2.8 19.3 1.0 H1 A:HOH403 2.8 25.9 1.0 H1 A:HOH401 2.8 26.0 1.0 H1 C:HOH101 2.8 27.9 1.0 CG A:ASP23 3.5 21.1 1.0 OD1 A:ASP125 3.8 17.9 1.0 OD2 A:ASP23 3.8 24.5 1.0 O A:HOH465 4.0 15.3 1.0 OP1 C:DG2 4.1 22.5 1.0 O A:HOH407 4.1 14.7 1.0 O A:HOH484 4.1 18.4 1.0 O A:VAL24 4.2 17.1 1.0 O A:HOH486 4.2 28.4 1.0 OD2 A:ASP125 4.5 19.3 1.0 O A:HOH529 4.5 23.7 1.0 CG A:ASP125 4.5 18.5 1.0 O A:HIS120 4.6 15.6 1.0 OD2 A:ASP186 4.7 23.6 1.0 CB A:ASP23 4.8 15.4 1.0 N A:VAL24 4.8 16.3 1.0 O3' C:DG1 5.0 20.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site


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 Rnase T in Complex with A Di-Nucleotide Product (Gg) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:24.4 occ:1.00 O D:HOH101 2.2 25.3 1.0 O B:HOH403 2.2 17.1 1.0 O B:HOH402 2.2 17.9 1.0 O B:HOH401 2.2 24.6 1.0 O B:HOH404 2.2 18.7 1.0 OD1 B:ASP23 2.5 19.2 1.0 H1 D:HOH101 2.8 30.3 1.0 H1 B:HOH402 2.8 21.4 1.0 H1 B:HOH403 2.8 20.6 1.0 H1 B:HOH401 2.8 29.6 1.0 H1 B:HOH404 2.8 22.4 1.0 CG B:ASP23 3.4 20.5 1.0 OD2 B:ASP23 3.6 25.3 1.0 OP1 D:DG2 3.8 27.5 1.0 OD1 B:ASP125 3.9 19.5 1.0 O B:HOH466 4.1 22.4 1.0 O B:VAL24 4.1 15.5 1.0 OD2 B:ASP125 4.1 18.6 1.0 O B:HOH426 4.2 19.0 1.0 O B:HOH508 4.2 26.6 1.0 CG B:ASP125 4.5 16.4 1.0 O B:HOH613 4.5 26.7 1.0 OD2 B:ASP186 4.6 21.6 1.0 N B:VAL24 4.7 16.7 1.0 O B:HIS120 4.8 16.3 1.0 CB B:ASP23 4.8 17.7 1.0 O D:HOH106 4.8 28.9 1.0 C5' D:DG2 5.0 23.2 1.0

Y.-Y.Hsiao, Y.Duh, Y.P.Chen, Y.T.Wang, H.S.Yuan. How An Exonuclease Decides Where to Stop in Trimming of Nucleic Acids: Crystal Structures of Rnase T-Product Complexes Nucleic Acids Res. V. 40 8144 2012.
ISSN: ISSN 0305-1048
PubMed: 22718982
DOI: 10.1093/NAR/GKS548