Magnesium in PDB 3v9s: Crystal Structure of Rnase T in Complex with A Product Ssdna (Aac) with One Mg in the Active Site

The structure of Crystal Structure of Rnase T in Complex with A Product Ssdna (Aac) with One Mg in the Active Site, PDB code: 3v9s 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)	25.66 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.063, 105.840, 46.918, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.6

The structure of Crystal Structure of Rnase T in Complex with A Product Ssdna (Aac) 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 Product Ssdna (Aac) with One Mg in the Active Site (pdb code 3v9s). 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 Product Ssdna (Aac) with One Mg in the Active Site, PDB code: 3v9s:
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 Product Ssdna (Aac) 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 Product Ssdna (Aac) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:51.9 occ:1.00 O A:HOH472 2.3 27.6 1.0 O A:HOH489 2.4 30.7 1.0 O3' C:DA6 2.6 28.3 1.0 OD1 A:ASP23 2.7 24.7 1.0 O A:HOH419 2.9 24.3 1.0 OP1 C:DC7 3.0 38.2 1.0 OD2 A:ASP23 3.3 24.8 1.0 CG A:ASP23 3.4 22.5 1.0 P C:DC7 3.4 28.8 1.0 C3' C:DA6 3.7 31.1 1.0 O A:VAL24 3.8 17.9 1.0 C2' C:DA6 3.9 28.8 1.0 C5' C:DC7 4.0 17.4 1.0 OD2 A:ASP186 4.1 27.5 1.0 O5' C:DC7 4.2 29.2 1.0 C4' C:DA6 4.2 32.8 1.0 O C:HOH103 4.3 33.3 1.0 OD1 A:ASP125 4.3 25.4 1.0 OE1 A:GLU25 4.5 29.0 1.0 O A:HOH451 4.6 23.3 1.0 OP2 C:DC7 4.6 32.2 1.0 CB A:ASP23 4.8 15.2 1.0 CG A:ASP186 4.9 26.4 1.0 N A:VAL24 5.0 10.6 1.0 OD2 A:ASP125 5.0 20.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rnase T in Complex with A Product Ssdna (Aac) 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 Product Ssdna (Aac) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:54.3 occ:1.00 O B:HOH569 2.4 26.0 1.0 O B:HOH470 2.5 24.8 1.0 OP1 D:DC7 2.6 39.9 1.0 O3' D:DA6 2.7 30.1 1.0 OD1 B:ASP23 2.8 28.2 1.0 OD2 B:ASP23 2.9 31.4 1.0 CG B:ASP23 3.2 24.2 1.0 P D:DC7 3.3 25.1 1.0 O B:HOH426 3.3 26.2 1.0 O B:VAL24 3.7 16.4 1.0 OD2 B:ASP186 3.7 26.7 1.0 O D:HOH103 3.8 27.0 1.0 C5' D:DC7 3.9 18.9 1.0 C3' D:DA6 4.0 22.6 1.0 OE1 B:GLU25 4.0 26.4 1.0 O5' D:DC7 4.1 26.4 1.0 C2' D:DA6 4.4 24.5 1.0 O B:HOH545 4.4 19.2 1.0 OP2 D:DC7 4.5 26.3 1.0 C4' D:DA6 4.5 27.4 1.0 CG B:ASP186 4.6 24.7 1.0 CD B:GLU25 4.6 22.4 1.0 OD1 B:ASP125 4.7 22.4 1.0 CB B:ASP23 4.7 16.8 1.0 CB B:ASP186 4.8 18.8 1.0 OE2 B:GLU25 4.8 18.5 1.0 C B:VAL24 4.8 20.6 1.0 N B:VAL24 4.9 14.7 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