Magnesium in PDB 3v9z: Crystal Structure of Rnase T in Complex with A Product Ssdna (Acc) with One Mg in the Active Site

The structure of Crystal Structure of Rnase T in Complex with A Product Ssdna (Acc) with One Mg in the Active Site, PDB code: 3v9z 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)	28.52 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.422, 106.092, 46.952, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.7

The structure of Crystal Structure of Rnase T in Complex with A Product Ssdna (Acc) 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 (Acc) with One Mg in the Active Site (pdb code 3v9z). 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 (Acc) with One Mg in the Active Site, PDB code: 3v9z:
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 (Acc) 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 (Acc) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:25.6 occ:1.00 O A:HOH434 2.1 15.5 1.0 O A:HOH425 2.5 14.7 1.0 OD1 A:ASP23 2.5 13.7 1.0 O A:HOH415 2.5 12.4 1.0 O3' C:DC6 2.5 16.9 1.0 OP1 C:DC7 3.2 27.7 1.0 CG A:ASP23 3.4 13.7 1.0 P C:DC7 3.5 19.6 1.0 C3' C:DC6 3.5 12.8 1.0 OD2 A:ASP23 3.6 18.0 1.0 C4' C:DC6 3.8 18.8 1.0 C2' C:DC6 3.8 12.1 1.0 O A:HOH445 4.0 13.9 1.0 O C:HOH105 4.0 14.0 1.0 OD1 A:ASP125 4.2 12.3 1.0 O A:HOH431 4.3 13.7 1.0 C5' C:DC7 4.3 11.8 1.0 O A:VAL24 4.4 8.8 1.0 O5' C:DC7 4.5 19.9 1.0 OD2 A:ASP125 4.6 13.7 1.0 OD2 A:ASP186 4.6 17.1 1.0 OP2 C:DC7 4.6 21.1 1.0 O A:HIS120 4.7 13.8 1.0 C5' C:DC6 4.7 17.8 1.0 O4' C:DC6 4.8 17.7 1.0 C1' C:DC6 4.8 20.1 1.0 CB A:ASP23 4.8 7.4 1.0 CG A:ASP125 4.9 12.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rnase T in Complex with A Product Ssdna (Acc) 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 (Acc) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:19.6 occ:1.00 O B:HOH430 2.4 16.2 1.0 O B:HOH465 2.5 17.2 1.0 OD1 B:ASP23 2.5 19.2 1.0 O B:HOH419 2.5 13.1 1.0 O3' D:DC6 2.6 15.4 1.0 OP1 D:DC7 3.2 24.1 1.0 CG B:ASP23 3.4 16.5 1.0 OD2 B:ASP23 3.5 16.5 1.0 P D:DC7 3.6 21.5 1.0 C3' D:DC6 3.6 14.5 1.0 C2' D:DC6 3.9 14.2 1.0 C4' D:DC6 3.9 17.6 1.0 OD1 B:ASP125 4.1 14.2 1.0 O B:HOH415 4.2 14.3 1.0 O B:VAL24 4.2 10.0 1.0 O B:HOH487 4.3 13.1 1.0 O D:HOH103 4.3 21.3 1.0 C5' D:DC7 4.3 15.7 1.0 O5' D:DC7 4.5 16.6 1.0 OD2 B:ASP125 4.5 13.1 1.0 OD2 B:ASP186 4.6 18.6 1.0 OP2 D:DC7 4.7 21.9 1.0 O B:HIS120 4.7 12.5 1.0 CG B:ASP125 4.8 15.0 1.0 CB B:ASP23 4.8 8.5 1.0 C5' D:DC6 4.9 19.1 1.0 O4' D:DC6 4.9 16.6 1.0 C1' D:DC6 4.9 16.5 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