Magnesium in PDB 3ngz: Crystal Structure of Rnase T in Complex with A Non-Preferred Ssdna (Gc) with One Mg in the Active Site

The structure of Crystal Structure of Rnase T in Complex with A Non-Preferred Ssdna (Gc) with One Mg in the Active Site, PDB code: 3ngz 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)	28.46 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.747, 105.585, 47.180, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 26

The structure of Crystal Structure of Rnase T in Complex with A Non-Preferred Ssdna (Gc) with One Mg in the Active Site also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Rnase T in Complex with A Non-Preferred Ssdna (Gc) with One Mg in the Active Site (pdb code 3ngz). 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 Non-Preferred Ssdna (Gc) with One Mg in the Active Site, PDB code: 3ngz:
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 Non-Preferred Ssdna (Gc) 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 Non-Preferred Ssdna (Gc) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:25.9 occ:1.00 O C:HOH1003 2.2 22.9 1.0 O A:HOH1002 2.3 9.7 1.0 O A:HOH1001 2.3 14.9 1.0 O A:HOH1004 2.4 16.2 1.0 OD2 A:ASP23 2.4 15.3 1.0 O C:HOH1005 2.4 22.8 1.0 H1 A:HOH1004 2.5 19.3 1.0 H1 A:HOH1001 2.8 17.8 1.0 H1 A:HOH1002 3.1 11.6 1.0 H1 C:HOH1003 3.1 27.3 1.0 H1 C:HOH1005 3.2 27.2 1.0 CG A:ASP23 3.6 19.3 1.0 O C:HOH296 3.7 26.7 1.0 OP1 C:DC2 3.7 18.8 1.0 O C:HOH385 3.9 29.4 1.0 O A:HOH292 3.9 20.2 1.0 OD1 A:ASP125 4.0 15.8 1.0 O3' C:DG1 4.0 24.8 1.0 O A:HOH390 4.1 18.2 1.0 OD1 A:ASP23 4.1 21.4 1.0 OD2 A:ASP125 4.1 19.1 1.0 O A:HOH226 4.2 16.9 1.0 O A:VAL24 4.3 10.9 1.0 O A:HIS120 4.3 17.8 1.0 CG A:ASP125 4.5 12.7 1.0 P C:DC2 4.6 22.3 1.0 C5' C:DC2 4.7 14.3 1.0 CB A:ASP23 4.8 15.0 1.0 OD2 A:ASP186 4.9 23.2 1.0 OE1 A:GLU25 5.0 25.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rnase T in Complex with A Non-Preferred Ssdna (Gc) 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 Non-Preferred Ssdna (Gc) with One Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2000 b:21.9 occ:1.00 O B:HOH2003 2.2 12.9 1.0 O D:HOH2001 2.2 22.2 1.0 O B:HOH2002 2.3 13.8 1.0 O D:HOH2004 2.4 20.1 1.0 O B:HOH2005 2.4 14.2 1.0 OD1 B:ASP23 2.5 16.7 1.0 H1 B:HOH2005 2.5 16.9 1.0 H1 D:HOH2001 2.7 26.6 1.0 H1 B:HOH2003 2.9 15.4 1.0 H1 B:HOH2002 2.9 16.5 1.0 H1 D:HOH2004 3.0 24.0 1.0 CG B:ASP23 3.6 17.7 1.0 OP1 D:DC2 3.8 15.2 1.0 O B:HOH355 3.8 23.5 1.0 OD2 B:ASP23 4.0 22.3 1.0 O3' D:DG1 4.1 25.6 1.0 O B:HOH305 4.1 14.7 1.0 OD2 B:ASP125 4.1 18.6 1.0 OD1 B:ASP125 4.1 15.3 1.0 O B:HOH243 4.2 14.8 1.0 O B:HOH384 4.2 26.1 1.0 O B:VAL24 4.3 10.7 1.0 O B:HIS120 4.4 15.3 1.0 CG B:ASP125 4.5 11.2 1.0 P D:DC2 4.7 21.8 1.0 C5' D:DC2 4.8 17.8 1.0 OD2 B:ASP186 4.8 20.1 1.0 CB B:ASP23 4.8 11.7 1.0 OE1 B:GLU25 4.9 24.3 1.0 C4' D:DG1 5.0 42.2 1.0

Y.-Y.Hsiao, C.-C.Yang, C.L.Lin, J.L.J.Lin, Y.Duh, H.S.Yuan. Structural Basis For Rna Trimming By Rnase T in Stable Rna 3'-End Maturation Nat.Chem.Biol. V. 7 236 2011.
ISSN: ISSN 1552-4450
PubMed: 21317904
DOI: 10.1038/NCHEMBIO.524