Magnesium in PDB 3v9u: Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site

The structure of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site, PDB code: 3v9u 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)	23.23 / 2.30
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	46.254, 46.254, 313.646, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 24.5

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

Cobalt

(Co)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site (pdb code 3v9u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site, PDB code: 3v9u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two 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 Preferred Ssdna (Aat) with Two Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:39.1 occ:1.00 OP1 E:DT7 2.3 33.0 1.0 OE1 A:GLU25 2.4 40.2 1.0 OD2 A:ASP186 2.4 35.5 1.0 OD2 A:ASP23 2.6 34.8 1.0 OD1 A:ASP23 3.1 35.6 1.0 CG A:ASP23 3.2 31.0 1.0 CD A:GLU25 3.3 33.7 1.0 CG A:ASP186 3.4 39.4 1.0 OE2 A:GLU25 3.5 37.0 1.0 CB A:ASP186 3.6 28.2 1.0 H1 A:HOH402 3.6 42.0 1.0 MG E:MG101 3.7 41.0 1.0 P E:DT7 3.8 42.5 1.0 CA A:HIS181 3.9 44.6 1.0 O A:HOH402 4.0 35.1 1.0 C A:HIS181 4.1 43.8 1.0 O A:SER182 4.2 40.6 1.0 O A:VAL24 4.2 26.2 1.0 N A:SER182 4.3 46.4 1.0 C A:SER182 4.3 37.1 1.0 H1 A:HOH403 4.3 36.2 1.0 O A:HIS181 4.5 44.9 1.0 OD1 A:ASP186 4.5 40.1 1.0 O5' E:DT7 4.5 35.4 1.0 N A:HIS181 4.5 44.0 1.0 N A:ALA183 4.5 37.2 1.0 O A:HOH403 4.6 30.3 1.0 CA A:ALA183 4.6 32.7 1.0 O3' E:DA6 4.6 44.3 1.0 O E:HOH204 4.7 43.8 1.0 CB A:ASP23 4.7 27.6 1.0 C5' E:DT7 4.7 27.1 1.0 OP2 E:DT7 4.7 49.4 1.0 CG A:GLU25 4.7 31.8 1.0 CA A:SER182 4.9 46.0 1.0 C A:VAL24 4.9 26.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two 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 Preferred Ssdna (Aat) with Two Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:39.1 occ:1.00 OE1 B:GLU25 2.3 37.2 1.0 OD2 B:ASP186 2.4 36.1 1.0 OP1 F:DT7 2.4 34.3 1.0 OD2 B:ASP23 2.6 31.8 1.0 OD1 B:ASP23 3.0 34.7 1.0 CG B:ASP23 3.1 30.3 1.0 CG B:ASP186 3.3 37.8 1.0 CD B:GLU25 3.3 36.5 1.0 CB B:ASP186 3.4 27.0 1.0 OE2 B:GLU25 3.7 38.4 1.0 O B:HOH428 3.7 32.5 1.0 MG F:MG101 3.7 42.5 1.0 P F:DT7 3.9 42.7 1.0 O B:SER182 3.9 36.5 1.0 CA B:HIS181 4.0 47.8 1.0 C B:HIS181 4.0 46.4 1.0 C B:SER182 4.2 35.9 1.0 O B:VAL24 4.2 26.6 1.0 N B:SER182 4.2 48.5 1.0 O B:HIS181 4.5 47.2 1.0 OD1 B:ASP186 4.5 41.5 1.0 N B:ALA183 4.6 35.4 1.0 N B:HIS181 4.6 44.6 1.0 CB B:ASP23 4.6 27.7 1.0 CA B:ALA183 4.6 31.2 1.0 CG B:GLU25 4.6 28.4 1.0 O3' F:DA6 4.7 42.9 1.0 O5' F:DT7 4.7 35.5 1.0 OP2 F:DT7 4.7 47.0 1.0 CA B:SER182 4.8 46.1 1.0 O B:HOH423 4.8 36.1 1.0 C5' F:DT7 4.8 30.1 1.0 O B:HOH419 4.9 21.7 1.0 CA B:ASP186 4.9 29.9 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two 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 3 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:41.0 occ:1.00 O A:HOH401 2.2 28.8 1.0 O A:HOH403 2.2 30.3 1.0 O A:HOH402 2.2 35.1 1.0 OD1 A:ASP23 2.5 35.6 1.0 O3' E:DA6 2.6 44.3 1.0 H1 A:HOH401 2.8 34.5 1.0 H1 A:HOH403 2.8 36.2 1.0 H1 A:HOH402 2.8 42.0 1.0 OP1 E:DT7 2.9 33.0 1.0 P E:DT7 3.4 42.5 1.0 CG A:ASP23 3.7 31.0 1.0 O A:HOH409 3.7 24.9 1.0 C3' E:DA6 3.7 41.9 1.0 MG A:MG301 3.7 39.1 1.0 OD1 A:ASP125 3.8 29.2 1.0 OD2 A:ASP125 4.0 28.8 1.0 C2' E:DA6 4.1 40.4 1.0 C4' E:DA6 4.1 43.3 1.0 C5' E:DT7 4.2 27.1 1.0 O A:HOH423 4.2 28.7 1.0 OD2 A:ASP23 4.2 34.8 1.0 O5' E:DT7 4.3 35.4 1.0 CG A:ASP125 4.3 30.3 1.0 O A:VAL24 4.3 26.2 1.0 O A:HIS120 4.5 22.9 1.0 OP2 E:DT7 4.5 49.4 1.0 CB A:ASP23 4.8 27.6 1.0 N A:VAL24 4.8 22.0 1.0 O E:HOH204 4.9 43.8 1.0 C5' E:DA6 5.0 42.5 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two 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 4 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg101 b:42.5 occ:1.00 O B:HOH410 2.1 29.1 1.0 O B:HOH428 2.2 32.5 1.0 O3' F:DA6 2.5 42.9 1.0 O B:HOH423 2.5 36.1 1.0 OD1 B:ASP23 2.6 34.7 1.0 OP1 F:DT7 2.9 34.3 1.0 P F:DT7 3.3 42.7 1.0 CG B:ASP23 3.6 30.3 1.0 C3' F:DA6 3.7 42.6 1.0 OD1 B:ASP125 3.7 27.9 1.0 MG B:MG301 3.7 39.1 1.0 O B:HOH419 3.9 21.7 1.0 O B:HOH414 3.9 22.3 1.0 OD2 B:ASP125 4.0 25.4 1.0 C4' F:DA6 4.0 47.5 1.0 C2' F:DA6 4.0 42.4 1.0 OD2 B:ASP23 4.1 31.8 1.0 C5' F:DT7 4.2 30.1 1.0 O B:VAL24 4.2 26.6 1.0 CG B:ASP125 4.3 30.9 1.0 O5' F:DT7 4.3 35.5 1.0 OP2 F:DT7 4.4 47.0 1.0 O B:HIS120 4.6 23.4 1.0 CB B:ASP23 4.7 27.7 1.0 N B:VAL24 4.8 23.5 1.0 C5' F:DA6 4.9 48.6 1.0 CA B:ASP23 5.0 23.5 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two 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 5 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:32.0 occ:1.00 O C:HOH417 2.4 29.3 1.0 OD1 C:ASP23 2.4 24.7 1.0 O3' G:DA6 2.5 32.4 1.0 O C:HOH423 2.5 29.9 1.0 OP1 G:DT7 2.5 30.2 1.0 O C:HOH414 2.6 21.6 1.0 P G:DT7 3.1 27.2 1.0 CG C:ASP23 3.6 26.8 1.0 C3' G:DA6 3.7 25.3 1.0 OD2 C:ASP186 3.8 38.0 1.0 CO C:CO301 4.0 39.5 1.0 O C:HOH411 4.0 22.3 1.0 O C:HOH410 4.0 23.8 1.0 O G:HOH205 4.0 33.1 1.0 C5' G:DT7 4.0 21.8 1.0 O5' G:DT7 4.1 25.0 1.0 OD2 C:ASP23 4.1 29.0 1.0 OD1 C:ASP125 4.1 28.5 1.0 C4' G:DA6 4.1 32.2 1.0 C2' G:DA6 4.1 29.5 1.0 O C:VAL24 4.2 20.3 1.0 OP2 G:DT7 4.2 26.9 1.0 OD2 C:ASP125 4.3 24.2 1.0 OE1 C:GLU25 4.6 28.6 1.0 CG C:ASP125 4.7 26.0 1.0 CB C:ASP23 4.8 24.1 1.0 N C:VAL24 4.8 27.0 1.0 O C:HIS120 4.8 17.0 1.0 CG C:ASP186 4.9 32.7 1.0 C5' G:DA6 5.0 27.2 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two 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 6 of Crystal Structure of Rnase T in Complex with A Preferred Ssdna (Aat) with Two Mg in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:33.2 occ:1.00 O D:HOH409 2.2 24.9 1.0 O3' H:DA6 2.5 29.7 1.0 OD1 D:ASP23 2.5 26.3 1.0 O D:HOH412 2.6 22.5 1.0 OP1 H:DT7 2.7 26.2 1.0 O D:HOH424 2.7 30.8 1.0 P H:DT7 3.2 23.8 1.0 CG D:ASP23 3.7 27.5 1.0 C3' H:DA6 3.7 22.2 1.0 OD2 D:ASP186 3.7 41.0 1.0 O D:HOH430 3.8 21.8 1.0 O D:HOH432 3.8 26.4 1.0 OD1 D:ASP125 3.9 24.2 1.0 C2' H:DA6 4.0 22.8 1.0 C5' H:DT7 4.0 22.7 1.0 CO D:CO301 4.1 41.4 1.0 O5' H:DT7 4.1 22.7 1.0 O D:VAL24 4.2 23.3 1.0 C4' H:DA6 4.2 29.9 1.0 O H:HOH202 4.2 30.8 1.0 OD2 D:ASP125 4.3 22.6 1.0 OD2 D:ASP23 4.3 24.9 1.0 OP2 H:DT7 4.4 23.2 1.0 CG D:ASP125 4.5 23.2 1.0 OE1 D:GLU25 4.7 30.5 1.0 CB D:ASP23 4.7 24.3 1.0 O D:HIS120 4.8 19.4 1.0 CG D:ASP186 4.8 29.2 1.0 N D:VAL24 4.9 23.0 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