Cobalt 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:

Magnesium

(Mg)

6 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 5 binding sites of Cobalt 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 Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 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 Cobalt with other atoms in the Co 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:Co302 b:56.6 occ:1.00 O A:HOH418 3.1 32.4 1.0 NH2 A:ARG135 3.2 27.1 1.0 O A:HOH415 3.2 28.5 1.0 NE A:ARG135 3.4 29.3 1.0 CZ A:ARG135 3.7 29.7 1.0 CA A:GLY92 3.8 24.8 1.0 CB A:PHE65 3.9 31.0 1.0 CD2 A:PHE65 3.9 29.2 1.0 N A:GLY92 4.3 24.9 1.0 CB A:LEU36 4.3 28.5 1.0 CB A:ALA132 4.3 25.3 1.0 CG A:PHE65 4.3 40.8 1.0 CG1 A:VAL62 4.4 29.2 1.0 CA A:ALA132 4.5 27.4 1.0 CD2 A:LEU36 4.6 26.3 1.0 CD A:ARG135 4.6 29.2 1.0 O A:GLU63 4.7 29.4 1.0 N A:PHE65 4.7 34.2 1.0 CA A:PHE65 4.8 33.4 1.0 CE2 A:PHE65 4.9 31.0 1.0

Cobalt binding site 2 out of 5 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 Cobalt with other atoms in the Co 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:Co302 b:55.9 occ:1.00 NH2 B:ARG135 3.1 29.9 1.0 O B:HOH409 3.1 28.2 1.0 O B:HOH411 3.2 30.6 1.0 CA B:GLY92 3.7 24.9 1.0 NE B:ARG135 3.8 35.1 1.0 CZ B:ARG135 3.9 32.7 1.0 CB B:PHE65 4.0 27.8 1.0 CB B:ALA132 4.1 32.2 1.0 N B:GLY92 4.2 23.8 1.0 CD2 B:PHE65 4.2 27.1 1.0 CG1 B:VAL62 4.3 28.7 1.0 CB B:LEU36 4.4 27.9 1.0 CA B:ALA132 4.5 31.3 1.0 CG B:PHE65 4.5 36.4 1.0 CD2 B:LEU36 4.6 22.8 1.0 N B:PHE65 4.8 31.1 1.0 O B:GLU63 4.8 31.1 1.0 C B:GLY92 4.8 27.4 1.0 CA B:PHE65 4.9 31.7 1.0 O B:HOH444 5.0 39.8 1.0

Cobalt binding site 3 out of 5 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 Cobalt with other atoms in the Co 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 C:Co301 b:39.5 occ:1.00 OP1 G:DT7 2.2 30.2 1.0 OE1 C:GLU25 2.2 28.6 1.0 OD2 C:ASP186 2.3 38.0 1.0 ND1 C:HIS181 2.6 33.7 1.0 CG C:ASP186 2.9 32.7 1.0 CD C:GLU25 3.0 26.8 1.0 CB C:HIS181 3.0 33.4 1.0 OE2 C:GLU25 3.1 27.1 1.0 CG C:HIS181 3.2 37.6 1.0 OD1 C:ASP186 3.3 37.6 1.0 P G:DT7 3.5 27.2 1.0 O C:HOH423 3.7 29.9 1.0 CE1 C:HIS181 3.8 40.4 1.0 OD2 C:ASP23 3.8 29.0 1.0 CA C:HIS181 3.8 37.1 1.0 MG G:MG101 4.0 32.0 1.0 CB C:ASP186 4.0 24.7 1.0 OP2 G:DT7 4.1 26.9 1.0 O5' G:DT7 4.2 25.0 1.0 O G:HOH205 4.2 33.1 1.0 OD1 C:ASP23 4.2 24.7 1.0 C C:HIS181 4.3 40.7 1.0 O C:HIS181 4.3 41.2 1.0 O C:HOH428 4.4 35.0 1.0 CG C:ASP23 4.4 26.8 1.0 CG C:GLU25 4.4 23.4 1.0 CD2 C:HIS181 4.5 38.5 1.0 C5' G:DT7 4.6 21.8 1.0 O3' G:DA6 4.6 32.4 1.0 NE2 C:HIS181 4.7 41.7 1.0 O C:VAL24 4.9 20.3 1.0 O C:SER182 5.0 26.3 1.0

Cobalt binding site 4 out of 5 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 Cobalt with other atoms in the Co 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 D:Co301 b:41.4 occ:1.00 OP1 H:DT7 2.1 26.2 1.0 OD2 D:ASP186 2.1 41.0 1.0 OE1 D:GLU25 2.3 30.5 1.0 ND1 D:HIS181 2.6 33.5 1.0 CD D:GLU25 3.0 23.4 1.0 OE2 D:GLU25 3.0 22.8 1.0 CG D:ASP186 3.0 29.2 1.0 CA D:HIS181 3.2 30.6 1.0 P H:DT7 3.4 23.8 1.0 OD1 D:ASP186 3.4 32.0 1.0 CG D:HIS181 3.5 32.4 1.0 CE1 D:HIS181 3.6 37.1 1.0 N D:HIS181 3.6 26.3 1.0 CB D:HIS181 3.7 31.1 1.0 O D:HOH424 4.0 30.8 1.0 OP2 H:DT7 4.0 23.2 1.0 OD2 D:ASP23 4.0 24.9 1.0 OD1 D:ASP23 4.1 26.3 1.0 MG H:MG101 4.1 33.2 1.0 O5' H:DT7 4.1 22.7 1.0 CB D:ASP186 4.2 22.6 1.0 C D:HIS181 4.2 37.1 1.0 O D:HOH414 4.3 34.2 1.0 O H:HOH202 4.4 30.8 1.0 CG D:GLU25 4.4 23.3 1.0 CG D:ASP23 4.5 27.5 1.0 C5' H:DT7 4.5 22.7 1.0 O3' H:DA6 4.5 29.7 1.0 O D:HIS181 4.6 38.5 1.0 CD2 D:HIS181 4.7 32.6 1.0 NE2 D:HIS181 4.7 42.1 1.0 C D:ALA180 4.9 35.3 1.0 O D:VAL24 4.9 23.3 1.0

Cobalt binding site 5 out of 5 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 Cobalt with other atoms in the Co 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 D:Co302 b:58.7 occ:1.00 O D:HOH428 3.2 28.8 1.0 NH2 D:ARG135 3.3 31.6 1.0 O D:HOH440 3.3 37.3 1.0 CA D:GLY92 3.6 36.2 1.0 CB D:ALA132 3.9 34.4 1.0 CG1 D:VAL62 4.0 30.9 1.0 N D:GLY92 4.1 39.1 1.0 CB D:LEU36 4.1 27.8 1.0 CB D:PHE65 4.2 32.7 1.0 CZ D:ARG135 4.2 33.8 1.0 NE D:ARG135 4.3 41.8 1.0 CD2 D:LEU36 4.3 26.8 1.0 CD2 D:PHE65 4.5 34.6 1.0 O D:GLU63 4.6 34.5 1.0 CA D:ALA132 4.6 35.8 1.0 CG D:LEU36 4.7 30.8 1.0 N D:PHE65 4.7 36.6 1.0 CG D:PHE65 4.8 38.9 1.0 O D:LEU36 4.9 27.8 1.0 CA D:PHE65 4.9 33.8 1.0 C D:GLY92 4.9 36.9 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