Cobalt in PDB 3ngy: Crystal Structure of Rnase T (E92G Mutant)

The structure of Crystal Structure of Rnase T (E92G Mutant), PDB code: 3ngy 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)	27.61 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.763, 107.718, 121.745, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.4

The binding sites of Cobalt atom in the Crystal Structure of Rnase T (E92G Mutant) (pdb code 3ngy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of Rnase T (E92G Mutant), PDB code: 3ngy:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of Rnase T (E92G Mutant)


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 (E92G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co216 b:39.5 occ:1.00 O A:HOH224 3.0 17.3 1.0 O A:HOH226 3.0 16.1 1.0 NH2 A:ARG135 3.1 22.1 1.0 O A:HOH295 3.1 29.4 1.0 NE A:ARG135 3.7 28.6 1.0 CA A:GLY92 3.8 20.3 1.0 CZ A:ARG135 3.8 25.4 1.0 CB A:PHE65 4.0 17.1 1.0 CD2 A:PHE65 4.1 19.6 1.0 CB A:ALA132 4.2 20.8 1.0 N A:GLY92 4.3 15.5 1.0 CB A:LEU36 4.3 14.6 1.0 CG1 A:VAL62 4.3 13.7 1.0 CD2 A:LEU36 4.4 20.1 1.0 CG A:PHE65 4.5 23.9 1.0 O A:GLU63 4.6 20.9 1.0 N A:PHE65 4.7 19.6 1.0 CA A:ALA132 4.8 14.1 1.0 O A:HOH254 4.8 30.1 1.0 CA A:PHE65 4.8 21.2 1.0 CG A:LEU36 4.9 20.0 1.0 O A:HOH259 4.9 26.1 1.0 C A:GLY92 4.9 18.7 1.0 O A:LEU36 5.0 18.6 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of Rnase T (E92G Mutant)


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 (E92G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co216 b:43.0 occ:1.00 O B:HOH225 3.1 22.3 1.0 O B:HOH222 3.2 16.6 1.0 O B:HOH252 3.2 33.4 1.0 NH2 B:ARG135 3.2 20.6 1.0 NE B:ARG135 3.6 27.5 1.0 CA B:GLY92 3.8 27.2 1.0 CZ B:ARG135 3.9 24.6 1.0 CB B:PHE65 4.0 27.8 1.0 CD2 B:PHE65 4.1 22.7 1.0 CB B:ALA132 4.1 20.7 1.0 N B:GLY92 4.2 31.8 1.0 CG1 B:VAL62 4.3 23.1 1.0 CB B:LEU36 4.5 20.6 1.0 CG B:PHE65 4.5 26.8 1.0 CA B:ALA132 4.6 23.3 1.0 O B:GLU63 4.6 28.3 1.0 CD2 B:LEU36 4.7 18.6 1.0 N B:PHE65 4.7 26.5 1.0 O B:HOH273 4.8 34.6 1.0 CA B:PHE65 4.8 25.8 1.0 CD B:ARG135 4.9 24.5 1.0 C B:GLY92 4.9 26.6 1.0 O B:HOH249 5.0 35.1 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of Rnase T (E92G Mutant)


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 (E92G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co216 b:37.4 occ:1.00 O D:HOH223 3.1 15.1 1.0 O D:HOH217 3.2 14.2 1.0 NH2 D:ARG135 3.2 23.5 1.0 O D:HOH230 3.2 20.9 1.0 NE D:ARG135 3.5 19.6 1.0 CA D:GLY92 3.7 16.2 1.0 CZ D:ARG135 3.8 20.8 1.0 CB D:PHE65 3.9 16.7 1.0 N D:GLY92 4.1 17.6 1.0 CD2 D:PHE65 4.2 20.3 1.0 CB D:ALA132 4.2 18.8 1.0 CG1 D:VAL62 4.4 18.9 1.0 CB D:LEU36 4.5 15.3 1.0 CG D:PHE65 4.5 21.3 1.0 CA D:ALA132 4.6 20.6 1.0 N D:PHE65 4.7 16.8 1.0 CD2 D:LEU36 4.7 13.7 1.0 O D:GLU63 4.7 21.5 1.0 CA D:PHE65 4.7 20.4 1.0 CD D:ARG135 4.7 21.0 1.0 O D:HOH269 4.8 20.7 1.0 C D:GLY92 4.8 14.8 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