Cobalt in PDB 3va3: Crystal Structure of Rnase T in Complex with A Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang)

The structure of Crystal Structure of Rnase T in Complex with A Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang), PDB code: 3va3 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)	28.93 / 2.71
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.266, 112.684, 57.793, 90.00, 90.00, 90.00
R / Rfree (%)	26.3 / 29

The binding sites of Cobalt atom in the Crystal Structure of Rnase T in Complex with A Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang) (pdb code 3va3). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Rnase T in Complex with A Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang), PDB code: 3va3:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Rnase T in Complex with A Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang)


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 Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:78.4 occ:1.00 O A:HOH402 3.1 53.4 1.0 CA A:GLY92 3.5 62.0 1.0 NE A:ARG135 3.8 58.5 1.0 N A:GLY92 3.9 60.1 1.0 CB A:PHE65 4.2 54.5 1.0 NH2 A:ARG135 4.2 57.5 1.0 CG1 A:VAL62 4.3 60.6 1.0 CD2 A:PHE65 4.3 54.1 1.0 CZ A:ARG135 4.5 58.9 1.0 CB A:ALA132 4.6 59.7 1.0 N A:PHE65 4.6 54.6 1.0 C A:GLY92 4.6 62.0 1.0 CB A:LEU36 4.7 51.4 1.0 CG A:PHE65 4.7 54.0 1.0 O A:GLU63 4.7 58.1 1.0 CD A:ARG135 4.8 58.5 1.0 CA A:PHE65 4.8 53.7 1.0 CA A:ALA132 4.9 59.7 1.0 O A:ALA132 4.9 60.6 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Rnase T in Complex with A Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang)


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 Duplex Dna Product (Stem Loop Dna with 2 Nucleotide 3' Overhang) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:82.9 occ:1.00 NH2 B:ARG135 3.3 62.7 1.0 CA B:GLY92 3.5 64.1 1.0 NE B:ARG135 3.7 61.8 1.0 CZ B:ARG135 3.9 62.0 1.0 N B:GLY92 4.2 64.4 1.0 CG1 B:VAL62 4.4 60.1 1.0 CB B:ALA132 4.4 62.6 1.0 C B:GLY92 4.4 65.9 1.0 CB B:PHE65 4.5 60.2 1.0 CB B:LEU36 4.7 56.2 1.0 CA B:ALA132 4.7 62.3 1.0 O B:GLU63 4.7 61.7 1.0 CD2 B:PHE65 4.8 58.7 1.0 O B:ALA132 4.9 64.3 1.0 CB B:ARG135 4.9 63.4 1.0 CD B:ARG135 4.9 60.8 1.0 N B:TYR93 5.0 64.4 1.0 O B:GLY92 5.0 64.0 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