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

Protein crystallography data

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

Other elements in 3ngz:

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:

Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 2 in 3ngz

Go back to Cobalt Binding Sites List in 3ngz
Cobalt 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 Cobalt with other atoms in the Co 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:Co217

b:30.7
occ:1.00
O A:HOH227 3.0 10.2 1.0
O A:HOH243 3.1 18.5 1.0
NH2 A:ARG135 3.2 14.1 1.0
O A:HOH352 3.3 15.3 1.0
NE A:ARG135 3.5 15.2 1.0
CA A:GLY92 3.8 15.1 1.0
CZ A:ARG135 3.8 15.5 1.0
CB A:PHE65 3.9 14.7 1.0
CD2 A:PHE65 4.1 12.1 1.0
CB A:ALA132 4.3 14.1 1.0
CG1 A:VAL62 4.3 10.2 1.0
N A:GLY92 4.3 11.9 1.0
CB A:LEU36 4.4 8.8 1.0
CG A:PHE65 4.5 16.0 1.0
CD2 A:LEU36 4.6 8.1 1.0
O A:GLU63 4.6 15.0 1.0
N A:PHE65 4.7 10.1 1.0
CA A:ALA132 4.7 15.1 1.0
O A:HOH353 4.8 15.8 1.0
CA A:PHE65 4.8 13.8 1.0
CD A:ARG135 4.8 11.1 1.0
C A:GLY92 4.9 15.5 1.0

Cobalt binding site 2 out of 2 in 3ngz

Go back to Cobalt Binding Sites List in 3ngz
Cobalt 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 Cobalt with other atoms in the Co 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:Co217

b:32.4
occ:1.00
O B:HOH233 3.0 11.4 1.0
NH2 B:ARG135 3.2 13.6 1.0
O B:HOH248 3.3 17.5 1.0
O B:HOH223 3.3 12.7 1.0
NE B:ARG135 3.6 18.4 1.0
CZ B:ARG135 3.8 18.8 1.0
CA B:GLY92 3.9 17.9 1.0
CB B:PHE65 4.0 12.0 1.0
CD2 B:PHE65 4.1 11.0 1.0
CB B:ALA132 4.2 13.6 1.0
CG1 B:VAL62 4.3 12.8 1.0
CB B:LEU36 4.4 10.6 1.0
N B:GLY92 4.4 12.0 1.0
CG B:PHE65 4.5 14.4 1.0
CA B:ALA132 4.5 14.4 1.0
O B:GLU63 4.7 13.7 1.0
CD2 B:LEU36 4.7 13.4 1.0
N B:PHE65 4.7 8.3 1.0
O B:HOH331 4.7 18.7 1.0
CD B:ARG135 4.8 12.7 1.0
CA B:PHE65 4.8 12.5 1.0

Reference:

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
Page generated: Sun Dec 13 10:41:37 2020

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