Sodium in PDB 3syu: Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp

All present enzymatic activity of Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp:
3.1.27.3;

The structure of Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp, PDB code: 3syu was solved by O.S.Smart, T.O.Womack, G.Bricogne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.44 / 1.95
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	88.690, 88.690, 88.690, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.5

The binding sites of Sodium atom in the Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp (pdb code 3syu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp, PDB code: 3syu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:39.2 occ:1.00 O A:HOH236 2.2 41.1 1.0 O A:GLY30 2.4 31.1 1.0 O A:HOH992 2.5 55.5 1.0 HA A:GLU31 3.2 28.1 1.0 C A:GLY30 3.6 31.0 1.0 HG2 A:GLU31 4.0 31.6 1.0 O A:HOH256 4.0 37.5 1.0 CA A:GLU31 4.1 26.9 1.0 N A:GLU31 4.3 28.0 1.0 O A:HOH242 4.3 53.0 1.0 HG3 A:GLU31 4.6 30.7 1.0 HA3 A:GLY30 4.7 28.2 1.0 CG A:GLU31 4.7 30.4 1.0 CA A:GLY30 4.7 30.0 1.0 H A:THR32 4.7 29.9 1.0 O A:HOH994 4.9 61.7 1.0

Sodium binding site 2 out of 2 in the Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Re-Refined Coordinates For Pdb Entry 1DET - Ribonuclease T1 Carboxymethylated at Glu 58 in Complex with 2'Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:38.3 occ:1.00 O A:HOH268 2.4 37.8 1.0 H A:GLY97 3.6 39.2 1.0 HA2 A:GLY97 4.0 38.8 1.0 N A:GLY97 4.3 37.2 1.0 CA A:GLY97 4.6 36.0 1.0 O A:GLY97 4.6 32.7 1.0 HA A:SER96 4.8 37.0 1.0

O.S.Smart, T.O.Womack, C.Flensburg, P.Keller, W.Paciorek, A.Sharff, C.Vonrhein, G.Bricogne. Exploiting Structure Similarity in Refinement: Automated Ncs and Target-Structure Restraints in Buster. Acta Crystallogr.,Sect.D V. 68 368 2012.
ISSN: ISSN 0907-4449
PubMed: 22505257
DOI: 10.1107/S0907444911056058