Sodium in PDB 6enp: Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.

The structure of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group., PDB code: 6enp was solved by G.Prats-Ejarque, M.Moussaoui, E.Boix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.93 / 1.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	27.734, 38.557, 98.965, 90.00, 90.00, 90.00
R / Rfree (%)	12.2 / 14.5

The structure of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. (pdb code 6enp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group., PDB code: 6enp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:43.4 occ:1.00 O A:HOH516 2.4 39.4 0.9 HH11 A:ARG4 2.5 74.4 0.0 HH12 A:ARG4 2.8 74.4 0.0 NH1 A:ARG4 2.9 62.0 0.0 HD2 A:ARG4 3.8 66.1 0.0 CZ A:ARG4 4.1 61.0 0.0 CD A:ARG4 4.6 55.1 0.0 NE A:ARG4 4.8 58.6 0.0 HH22 A:ARG4 4.9 73.8 0.0 HD3 A:ARG4 4.9 66.1 0.0 NH2 A:ARG4 5.0 61.5 0.0

Sodium binding site 2 out of 3 in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:22.7 occ:0.53 CB A:PRO18 0.4 13.8 0.4 CA A:PRO18 1.4 13.8 0.4 CG A:PRO18 1.8 14.1 0.4 C A:PRO18 2.4 13.6 0.4 N A:PRO18 2.5 12.5 0.4 CD A:PRO18 2.7 13.3 0.4 O A:HOH430 2.7 18.7 0.6 CL A:CL208 2.9 24.1 0.4 O A:PRO18 2.9 14.7 0.4 N A:SER19 3.3 14.3 0.4 HA A:ASP46 3.4 21.0 1.0 C A:ASP46 3.6 17.3 1.0 N A:ASP46 3.6 16.2 1.0 C A:GLN17 3.7 10.1 0.4 CA A:ASP46 3.7 17.5 1.0 O A:ASP46 3.8 17.9 1.0 C A:HIS45 3.8 14.2 1.0 CB A:PRO18 3.9 13.4 0.6 H A:ASP46 3.9 19.4 1.0 CA A:PRO18 3.9 11.1 0.6 HA A:HIS45 4.0 16.0 1.0 N A:SER47 4.0 21.0 1.0 O A:GLN17 4.1 12.8 0.4 O A:HIS45 4.1 15.3 1.0 HA A:SER47 4.1 24.5 1.0 H A:SER47 4.3 25.1 1.0 HB3 A:HIS45 4.4 17.1 1.0 CA A:HIS45 4.4 13.3 1.0 N A:PRO18 4.6 10.5 0.6 CA A:SER47 4.6 20.4 1.0 CA A:SER19 4.6 15.6 0.4 HB3 A:SER47 4.6 27.8 1.0 CA A:GLN17 4.9 13.1 0.4 CB A:HIS45 5.0 14.2 1.0 O A:GLN17 5.0 10.5 0.6 C A:GLN17 5.0 10.3 0.6

Sodium binding site 3 out of 3 in the Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Atomic Resolution Structure of Human Rnase 6 in the Presence of Phosphate Anions in P21 Space Group. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:14.4 occ:0.53 O A:GLN71 2.6 10.7 0.4 O A:GLN71 2.7 11.1 0.6 O A:HOH505 2.8 23.1 0.8 O A:HOH332 2.8 13.9 1.0 HB3 A:GLN71 3.0 12.9 0.6 HD13 A:LEU57 3.0 15.5 1.0 HD23 A:LEU58 3.0 29.1 0.5 HB3 A:GLN71 3.0 13.9 0.4 HB3 A:LEU57 3.1 13.8 1.0 HD21 A:LEU58 3.2 29.1 0.5 CD2 A:LEU58 3.4 24.2 0.5 H A:GLN71 3.5 11.7 0.4 H A:GLN71 3.6 10.6 0.6 C A:GLN71 3.6 10.3 0.4 C A:GLN71 3.6 9.4 0.6 HD22 A:LEU58 3.6 29.1 0.5 HD12 A:LEU57 3.7 15.5 1.0 HB2 A:LEU57 3.7 13.8 1.0 CD1 A:LEU57 3.8 12.9 1.0 CB A:LEU57 3.8 11.5 1.0 CB A:GLN71 3.9 10.7 0.6 O A:HOH493 3.9 34.4 0.5 CB A:GLN71 3.9 11.6 0.4 CA A:GLN71 4.1 8.6 0.6 CA A:GLN71 4.1 11.1 0.4 HA A:SER73 4.1 21.7 1.0 N A:GLN71 4.1 9.7 0.4 N A:GLN71 4.1 8.8 0.6 HB2 A:LEU58 4.2 17.7 0.5 H A:LEU58 4.3 15.9 0.5 O A:SER72 4.3 13.2 1.0 CG A:LEU57 4.4 12.2 1.0 H A:LEU58 4.4 14.4 0.5 HG2 A:GLN71 4.4 14.1 0.4 HB2 A:GLN71 4.4 12.9 0.6 C A:SER72 4.5 13.0 1.0 O A:HOH333 4.5 22.9 0.4 HB2 A:GLN71 4.5 13.9 0.4 O A:HOH379 4.5 17.6 0.6 HD11 A:LEU57 4.5 15.5 1.0 HE21 A:GLN71 4.5 18.6 0.6 HB3 A:SER73 4.6 26.9 1.0 NE2 A:GLN71 4.6 15.5 0.6 HD22 A:LEU57 4.6 17.0 1.0 CD A:GLN71 4.6 13.8 0.6 CG A:GLN71 4.7 12.7 0.6 N A:SER73 4.7 14.0 1.0 HG2 A:GLN71 4.7 15.2 0.6 N A:SER72 4.7 9.5 1.0 CG A:GLN71 4.8 11.8 0.4 CA A:SER73 4.8 18.1 1.0 N A:LEU58 4.8 12.0 0.5 N A:LEU58 4.8 13.3 0.5 HE22 A:GLN71 4.9 18.6 0.6 CG A:LEU58 4.9 20.8 0.5 O A:LEU58 4.9 10.9 0.5 OE1 A:GLN71 5.0 23.5 0.4 O A:LEU58 5.0 12.3 0.5

G.Prats-Ejarque, J.A.Blanco, V.A.Salazar, V.M.Nogues, M.Moussaoui, E.Boix. Characterization of An Rnase with Two Catalytic Centers. Human RNASE6 Catalytic and Phosphate-Binding Site Arrangement Favors the Endonuclease Cleavage of Polymeric Substrates. Biochim Biophys Acta Gen V.1863 105 2019SUBJ.
ISSN: ISSN 1872-8006
PubMed: 30287244
DOI: 10.1016/J.BBAGEN.2018.09.021