Sodium in PDB 5oab: A Novel Crystal Form of Human RNASE6 at Atomic Resolution

The structure of A Novel Crystal Form of Human RNASE6 at Atomic Resolution, PDB code: 5oab 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)	47.70 / 1.11
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	95.405, 95.405, 95.405, 90.00, 90.00, 90.00
R / Rfree (%)	11.7 / 14.1

The structure of A Novel Crystal Form of Human RNASE6 at Atomic Resolution also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution (pdb code 5oab). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution, PDB code: 5oab:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Novel Crystal Form of Human RNASE6 at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:38.3 occ:1.00 HZ3 A:TRP1 2.4 13.8 0.5 HH2 A:TRP1 2.5 12.4 0.5 HZ2 A:LYS7 2.5 12.4 1.0 CL A:CL210 2.9 45.9 1.0 CZ3 A:TRP1 3.0 11.5 0.5 HE3 A:LYS7 3.0 10.8 1.0 CH2 A:TRP1 3.0 10.3 0.5 O A:HOH510 3.0 12.1 0.5 HZ3 A:TRP1 3.1 10.2 0.5 NZ A:LYS7 3.1 10.4 1.0 HZ1 A:LYS7 3.1 12.4 1.0 CE A:LYS7 3.5 9.0 1.0 HD2 A:LYS7 3.7 9.7 1.0 CZ3 A:TRP1 3.9 8.5 0.5 HZ3 A:LYS7 3.9 12.4 1.0 HE1 A:HIS122 4.1 12.7 0.8 CD A:LYS7 4.2 8.1 1.0 CE3 A:TRP1 4.3 11.4 0.5 NE2 A:HIS122 4.3 10.3 0.8 CZ2 A:TRP1 4.3 10.3 0.5 HE3 A:TRP1 4.3 9.9 0.5 HE2 A:LYS7 4.3 10.8 1.0 CE3 A:TRP1 4.5 8.2 0.5 CE1 A:HIS122 4.5 10.6 0.8 O A:HOH510 4.6 14.3 0.5 HE3 A:TRP1 4.6 13.7 0.5 O A:HOH439 4.7 13.8 1.0 HZ2 A:TRP1 4.7 12.3 0.5 HH2 A:TRP1 4.7 10.9 0.5 CH2 A:TRP1 4.8 9.1 0.5 HD3 A:LYS7 4.8 9.7 1.0 HG2 A:LYS7 4.9 9.7 1.0

Sodium binding site 2 out of 3 in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Novel Crystal Form of Human RNASE6 at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:23.0 occ:1.00 O A:TRP1 2.6 9.2 0.5 O A:HOH474 2.8 13.1 1.0 O A:HOH586 2.8 26.5 0.9 O A:TRP1 2.8 9.7 0.5 HA A:PRO2 3.4 12.0 1.0 SD A:MET0 3.4 25.1 0.6 C A:TRP1 3.5 9.8 0.5 C A:TRP1 3.6 9.6 0.5 H A:TRP1 3.8 14.7 0.5 H A:TRP1 3.8 14.1 0.5 H A:LYS3 4.0 11.2 1.0 CA A:PRO2 4.1 10.0 1.0 N A:PRO2 4.1 9.7 1.0 N A:TRP1 4.2 12.2 0.5 N A:TRP1 4.2 11.8 0.5 N A:LYS3 4.3 9.3 1.0 HB3 A:LYS3 4.3 12.6 1.0 CB A:MET0 4.4 20.1 1.0 O A:HOH429 4.4 17.1 0.8 CA A:TRP1 4.4 10.7 0.5 CA A:TRP1 4.5 10.0 0.5 CG A:MET0 4.5 23.0 1.0 C A:PRO2 4.6 9.7 1.0 O A:HOH522 4.6 13.6 1.0 HA A:TRP1 4.7 12.9 0.5 O A:HOH582 4.8 18.4 1.0 HA A:TRP1 4.8 12.0 0.5 CE A:MET0 4.9 25.9 0.6 C A:MET0 4.9 14.7 1.0

Sodium binding site 3 out of 3 in the A Novel Crystal Form of Human RNASE6 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Novel Crystal Form of Human RNASE6 at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:14.4 occ:1.00 O A:VAL121 2.7 8.4 1.0 O A:HOH521 2.8 14.6 0.5 O A:LYS7 2.8 6.7 1.0 HD1 A:TRP10 3.0 10.6 1.0 CL A:CL211 3.0 15.3 0.6 O A:HOH349 3.0 20.9 0.9 HB3 A:TRP10 3.2 8.3 1.0 HB3 A:LYS7 3.2 8.5 1.0 HB2 A:PHE11 3.3 8.2 1.0 HA A:LYS7 3.4 8.5 1.0 H A:PHE11 3.4 7.7 1.0 C A:LYS7 3.6 6.8 1.0 N A:PHE11 3.7 6.4 1.0 CD1 A:TRP10 3.8 8.8 1.0 C A:VAL121 3.8 7.6 1.0 CA A:LYS7 3.8 7.1 1.0 HA A:PHE11 3.9 7.4 1.0 CB A:LYS7 3.9 7.1 1.0 HA A:VAL121 4.0 8.6 1.0 CB A:TRP10 4.0 7.0 1.0 CB A:PHE11 4.1 6.8 1.0 CA A:PHE11 4.1 6.2 1.0 HD1 A:HIS122 4.1 11.2 0.8 HG2 A:LYS7 4.2 9.7 1.0 HB3 A:TRP1 4.2 13.3 0.5 HE2 A:LYS7 4.2 10.8 1.0 HB3 A:TRP1 4.2 11.5 0.5 HB A:VAL121 4.2 8.9 1.0 HA A:HIS122 4.3 10.8 0.2 ND1 A:HIS122 4.3 9.3 0.8 HA A:HIS122 4.3 8.6 0.8 CG A:TRP10 4.3 7.5 1.0 C A:TRP10 4.3 6.0 1.0 HE1 A:HIS122 4.3 12.7 0.8 CE1 A:HIS122 4.4 10.6 0.8 CA A:VAL121 4.4 7.1 1.0 HB3 A:PHE11 4.5 8.2 1.0 O3 A:PO4202 4.5 13.6 0.7 HE21 A:GLN14 4.6 14.1 1.0 CG A:LYS7 4.6 8.1 1.0 HE3 A:LYS7 4.6 10.8 1.0 HD2 A:PHE11 4.6 9.1 1.0 HB2 A:TRP10 4.7 8.3 1.0 HB2 A:LYS7 4.7 8.5 1.0 CA A:TRP10 4.7 6.0 1.0 HE3 A:TRP1 4.7 13.7 0.5 HD1 A:HIS122 4.8 14.8 0.2 HB2 A:TRP1 4.8 11.5 0.5 N A:HIS122 4.8 8.1 0.2 CE A:LYS7 4.8 9.0 1.0 N A:HIS122 4.8 6.7 0.8 N A:ALA8 4.8 6.3 1.0 HB2 A:HIS122 4.9 12.5 0.2 CB A:VAL121 4.9 7.5 1.0 H A:TRP10 4.9 7.0 1.0 HA A:ALA8 4.9 7.3 1.0 NE1 A:TRP10 4.9 9.4 1.0 CB A:TRP1 5.0 9.6 0.5 CA A:HIS122 5.0 9.0 0.2 O2 A:PO4202 5.0 11.0 0.7

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